Ticket #19302: log_06_11_25.html

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4<title> ChimeraX Log </title>
5<script type="text/javascript">
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43<body>
44<h1> ChimeraX Log </h1>
45UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Wed Nov 5 11:09:20 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Wed Oct 29 10:26:11 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot; format session">open &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Wed Oct 22 19:01:49 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot; format session">open &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Wed Oct 22 18:27:07 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/Dropbox/Design to Martin/PSI-DdHyd design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/Dropbox/Design to Martin/PSI-DdHyd design.cxs&quot;">open &quot;/Users/drornoy/Library/CloudStorage/Dropbox/Design to Martin/PSI-DdHyd design.cxs&quot;</a></div></div><p style="color:#ffb961">Frozen name &quot;Hbonding&quot; not restored: Nothing is selected by specifier<br>
46</p><details style="background-color: #ebf5fb"><summary>Log from Wed Sep 17 15:57:48 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot; format session">open &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Mon Sep 15 21:24:55 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;">open &quot;/Users/drornoy/Library/CloudStorage/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Mon Sep 15 20:51:36 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot; format session">open &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Mon Sep 15 19:12:58 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs&quot; format session">open &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sun Sep 14 07:49:27 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs&quot; format session">open &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sat Sep 13 22:23:04 2025</summary>UCSF ChimeraX version: 1.10 (2025-06-26)<br>© 2016-2025 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Tue Oct 22 11:40:52 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot; format session</a></div></div>Associated PSI_BFD_SF4_opt_chains.pdb chain F to PSI_BFd_SF4_opt.pdb, chain F with 0 mismatches<br>
47<details style="background-color: #ebf5fb"><summary>Log from Tue Oct 22 11:39:31 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs&quot; format session</a></div></div>Associated PSI_BFD_SF4_opt_chains.pdb chain F to PSI_BFd_SF4_opt.pdb, chain F with 0 mismatches<br>
48<details style="background-color: #ebf5fb"><summary>Log from Tue Oct 22 09:43:01 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd PSI-BFd AMBER opt.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd PSI-BFd AMBER opt.cxs&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd PSI-BFd AMBER opt.cxs&quot;</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Mon Oct 21 23:18:11 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot; format session">open &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Mon Oct 14 21:44:01 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot; format session">open &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot; format session</a></div></div>Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M, PSI_BFd_SF4_opt.pdb #4/F<br>
49<details style="background-color: #ebf5fb"><summary>Log from Mon Oct 14 18:11:28 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot; format session">open &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Mon Oct 14 17:57:44 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Fri Oct 11 10:32:45 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Thu Oct 10 08:30:31 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Wed Oct 9 21:29:02 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for relaxation.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for relaxation.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for relaxation.cxs&quot; format session</a></div></div><p style="color:darkorange">Frozen name &quot;minAB&quot; not restored: nothing is selected by specifier<br>
50</p><details style="background-color: #ebf5fb"><summary>Log from Tue Oct 8 17:54:27 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session">open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sun Oct 6 13:38:31 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session">open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Fri Oct 4 15:14:28 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session">open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Fri Oct 4 10:09:32 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session">open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Fri Oct 4 09:37:44 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session">open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Thu Oct 3 21:28:49 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Thu Oct 3 09:47:21 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot; format session">open &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Mon Sep 30 14:03:27 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs&quot;</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Thu Sep 19 17:01:48 2024</summary>UCSF ChimeraX version: 1.8 (2024-06-10)<br>© 2016-2024 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Tue Jun 4 19:01:21 2024</summary>UCSF ChimeraX version: 1.7.1 (2024-01-23)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Tue Jun 4 18:24:08 2024</summary>UCSF ChimeraX version: 1.7.1 (2024-01-23)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sat Jun 1 14:26:44 2024</summary>UCSF ChimeraX version: 1.7.1 (2024-01-23)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sun May 19 17:29:55 2024</summary>UCSF ChimeraX version: 1.7.1 (2024-01-23)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs&quot;</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sat May 18 22:45:24 2024</summary>UCSF ChimeraX version: 1.7.1 (2024-01-23)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sat May 18 17:13:54 2024</summary>UCSF ChimeraX version: 1.7.1 (2024-01-23)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sat May 18 14:49:43 2024</summary>UCSF ChimeraX version: 1.7.1 (2024-01-23)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI Fdx Fld combined.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI Fdx Fld combined.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI Fdx Fld combined.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Fri May 17 15:09:06 2024</summary>UCSF ChimeraX version: 1.7.1 (2024-01-23)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI base for design.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI base for design.cxs&quot; format session">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI base for design.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Fri May 17 13:23:40 2024</summary>UCSF ChimeraX version: 1.7.1 (2024-01-23)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge PetF truncated for docking.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge PetF truncated for docking.cxs&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge PetF truncated for docking.cxs&quot;</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sun Sep 3 21:12:02 2023</summary>UCSF ChimeraX version: 1.6.1 (2023-05-09)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs&quot; format session">open &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sun Sep 3 20:48:37 2023</summary>UCSF ChimeraX version: 1.6.1 (2023-05-09)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF PshB PscB.cxs&quot; format session</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF PshB PscB.cxs&quot; format session">open &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF PshB PscB.cxs&quot; format session</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Sun Sep 3 20:15:18 2023</summary>UCSF ChimeraX version: 1.6.1 (2023-05-09)<br>© 2016-2023 Regents of the University of California. All rights reserved.<br><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs&quot;">open &quot;/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs&quot;</a></div></div><details style="background-color: #ebf5fb"><summary>Log from Tue Dec 20 17:39:04 2022</summary>UCSF ChimeraX version: 1.5 (2022-11-24)<br>
51© 2016-2022 Regents of the University of California. All rights reserved.<br>
52<a href="cxcmd:help help:credits.html">How to cite UCSF ChimeraX</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> /Users/drornoy/Downloads/ChimeraX/AlphaFold/AF-A1Z1D6-F1-model_v4.cif format mmcif</div><div class="cxcmd_as_cmd"><a href="cxcmd:open /Users/drornoy/Downloads/ChimeraX/AlphaFold/AF-A1Z1D6-F1-model_v4.cif format mmcif">open /Users/drornoy/Downloads/ChimeraX/AlphaFold/AF-A1Z1D6-F1-model_v4.cif format mmcif</a></div></div><table border=1 cellpadding=4 cellspacing=0>
53 <thead>
54 <tr>
55 <th colspan="3">Chain information for AF-A1Z1D6-F1-model_v4.cif #1</th>
56 </tr>
57 <tr>
58 <th>Chain</th>
59 <th>Description</th>
60 <th>UniProt</th>
61 </tr>
62 </thead>
63 <tbody>
64 <tr>
65 <td style="text-align:center"><a title="Select chain" href="cxcmd:select /A:1-54">A</a></td>
66 <td><a title="Show sequence" href="cxcmd:sequence chain #1/A">PshB</a></td>
67 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open A1Z1D6 from uniprot">A1Z1D6_9FIRM</a></td>
68 </tr>
69 </tbody>
70</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :Cys">select :Cys</a></div></div>54 atoms, 46 bonds, 9 residues, 1 model selected<br>
71<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
72Coulombic values for AF-A1Z1D6-F1-model_v4.cif_A SES surface #1.1: minimum, -13.99, mean -2.80, maximum 7.54<br>
73<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #1.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #1.1">close #1.1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic">coulombic</a></div></div>Coulombic values for AF-A1Z1D6-F1-model_v4.cif_A SES surface #1.1: minimum, -13.99, mean -2.80, maximum 7.54<br>
74<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.1 models">hide #1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 6yez</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 6yez">open 6yez</a></div></div><i>6yez</i> title:<br><b>Plant PSI-ferredoxin-plastocyanin supercomplex</b> <a href="cxcmd:log metadata #2">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
75 <thead>
76 <tr>
77 <th colspan="3">Chain information for 6yez #2</th>
78 </tr>
79 <tr>
80 <th>Chain</th>
81 <th>Description</th>
82 <th>UniProt</th>
83 </tr>
84 </thead>
85 <tbody>
86 <tr>
87 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/1:40-232">1</a></td>
88 <td><a title="Show sequence" href="cxcmd:sequence chain #2/1">Lhca1</a></td>
89 <td style="text-align:center"></td>
90 </tr>
91 <tr>
92 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/2:58-265">2</a></td>
93 <td><a title="Show sequence" href="cxcmd:sequence chain #2/2">Chlorophyll a-b binding protein, chloroplastic</a></td>
94 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q41038 from uniprot">Q41038_PEA</a></td>
95 </tr>
96 <tr>
97 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/3:55-275">3</a></td>
98 <td><a title="Show sequence" href="cxcmd:sequence chain #2/3">Chlorophyll a-b binding protein 3, chloroplastic</a></td>
99 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q32904 from uniprot">CB23_PEA</a></td>
100 </tr>
101 <tr>
102 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/4:52-249">4</a></td>
103 <td><a title="Show sequence" href="cxcmd:sequence chain #2/4">Chlorophyll a-b binding protein P4, chloroplastic</a></td>
104 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q9SQL2 from uniprot">CB24_PEA</a></td>
105 </tr>
106 <tr>
107 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/A:16-758">A</a></td>
108 <td><a title="Show sequence" href="cxcmd:sequence chain #2/A">Photosystem I P700 chlorophyll a apoprotein A1</a></td>
109 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open A0A0F6NFW5 from uniprot">A0A0F6NFW5_PEA</a></td>
110 </tr>
111 <tr>
112 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/B:2-734">B</a></td>
113 <td><a title="Show sequence" href="cxcmd:sequence chain #2/B">Photosystem I P700 chlorophyll a apoprotein A2</a></td>
114 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open A0A0F6NGI2 from uniprot">A0A0F6NGI2_PEA</a></td>
115 </tr>
116 <tr>
117 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/C:2-81">C</a></td>
118 <td><a title="Show sequence" href="cxcmd:sequence chain #2/C">Photosystem I iron-sulfur center</a></td>
119 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P10793 from uniprot">PSAC_PEA</a></td>
120 </tr>
121 <tr>
122 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/D:69-211">D</a></td>
123 <td><a title="Show sequence" href="cxcmd:sequence chain #2/D">PsaD</a></td>
124 <td style="text-align:center"></td>
125 </tr>
126 <tr>
127 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/E:64-129">E</a></td>
128 <td><a title="Show sequence" href="cxcmd:sequence chain #2/E">PsaE</a></td>
129 <td style="text-align:center"></td>
130 </tr>
131 <tr>
132 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/F:78-231">F</a></td>
133 <td><a title="Show sequence" href="cxcmd:sequence chain #2/F">PsaF</a></td>
134 <td style="text-align:center"></td>
135 </tr>
136 <tr>
137 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/G:58-154">G</a></td>
138 <td><a title="Show sequence" href="cxcmd:sequence chain #2/G">PsaG</a></td>
139 <td style="text-align:center"></td>
140 </tr>
141 <tr>
142 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/H:48-140">H</a></td>
143 <td><a title="Show sequence" href="cxcmd:sequence chain #2/H">PsaH</a></td>
144 <td style="text-align:center"></td>
145 </tr>
146 <tr>
147 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/I:2-32">I</a></td>
148 <td><a title="Show sequence" href="cxcmd:sequence chain #2/I">Photosystem I reaction center subunit VIII</a></td>
149 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P17227 from uniprot">PSAI_PEA</a></td>
150 </tr>
151 <tr>
152 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/J:1-42">J</a></td>
153 <td><a title="Show sequence" href="cxcmd:sequence chain #2/J">PsaJ</a></td>
154 <td style="text-align:center"></td>
155 </tr>
156 <tr>
157 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/K:46-126">K</a></td>
158 <td><a title="Show sequence" href="cxcmd:sequence chain #2/K">Photosystem I reaction center subunit X psaK</a></td>
159 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open E1C9L3 from uniprot">E1C9L3_PEA</a></td>
160 </tr>
161 <tr>
162 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/L:54-212">L</a></td>
163 <td><a title="Show sequence" href="cxcmd:sequence chain #2/L">PsaL</a></td>
164 <td style="text-align:center"></td>
165 </tr>
166 <tr>
167 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/N:1-97">N</a></td>
168 <td><a title="Show sequence" href="cxcmd:sequence chain #2/N">Ferredoxin-1, chloroplastic</a></td>
169 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P09911 from uniprot">FER1_PEA</a></td>
170 </tr>
171 <tr>
172 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/P:1-99">P</a></td>
173 <td><a title="Show sequence" href="cxcmd:sequence chain #2/P">Plastocyanin</a></td>
174 <td style="text-align:center"></td>
175 </tr>
176 </tbody>
177</table><br/><table border=1 cellpadding=4 cellspacing=0>
178 <thead>
179 <tr>
180 <th>Non-standard residues in 6yez #2</th>
181 </tr>
182 </thead>
183 <tbody>
184 <tr>
185 <td><a title="select residue" href="cxcmd:sel :3PH">3PH</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/3PH">1,2-diacyl-glycerol-3-Sn-phosphate</a> (phosphatidic acid)</td>
186 </tr>
187 <tr>
188 <td><a title="select residue" href="cxcmd:sel :BCR">BCR</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/BCR">β-carotene</a></td>
189 </tr>
190 <tr>
191 <td><a title="select residue" href="cxcmd:sel :C7Z">C7Z</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/C7Z">(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol</a></td>
192 </tr>
193 <tr>
194 <td><a title="select residue" href="cxcmd:sel :CA">CA</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CA">calcium ion</a></td>
195 </tr>
196 <tr>
197 <td><a title="select residue" href="cxcmd:sel :CHL">CHL</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CHL">chlorophyll B</a></td>
198 </tr>
199 <tr>
200 <td><a title="select residue" href="cxcmd:sel :CL0">CL0</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CL0">chlorophyll A isomer</a></td>
201 </tr>
202 <tr>
203 <td><a title="select residue" href="cxcmd:sel :CLA">CLA</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CLA">chlorophyll A</a></td>
204 </tr>
205 <tr>
206 <td><a title="select residue" href="cxcmd:sel :CU">CU</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CU">copper (II) ion</a></td>
207 </tr>
208 <tr>
209 <td><a title="select residue" href="cxcmd:sel :DGD">DGD</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/DGD">digalactosyl diacyl glycerol (DGDG)</a></td>
210 </tr>
211 <tr>
212 <td><a title="select residue" href="cxcmd:sel :FES">FES</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/FES">FE2/S2 (inorganic) cluster</a></td>
213 </tr>
214 <tr>
215 <td><a title="select residue" href="cxcmd:sel :LHG">LHG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LHG">1,2-dipalmitoyl-phosphatidyl-glycerole</a></td>
216 </tr>
217 <tr>
218 <td><a title="select residue" href="cxcmd:sel :LMG">LMG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LMG">1,2-distearoyl-monogalactosyl-diglyceride</a></td>
219 </tr>
220 <tr>
221 <td><a title="select residue" href="cxcmd:sel :LMT">LMT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LMT">dodecyl-β-D-maltoside</a></td>
222 </tr>
223 <tr>
224 <td><a title="select residue" href="cxcmd:sel :LUT">LUT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LUT">(3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol</a> ((3R,3'R)-β,β-carotene-3,3'-diol; lutein)</td>
225 </tr>
226 <tr>
227 <td><a title="select residue" href="cxcmd:sel :PQN">PQN</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PQN">phylloquinone</a> (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)</td>
228 </tr>
229 <tr>
230 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
231 </tr>
232 <tr>
233 <td><a title="select residue" href="cxcmd:sel :XAT">XAT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/XAT">(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-β,β-carotene-3,3'-diol</a> (violaxanthin)</td>
234 </tr>
235 </tbody>
236</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view">view</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2">select #2</a></div></div>39226 atoms, 40742 bonds, 678 pseudobonds, 3684 residues, 2 models selected<br>
237<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E/N">select #2/A-E/N</a></div></div>21037 atoms, 21881 bonds, 372 pseudobonds, 1981 residues, 2 models selected<br>
238<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
239<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N &amp;protein">select #2/N &amp;protein</a></div></div>724 atoms, 736 bonds, 97 residues, 1 model selected<br>
240<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
241Coulombic values for 6yez_N SES surface #2.2: minimum, -22.35, mean -7.76, maximum 6.07<br>
242<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view">view</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> right &quot;translate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode right &quot;translate selected models&quot;">ui mousemode right &quot;translate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1">select #1</a></div></div>369 atoms, 372 bonds, 54 residues, 1 model selected<br>
243<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #1,1,0,0,38.794,0,1,0,146.26,0,0,1,93.086</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #1,1,0,0,38.794,0,1,0,146.26,0,0,1,93.086">view matrix models #1,1,0,0,38.794,0,1,0,146.26,0,0,1,93.086</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #1,1,0,0,80.971,0,1,0,155.21,0,0,1,92.043</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #1,1,0,0,80.971,0,1,0,155.21,0,0,1,92.043">view matrix models #1,1,0,0,80.971,0,1,0,155.21,0,0,1,92.043</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #1,1,0,0,118.66,0,1,0,188.05,0,0,1,73.54</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #1,1,0,0,118.66,0,1,0,188.05,0,0,1,73.54">view matrix models #1,1,0,0,118.66,0,1,0,188.05,0,0,1,73.54</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs&quot;">save &quot;/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.1 models">show #1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.1 models">hide #1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2 models">hide #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:Cys">select #2/N:Cys</a></div></div>30 atoms, 25 bonds, 5 residues, 1 model selected<br>
244<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 30 atom styles<br>
245<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:18</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:18">select #2/N:18</a></div></div>6 atoms, 5 bonds, 1 residue, 1 model selected<br>
246<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:39,44,47,77</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:39,44,47,77">select #2/N:39,44,47,77</a></div></div>24 atoms, 20 bonds, 4 residues, 1 model selected<br>
247<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1">select #1</a></div></div>369 atoms, 372 bonds, 54 residues, 1 model selected<br>
248<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #1,1,0,0,125.11,0,1,0,180.57,0,0,1,83.231</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #1,1,0,0,125.11,0,1,0,180.57,0,0,1,83.231">view matrix models #1,1,0,0,125.11,0,1,0,180.57,0,0,1,83.231</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #1,1,0,0,124.62,0,1,0,176.17,0,0,1,84.747</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #1,1,0,0,124.62,0,1,0,176.17,0,0,1,84.747">view matrix models #1,1,0,0,124.62,0,1,0,176.17,0,0,1,84.747</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.1 models">show #1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> right &quot;rotate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode right &quot;rotate selected models&quot;">ui mousemode right &quot;rotate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #1,0.45679,-0.5223,-0.7201,126.73,0.84237,0.51416,0.16142,175.23,0.28594,-0.68032,0.67483,85.358</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #1,0.45679,-0.5223,-0.7201,126.73,0.84237,0.51416,0.16142,175.23,0.28594,-0.68032,0.67483,85.358">view matrix models #1,0.45679,-0.5223,-0.7201,126.73,0.84237,0.51416,0.16142,175.23,0.28594,-0.68032,0.67483,85.358</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!1 &amp; sel) 50</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!1 &amp; sel) 50">transparency (#!1 &amp; sel) 50</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
249<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2 models">show #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!2 &amp; sel) 50</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!2 &amp; sel) 50">transparency (#!2 &amp; sel) 50</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1">select #1</a></div></div>369 atoms, 372 bonds, 54 residues, 1 model selected<br>
250<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.1 models">hide #1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2 models">hide #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> right &quot;move picked models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode right &quot;move picked models&quot;">ui mousemode right &quot;move picked models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #2,1,0,0,-0.12823,0,1,0,-1.3842,0,0,1,0.015386</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #2,1,0,0,-0.12823,0,1,0,-1.3842,0,0,1,0.015386">view matrix models #2,1,0,0,-0.12823,0,1,0,-1.3842,0,0,1,0.015386</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1">select #1</a></div></div>369 atoms, 372 bonds, 54 residues, 1 model selected<br>
251<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #1,0.45679,-0.5223,-0.7201,116.11,0.84237,0.51416,0.16142,145.16,0.28594,-0.68032,0.67483,88.372</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #1,0.45679,-0.5223,-0.7201,116.11,0.84237,0.51416,0.16142,145.16,0.28594,-0.68032,0.67483,88.372">view matrix models #1,0.45679,-0.5223,-0.7201,116.11,0.84237,0.51416,0.16142,145.16,0.28594,-0.68032,0.67483,88.372</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #1,0.45679,-0.5223,-0.7201,114.24,0.84237,0.51416,0.16142,146.41,0.28594,-0.68032,0.67483,87.683</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #1,0.45679,-0.5223,-0.7201,114.24,0.84237,0.51416,0.16142,146.41,0.28594,-0.68032,0.67483,87.683">view matrix models #1,0.45679,-0.5223,-0.7201,114.24,0.84237,0.51416,0.16142,146.41,0.28594,-0.68032,0.67483,87.683</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
252<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1">select #1</a></div></div>369 atoms, 372 bonds, 54 residues, 1 model selected<br>
253<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #2,1,0,0,0.65788,0,1,0,0.30648,0,0,1,0.70826</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #2,1,0,0,0.65788,0,1,0,0.30648,0,0,1,0.70826">view matrix models #2,1,0,0,0.65788,0,1,0,0.30648,0,0,1,0.70826</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#matrix">view matrix</a> models #2,1,0,0,-0.65234,0,1,0,1.2309,0,0,1,0.14732</div><div class="cxcmd_as_cmd"><a href="cxcmd:view matrix models #2,1,0,0,-0.65234,0,1,0,1.2309,0,0,1,0.14732">view matrix models #2,1,0,0,-0.65234,0,1,0,1.2309,0,0,1,0.14732</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs&quot;">save &quot;/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Tue Dec 20 17:39:04 2022 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
254<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.1 models">show #1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2 models">show #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2 models">hide #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.1 models">hide #2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.1 models">show #2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.1 models">hide #1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
255<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:FeS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:FeS">select #2:FeS</a></div></div>4 atoms, 4 bonds, 1 residue, 1 model selected<br>
256<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 4 atom styles<br>
257<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:FS4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:FS4">select #2:FS4</a></div></div>Nothing selected<br>
258<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:SF4">select #2:SF4</a></div></div>24 atoms, 36 bonds, 3 residues, 1 model selected<br>
259<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 24 atom styles<br>
260<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #2 enclose /C-D</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #2 enclose /C-D">surface #2 enclose /C-D</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.3">select add #2.3</a></div></div>1768 atoms, 36 bonds, 226 residues, 1 model selected<br>
261<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div><p style="color:darkorange">The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:<br>6yez #2/D LEU 211 OXT<br/></p>Using Amber 20 recommended default charges and atom types for standard residues<br>
262Coulombic values for 6yez_C SES surface #2.3: minimum, -12.54, mean -0.30, maximum 9.66<br>
263Coulombic values for 6yez_D SES surface #2.4: minimum, -11.93, mean 1.16, maximum 13.86<br>
264<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #2 enclose /E</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #2 enclose /E">surface #2 enclose /E</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.5">select add #2.5</a></div></div>2296 atoms, 36 bonds, 292 residues, 3 models selected<br>
265<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.4">select subtract #2.4</a></div></div>1164 atoms, 36 bonds, 149 residues, 4 models selected<br>
266<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.3">select subtract #2.3</a></div></div>552 atoms, 36 bonds, 69 residues, 3 models selected<br>
267<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div><p style="color:darkorange">The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:<br>6yez #2/E LYS 129 OXT<br/></p>Using Amber 20 recommended default charges and atom types for standard residues<br>
268Coulombic values for Surface /E #2.5: minimum, -13.31, mean 0.69, maximum 9.65<br>
269<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2 models">show #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.4">select add #2.4</a></div></div>1684 atoms, 36 bonds, 212 residues, 2 models selected<br>
270<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.5">select subtract #2.5</a></div></div>1156 atoms, 36 bonds, 146 residues, 3 models selected<br>
271<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!2 &amp; sel) 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!2 &amp; sel) 60">transparency (#!2 &amp; sel) 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!2 &amp; sel) 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!2 &amp; sel) 0">transparency (#!2 &amp; sel) 0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.4">select subtract #2.4</a></div></div>24 atoms, 36 bonds, 3 residues, 2 models selected<br>
272<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.3">select add #2.3</a></div></div>636 atoms, 36 bonds, 83 residues, 1 model selected<br>
273<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!2 &amp; sel) 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!2 &amp; sel) 60">transparency (#!2 &amp; sel) 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> AlphaFold</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show AlphaFold">ui tool show AlphaFold</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#match">alphafold match</a> Q8KCZ6</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold match Q8KCZ6">alphafold match Q8KCZ6</a></div></div>Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json<br>
2741 AlphaFold model found using UniProt identifier: Q8KCZ6 (UniProt Q8KCZ6)<br>
275<table border=1 cellpadding=4 cellspacing=0>
276 <thead>
277 <tr><th colspan=4>Sequence Similarity
278 <tr><th>AlphaFold Model<th>Query Sequence<th>Identity %<th>Coverage %
279 </thead>
280 <tbody>
281 <td style="text-align:center">Q8KCZ6
282 <td style="text-align:center">Q8KCZ6
283 <td style="text-align:center">100.0
284 <td style="text-align:center">100.0
285 </tbody>
286</table><br/>Opened 1 AlphaFold model<br>
287<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 &quot;AlphaFold Q8KCZ6 CbFdx&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 &quot;AlphaFold Q8KCZ6 CbFdx&quot;">rename #3 &quot;AlphaFold Q8KCZ6 CbFdx&quot;</a></div></div>Fetching A1Z1D6 UniProt info from https://www.uniprot.org/uniprot/A1Z1D6.xml<br>
288<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#match">alphafold match</a> A1Z1D6</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold match A1Z1D6">alphafold match A1Z1D6</a></div></div>Fetching compressed AlphaFold A1Z1D6 from https://alphafold.ebi.ac.uk/files/AF-A1Z1D6-F1-model_v4.cif<br>
2891 AlphaFold model found using UniProt identifier: A1Z1D6 (UniProt A1Z1D6)<br>
290<table border=1 cellpadding=4 cellspacing=0>
291 <thead>
292 <tr><th colspan=4>Sequence Similarity
293 <tr><th>AlphaFold Model<th>Query Sequence<th>Identity %<th>Coverage %
294 </thead>
295 <tbody>
296 <td style="text-align:center">A1Z1D6
297 <td style="text-align:center">A1Z1D6
298 <td style="text-align:center">100.0
299 <td style="text-align:center">100.0
300 </tbody>
301</table><br/>Opened 1 AlphaFold model<br>
302<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1 &quot;AlphaFold A1Z1D6 PshB&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1 &quot;AlphaFold A1Z1D6 PshB&quot;">rename #1 &quot;AlphaFold A1Z1D6 PshB&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #4">close #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #3 to #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #3 to #1">matchmaker #3 to #1</a></div></div>
303 <table border=1 cellpadding=4 cellspacing=0>
304 <tr>
305 <th colspan="2">Parameters</th>
306 </tr>
307 <tr>
308 <td>Chain pairing</td>
309 <td>bb</td>
310 </tr>
311 <tr>
312 <td>Alignment algorithm</td>
313 <td>Needleman-Wunsch</td>
314 </tr>
315 <tr>
316 <td>Similarity matrix</td>
317 <td>BLOSUM-62</td>
318 </tr>
319
320 <tr>
321 <td>SS fraction</td>
322 <td>0.3</td>
323 </tr>
324 <tr>
325 <td>Gap open (HH/SS/other)</td>
326 <td>18/18/6</td>
327 </tr>
328 <tr>
329 <td>Gap extend</td>
330 <td>1</td>
331 </tr>
332 <tr>
333 <td>SS matrix</td>
334 <td>
335 <table>
336 <tr>
337 <th></th> <th>H</th> <th>S</th> <th>O</th>
338 </tr>
339 <tr>
340 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
341 </tr>
342 <tr>
343 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
344 </tr>
345 <tr>
346 <th>O</th> <td></td> <td></td> <td align="right">4</td>
347 </tr>
348 </table>
349 </td>
350 </tr>
351
352 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
353 </table>
354 <br/>Matchmaker AlphaFold A1Z1D6 PshB, chain A (#1) with AlphaFold Q8KCZ6 CbFdx, chain A (#3), sequence alignment score = 92.4<br>
355RMSD between 42 pruned atom pairs is 0.750 angstroms; (across all 54 pairs: 3.659)<br>
356<br>
357<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2 models">hide #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
358<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3:cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3:cys">select #3:cys</a></div></div>54 atoms, 45 bonds, 9 residues, 1 model selected<br>
359<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF PshB PscB.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF PshB PscB.cxs&quot;">save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF PshB PscB.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sun Sep 3 20:15:18 2023 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
360<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:562-593</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:562-593">select #2/A:562-593</a></div></div>238 atoms, 243 bonds, 32 residues, 1 model selected<br>
361<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:417-442,562-593</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:417-442,562-593">select #2/A:417-442,562-593</a></div></div>466 atoms, 475 bonds, 58 residues, 1 model selected<br>
362<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:417-442,562-595</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:417-442,562-595">select #2/A:417-442,562-595</a></div></div>485 atoms, 496 bonds, 60 residues, 1 model selected<br>
363<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-73,417-442,562-595</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-73,417-442,562-595">select #2/A:16-73,417-442,562-595</a></div></div>959 atoms, 986 bonds, 118 residues, 1 model selected<br>
364<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-73,417-442,562-595,695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-73,417-442,562-595,695-729">select #2/A:16-73,417-442,562-595,695-729</a></div></div>1238 atoms, 1272 bonds, 153 residues, 1 model selected<br>
365<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-73,320-354,417-442,562-595,695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-73,320-354,417-442,562-595,695-729">select #2/A:16-73,320-354,417-442,562-595,695-729</a></div></div>1512 atoms, 1555 bonds, 188 residues, 1 model selected<br>
366<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #2 enclose #2/A:16-73,320-354,417-442,562-595,695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #2 enclose #2/A:16-73,320-354,417-442,562-595,695-729">surface #2 enclose #2/A:16-73,320-354,417-442,562-595,695-729</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #2.6">close #2.6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #2 enclose #2/A:16-73,191-200,320-354,417-442,562-595,695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #2 enclose #2/A:16-73,191-200,320-354,417-442,562-595,695-729">surface #2 enclose #2/A:16-73,191-200,320-354,417-442,562-595,695-729</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.6">select subtract #2.6</a></div></div>1 model selected<br>
367<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #2.6">close #2.6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #2 enclose #2/A:16-73,191-200,315-354,417-442,562-595,695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #2 enclose #2/A:16-73,191-200,315-354,417-442,562-595,695-729">surface #2 enclose #2/A:16-73,191-200,315-354,417-442,562-595,695-729</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3 models">hide #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.4 models">hide #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-41</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-41">select #2/B:2-41</a></div></div>327 atoms, 336 bonds, 40 residues, 1 model selected<br>
368<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-41,172-176,291-331</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-41,172-176,291-331">select #2/B:2-41,172-176,291-331</a></div></div>693 atoms, 710 bonds, 86 residues, 1 model selected<br>
369<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-41,172-176,291-331,392-421</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-41,172-176,291-331,392-421">select #2/B:2-41,172-176,291-331,392-421</a></div></div>945 atoms, 967 bonds, 116 residues, 1 model selected<br>
370<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-41,172-176,291-331,392-423</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-41,172-176,291-331,392-423">select #2/B:2-41,172-176,291-331,392-423</a></div></div>959 atoms, 981 bonds, 118 residues, 1 model selected<br>
371<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-41,172-176,291-331,392-419</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-41,172-176,291-331,392-419">select #2/B:2-41,172-176,291-331,392-419</a></div></div>929 atoms, 950 bonds, 114 residues, 1 model selected<br>
372<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-41,172-176,291-331,392-420</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-41,172-176,291-331,392-420">select #2/B:2-41,172-176,291-331,392-420</a></div></div>935 atoms, 956 bonds, 115 residues, 1 model selected<br>
373<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-41,172-176,291-331,392-420,535-573</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-41,172-176,291-331,392-420,535-573">select #2/B:2-41,172-176,291-331,392-420,535-573</a></div></div>1221 atoms, 1249 bonds, 154 residues, 1 model selected<br>
374<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-41,172-176,291-331,392-420,535-575</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-41,172-176,291-331,392-420,535-575">select #2/B:2-41,172-176,291-331,392-420,535-575</a></div></div>1234 atoms, 1262 bonds, 156 residues, 1 model selected<br>
375<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44,172-176,291-331,392-420,535-575</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44,172-176,291-331,392-420,535-575">select #2/B:2-44,172-176,291-331,392-420,535-575</a></div></div>1263 atoms, 1292 bonds, 159 residues, 1 model selected<br>
376<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44,162-176,291-331,392-420,535-575</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44,162-176,291-331,392-420,535-575">select #2/B:2-44,162-176,291-331,392-420,535-575</a></div></div>1345 atoms, 1378 bonds, 169 residues, 1 model selected<br>
377<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44,162-176,291-331,392-420,535-575,666-705</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44,162-176,291-331,392-420,535-575,666-705">select #2/B:2-44,162-176,291-331,392-420,535-575,666-705</a></div></div>1684 atoms, 1728 bonds, 209 residues, 1 model selected<br>
378<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44,162-176,291-331,392-420,535-575,665-707</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44,162-176,291-331,392-420,535-575,665-707">select #2/B:2-44,162-176,291-331,392-420,535-575,665-707</a></div></div>1711 atoms, 1755 bonds, 212 residues, 1 model selected<br>
379<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #2 enclose #2/B:2-44,162-176,291-331,392-420,535-575,665-707</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #2 enclose #2/B:2-44,162-176,291-331,392-420,535-575,665-707">surface #2 enclose #2/B:2-44,162-176,291-331,392-420,535-575,665-707</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.5 models">show #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.4 models">show #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.3 models">show #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2 models">show #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2 models">hide #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.7">select subtract #2.7</a></div></div>1 model selected<br>
380<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.7">select add #2.7</a></div></div>1711 atoms, 212 residues, 1 model selected<br>
381<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
382Coulombic values for 6yez_B SES surface #2.7: minimum, -15.22, mean -0.70, maximum 13.28<br>
383<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.7">select subtract #2.7</a></div></div>1 model selected<br>
384<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.6">select add #2.6</a></div></div>1649 atoms, 203 residues, 1 model selected<br>
385<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
386Coulombic values for 6yez_A SES surface #2.6: minimum, -15.63, mean -1.25, maximum 12.20<br>
387<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.6">select subtract #2.6</a></div></div>1 model selected<br>
388<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
389<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2 models">show #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.2">select subtract #2.2</a></div></div>4 atoms, 4 bonds, 1 residue, 2 models selected<br>
390<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.2">select add #2.2</a></div></div>728 atoms, 4 bonds, 98 residues, 1 model selected<br>
391<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Coulombic values for 6yez_N SES surface #2.2: minimum, -22.35, mean -7.76, maximum 6.07<br>
392<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.2">select subtract #2.2</a></div></div>4 atoms, 4 bonds, 1 residue, 2 models selected<br>
393<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.2">select add #2.2</a></div></div>728 atoms, 4 bonds, 98 residues, 1 model selected<br>
394<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!2 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!2 &amp; sel) 30">transparency (#!2 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2 models">hide #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3 models">hide #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:FES@FE1/C:3003@FE1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:FES@FE1/C:3003@FE1">select #2/N:FES@FE1/C:3003@FE1</a></div></div>2 atoms, 2 residues, 1 model selected<br>
395<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Distances</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Distances">ui tool show Distances</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> radius 0.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style radius 0.3">distance style radius 0.3</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> dashes 8</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style dashes 8">distance style dashes 8</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> dashes 7</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style dashes 7">distance style dashes 7</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> dashes 6</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style dashes 6">distance style dashes 6</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> color #00f900</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style color #00f900">distance style color #00f900</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #2/C:3003@FE1 #2/N:101@FE1</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #2/C:3003@FE1 #2/N:101@FE1">distance #2/C:3003@FE1 #2/N:101@FE1</a></div></div>Distance between 6yez #2/C SF4 3003 FE1 and /N FES 101 FE1: 9.664Å
396<br>
397<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2 models">show #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.3 models">show #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.5 models">show #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs&quot;">save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:CL1,CLA</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:CL1,CLA">select #2:CL1,CLA</a></div></div>8357 atoms, 8921 bonds, 564 pseudobonds, 141 residues, 2 models selected<br>
398<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:CL1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:CL1">select #2:CL1</a></div></div>Nothing selected<br>
399<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:CHL</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:CHL">select #2:CHL</a></div></div>802 atoms, 862 bonds, 60 pseudobonds, 15 residues, 2 models selected<br>
400<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:CHL</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:CHL">select #2:CHL</a></div></div>802 atoms, 862 bonds, 60 pseudobonds, 15 residues, 2 models selected<br>
401<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-B:CHL</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-B:CHL">select #2/A-B:CHL</a></div></div>Nothing selected<br>
402<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-B:CL0</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-B:CL0">select #2/A-B:CL0</a></div></div>65 atoms, 69 bonds, 4 pseudobonds, 1 residue, 2 models selected<br>
403<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-B:CL0,CLA</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-B:CL0,CLA">select #2/A-B:CL0,CLA</a></div></div>5318 atoms, 5662 bonds, 344 pseudobonds, 86 residues, 2 models selected<br>
404<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!2 &amp; sel) forest green</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!2 &amp; sel) forest green">color (#!2 &amp; sel) forest green</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs&quot;">save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF coulombic interactions.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sun Sep 3 20:48:37 2023 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
405<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A &amp;~:16-73,191-200,315-354,417-442,562-595,695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A &amp;~:16-73,191-200,315-354,417-442,562-595,695-729">select #2/A &amp;~:16-73,191-200,315-354,417-442,562-595,695-729</a></div></div>7373 atoms, 7698 bonds, 180 pseudobonds, 597 residues, 2 models selected<br>
406<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A &amp;~:16-73,191-200,315-354,417-442,562-595,695-729,SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A &amp;~:16-73,191-200,315-354,417-442,562-595,695-729,SF4">select #2/A &amp;~:16-73,191-200,315-354,417-442,562-595,695-729,SF4</a></div></div>7365 atoms, 7686 bonds, 180 pseudobonds, 596 residues, 2 models selected<br>
407<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#atoms">delete atoms</a> (#!2 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete atoms (#!2 &amp; sel)">delete atoms (#!2 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#bonds">delete bonds</a> (#!2 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete bonds (#!2 &amp; sel)">delete bonds (#!2 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B &amp;~:2-44,162-176,291-331,392-420,535-575,665-707</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B &amp;~:2-44,162-176,291-331,392-420,535-575,665-707">select #2/B &amp;~:2-44,162-176,291-331,392-420,535-575,665-707</a></div></div>7288 atoms, 7617 bonds, 177 pseudobonds, 580 residues, 2 models selected<br>
408<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B &amp;~:2-44,162-176,291-331,392-420,535-575,665-707,SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B &amp;~:2-44,162-176,291-331,392-420,535-575,665-707,SF4">select #2/B &amp;~:2-44,162-176,291-331,392-420,535-575,665-707,SF4</a></div></div>7288 atoms, 7617 bonds, 177 pseudobonds, 580 residues, 2 models selected<br>
409<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B &amp;~:2-44,162-176,291-331,392-420,535-575,665-707</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B &amp;~:2-44,162-176,291-331,392-420,535-575,665-707">select #2/B &amp;~:2-44,162-176,291-331,392-420,535-575,665-707</a></div></div>7288 atoms, 7617 bonds, 177 pseudobonds, 580 residues, 2 models selected<br>
410<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#atoms">delete atoms</a> (#!2 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete atoms (#!2 &amp; sel)">delete atoms (#!2 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#bonds">delete bonds</a> (#!2 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete bonds (#!2 &amp; sel)">delete bonds (#!2 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2 &amp;~/A-E/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2 &amp;~/A-E/N">select #2 &amp;~/A-E/N</a></div></div>18189 atoms, 18861 bonds, 305 pseudobonds, 1703 residues, 2 models selected<br>
411<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#atoms">delete atoms</a> (#!2 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete atoms (#!2 &amp; sel)">delete atoms (#!2 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#bonds">delete bonds</a> (#!2 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete bonds (#!2 &amp; sel)">delete bonds (#!2 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3 models">hide #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.4 models">hide #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.6 models">hide #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.7 models">hide #2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.3 models">show #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.4 models">show #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.5 models">show #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.6 models">show #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.6">select add #2.6</a></div></div>1649 atoms, 203 residues, 1 model selected<br>
412<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Coulombic values for 6yez_A SES surface #2.6: minimum, -23.39, mean -1.01, maximum 11.65<br>
413<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.6">select subtract #2.6</a></div></div>1 model selected<br>
414<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.7 models">show #2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.7">select add #2.7</a></div></div>1711 atoms, 212 residues, 1 model selected<br>
415<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Coulombic values for 6yez_B SES surface #2.7: minimum, -15.05, mean 0.76, maximum 12.84<br>
416<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI PetF truncated.pdb&quot; models #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI PetF truncated.pdb&quot; models #2">save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI PetF truncated.pdb&quot; models #2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF truncated for docking.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF truncated for docking.cxs&quot;">save &quot;/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI stromal ridge PetF truncated for docking.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sun Sep 3 21:12:02 2023 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
417<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.8 models">hide #2.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.8 models">show #2.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.7 models">hide #2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.6 models">hide #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.4 models">hide #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3 models">hide #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2 models">hide #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 2fdn</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 2fdn">open 2fdn</a></div></div><i>2fdn</i> title:<br><b>2[4FE-4S] ferredoxin from clostridium acidi-urici</b> <a href="cxcmd:log metadata #5">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
418 <thead>
419 <tr>
420 <th colspan="3">Chain information for 2fdn #5</th>
421 </tr>
422 <tr>
423 <th>Chain</th>
424 <th>Description</th>
425 <th>UniProt</th>
426 </tr>
427 </thead>
428 <tbody>
429 <tr>
430 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/A:1-55">A</a></td>
431 <td><a title="Show sequence" href="cxcmd:sequence chain #5/A">FERREDOXIN</a></td>
432 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P00198 from uniprot associate #5/A">FER_CLOAC</a> <a title="Select sequence" href="cxcmd:select #5/A:1-55">1-55</a></td>
433 </tr>
434 </tbody>
435</table><br/><table border=1 cellpadding=4 cellspacing=0>
436 <thead>
437 <tr>
438 <th>Non-standard residues in 2fdn #5</th>
439 </tr>
440 </thead>
441 <tbody>
442 <tr>
443 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
444 </tr>
445 </tbody>
446</table><br/><div class="cxcmd"><span style="color:white; background-color:crimson;">Align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2</span></div><font color="crimson"><b>Unknown command: Align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2">align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2</a></div></div>RMSD between 4 atom pairs is 0.181 angstroms<br>
447<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
448<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #2/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #2/A">sequence chain #2/A</a></div></div>Alignment identifier is 2/A<br>
449<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #2/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #2/B">sequence chain #2/B</a></div></div>Alignment identifier is 2/B<br>
450<div class="cxcmd"><a href="help:user/commands/select.html">select</a> <span style="color:white; background-color:crimson;">#sel #2/A</span></div><font color="crimson"><b>Expected an objects specifier or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A">select #2/A</a></div></div>1657 atoms, 1709 bonds, 7 pseudobonds, 204 residues, 3 models selected<br>
451<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI base for design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI base for design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI base for design.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Fri May 17 13:23:40 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
452<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI_IsiB_noFld.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI_IsiB_noFld.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI_PetF/PSI_IsiB_noFld.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
453 <thead>
454 <tr>
455 <th colspan="2">Chain information for PSI_IsiB_noFld.pdb #6</th>
456 </tr>
457 <tr>
458 <th>Chain</th>
459 <th>Description</th>
460
461 </tr>
462 </thead>
463 <tbody>
464 <tr>
465 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/A:1-704">A</a></td>
466 <td><a title="Show sequence" href="cxcmd:sequence chain #6/A">No description available</a></td>
467
468 </tr>
469 </tbody>
470</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!6 to #2 showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!6 to #2 showAlignment true">matchmaker #!6 to #2 showAlignment true</a></div></div>
471 <table border=1 cellpadding=4 cellspacing=0>
472 <tr>
473 <th colspan="2">Parameters</th>
474 </tr>
475 <tr>
476 <td>Chain pairing</td>
477 <td>bb</td>
478 </tr>
479 <tr>
480 <td>Alignment algorithm</td>
481 <td>Needleman-Wunsch</td>
482 </tr>
483 <tr>
484 <td>Similarity matrix</td>
485 <td>BLOSUM-62</td>
486 </tr>
487
488 <tr>
489 <td>SS fraction</td>
490 <td>0.3</td>
491 </tr>
492 <tr>
493 <td>Gap open (HH/SS/other)</td>
494 <td>18/18/6</td>
495 </tr>
496 <tr>
497 <td>Gap extend</td>
498 <td>1</td>
499 </tr>
500 <tr>
501 <td>SS matrix</td>
502 <td>
503 <table>
504 <tr>
505 <th></th> <th>H</th> <th>S</th> <th>O</th>
506 </tr>
507 <tr>
508 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
509 </tr>
510 <tr>
511 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
512 </tr>
513 <tr>
514 <th>O</th> <td></td> <td></td> <td align="right">4</td>
515 </tr>
516 </table>
517 </td>
518 </tr>
519
520 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
521 </table>
522 <br/>Matchmaker 6yez, chain D (#2) with PSI_IsiB_noFld.pdb, chain A (#6), sequence alignment score = 488.5<br>
523Alignment identifier is 1<br>
524Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
525Hiding conservation header for alignment 1<br>
526Chains used in RMSD evaluation for alignment 1: 6yez #2/D, PSI_IsiB_noFld.pdb #6/A<br>
527Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
528RMSD between 126 pruned atom pairs is 0.707 angstroms; (across all 142 pairs: 5.251)<br>
529<br>
530<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-73,191-200,315-354,417-442,562-595,695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-73,191-200,315-354,417-442,562-595,695-729">select #2/A:16-73,191-200,315-354,417-442,562-595,695-729</a></div></div>1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected<br>
531<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B">select #2/B</a></div></div>1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected<br>
532<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44,162-176,291-331,392-420,535-575,665-707</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44,162-176,291-331,392-420,535-575,665-707">select #2/B:2-44,162-176,291-331,392-420,535-575,665-707</a></div></div>1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected<br>
533<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-73,191-200,315-354,417-442,562-595,695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-73,191-200,315-354,417-442,562-595,695-729">select #2/A:16-73,191-200,315-354,417-442,562-595,695-729</a></div></div>1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected<br>
534<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_0.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_0.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_0.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
535 <thead>
536 <tr>
537 <th colspan="2">Chain information for PSI_6yez_A_B_for_docking_0.pdb #7</th>
538 </tr>
539 <tr>
540 <th>Chain</th>
541 <th>Description</th>
542
543 </tr>
544 </thead>
545 <tbody>
546 <tr>
547 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #7/A:1-615">A</a></td>
548 <td><a title="Show sequence" href="cxcmd:sequence chain #7/A">No description available</a></td>
549
550 </tr>
551 </tbody>
552</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #7 to #2 showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #7 to #2 showAlignment true">matchmaker #7 to #2 showAlignment true</a></div></div>
553 <table border=1 cellpadding=4 cellspacing=0>
554 <tr>
555 <th colspan="2">Parameters</th>
556 </tr>
557 <tr>
558 <td>Chain pairing</td>
559 <td>bb</td>
560 </tr>
561 <tr>
562 <td>Alignment algorithm</td>
563 <td>Needleman-Wunsch</td>
564 </tr>
565 <tr>
566 <td>Similarity matrix</td>
567 <td>BLOSUM-62</td>
568 </tr>
569
570 <tr>
571 <td>SS fraction</td>
572 <td>0.3</td>
573 </tr>
574 <tr>
575 <td>Gap open (HH/SS/other)</td>
576 <td>18/18/6</td>
577 </tr>
578 <tr>
579 <td>Gap extend</td>
580 <td>1</td>
581 </tr>
582 <tr>
583 <td>SS matrix</td>
584 <td>
585 <table>
586 <tr>
587 <th></th> <th>H</th> <th>S</th> <th>O</th>
588 </tr>
589 <tr>
590 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
591 </tr>
592 <tr>
593 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
594 </tr>
595 <tr>
596 <th>O</th> <td></td> <td></td> <td align="right">4</td>
597 </tr>
598 </table>
599 </td>
600 </tr>
601
602 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
603 </table>
604 <br/>Matchmaker 6yez, chain B (#2) with PSI_6yez_A_B_for_docking_0.pdb, chain A (#7), sequence alignment score = 572.4<br>
605Alignment identifier is 1<br>
606Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
607Hiding conservation header for alignment 1<br>
608Chains used in RMSD evaluation for alignment 1: 6yez #2/B, PSI_6yez_A_B_for_docking_0.pdb #7/A<br>
609Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
610RMSD between 211 pruned atom pairs is 0.247 angstroms; (across all 211 pairs: 0.247)<br>
611<br>
612<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #7 to #2 showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #7 to #2 showAlignment true">matchmaker #7 to #2 showAlignment true</a></div></div>
613 <table border=1 cellpadding=4 cellspacing=0>
614 <tr>
615 <th colspan="2">Parameters</th>
616 </tr>
617 <tr>
618 <td>Chain pairing</td>
619 <td>bb</td>
620 </tr>
621 <tr>
622 <td>Alignment algorithm</td>
623 <td>Needleman-Wunsch</td>
624 </tr>
625 <tr>
626 <td>Similarity matrix</td>
627 <td>BLOSUM-62</td>
628 </tr>
629
630 <tr>
631 <td>SS fraction</td>
632 <td>0.3</td>
633 </tr>
634 <tr>
635 <td>Gap open (HH/SS/other)</td>
636 <td>18/18/6</td>
637 </tr>
638 <tr>
639 <td>Gap extend</td>
640 <td>1</td>
641 </tr>
642 <tr>
643 <td>SS matrix</td>
644 <td>
645 <table>
646 <tr>
647 <th></th> <th>H</th> <th>S</th> <th>O</th>
648 </tr>
649 <tr>
650 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
651 </tr>
652 <tr>
653 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
654 </tr>
655 <tr>
656 <th>O</th> <td></td> <td></td> <td align="right">4</td>
657 </tr>
658 </table>
659 </td>
660 </tr>
661
662 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
663 </table>
664 <br/>Matchmaker 6yez, chain B (#2) with PSI_6yez_A_B_for_docking_0.pdb, chain A (#7), sequence alignment score = 572.4<br>
665Alignment identifier is 2<br>
666Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 2<br>
667Hiding conservation header for alignment 2<br>
668Chains used in RMSD evaluation for alignment 2: 6yez #2/B, PSI_6yez_A_B_for_docking_0.pdb #7/A<br>
669Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 2<br>
670RMSD between 211 pruned atom pairs is 0.247 angstroms; (across all 211 pairs: 0.247)<br>
671<br>
672<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:73,191,200,315,354,417,442,562,595,695,729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:73,191,200,315,354,417,442,562,595,695,729">select #2/A:73,191,200,315,354,417,442,562,595,695,729</a></div></div>108 atoms, 105 bonds, 5 pseudobonds, 11 residues, 2 models selected<br>
673<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!2 &amp; sel) yellow</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!2 &amp; sel) yellow">color (#!2 &amp; sel) yellow</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:44,162,176,291,331,392,420,535,575,665,707</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:44,162,176,291,331,392,420,535,575,665,707">select #2/B:44,162,176,291,331,392,420,535,575,665,707</a></div></div>90 atoms, 81 bonds, 5 pseudobonds, 11 residues, 2 models selected<br>
674<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!2 &amp; sel) yellow</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!2 &amp; sel) yellow">color (#!2 &amp; sel) yellow</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #7 models">hide #7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:707</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:707">select #2/B:707</a></div></div>8 atoms, 7 bonds, 1 residue, 1 model selected<br>
675<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!2 &amp; sel) hot pink</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!2 &amp; sel) hot pink">color (#!2 &amp; sel) hot pink</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2">select #2/B:2</a></div></div>5 atoms, 4 bonds, 1 residue, 1 model selected<br>
676<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!2 &amp; sel) blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!2 &amp; sel) blue">color (#!2 &amp; sel) blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:729/B:2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:729/B:2">select #2/A:729/B:2</a></div></div>14 atoms, 12 bonds, 2 residues, 1 model selected<br>
677<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:729">select #2/A:729</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
678<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!2 &amp; sel) magenta</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!2 &amp; sel) magenta">color (#!2 &amp; sel) magenta</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #7">close #7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_hike6_0.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_hike6_0.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_hike6_0.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
679 <thead>
680 <tr>
681 <th colspan="2">Chain information for PSI_6yez_A_B_for_docking_hike6_0.pdb #7</th>
682 </tr>
683 <tr>
684 <th>Chain</th>
685 <th>Description</th>
686
687 </tr>
688 </thead>
689 <tbody>
690 <tr>
691 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #7/A:1-479">A</a></td>
692 <td><a title="Show sequence" href="cxcmd:sequence chain #7/A">No description available</a></td>
693
694 </tr>
695 </tbody>
696</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #7 to #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #7 to #2">matchmaker #7 to #2</a></div></div>
697 <table border=1 cellpadding=4 cellspacing=0>
698 <tr>
699 <th colspan="2">Parameters</th>
700 </tr>
701 <tr>
702 <td>Chain pairing</td>
703 <td>bb</td>
704 </tr>
705 <tr>
706 <td>Alignment algorithm</td>
707 <td>Needleman-Wunsch</td>
708 </tr>
709 <tr>
710 <td>Similarity matrix</td>
711 <td>BLOSUM-62</td>
712 </tr>
713
714 <tr>
715 <td>SS fraction</td>
716 <td>0.3</td>
717 </tr>
718 <tr>
719 <td>Gap open (HH/SS/other)</td>
720 <td>18/18/6</td>
721 </tr>
722 <tr>
723 <td>Gap extend</td>
724 <td>1</td>
725 </tr>
726 <tr>
727 <td>SS matrix</td>
728 <td>
729 <table>
730 <tr>
731 <th></th> <th>H</th> <th>S</th> <th>O</th>
732 </tr>
733 <tr>
734 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
735 </tr>
736 <tr>
737 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
738 </tr>
739 <tr>
740 <th>O</th> <td></td> <td></td> <td align="right">4</td>
741 </tr>
742 </table>
743 </td>
744 </tr>
745
746 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
747 </table>
748 <br/>Matchmaker 6yez, chain B (#2) with PSI_6yez_A_B_for_docking_hike6_0.pdb, chain A (#7), sequence alignment score = 551.5<br>
749RMSD between 211 pruned atom pairs is 0.251 angstroms; (across all 212 pairs: 0.314)<br>
750<br>
751<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-B:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-B:CYS">select #2/A-B:CYS</a></div></div>24 atoms, 20 bonds, 4 residues, 1 model selected<br>
752<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 24 atom styles<br>
753<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A-B:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A-B:CYS">select #7/A-B:CYS</a></div></div>16 atoms, 12 bonds, 4 residues, 1 model selected<br>
754<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A-B:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A-B:CYS">select #7/A-B:CYS</a></div></div>16 atoms, 12 bonds, 4 residues, 1 model selected<br>
755<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI Fdx Fld combined.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI Fdx Fld combined.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI Fdx Fld combined.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Fri May 17 15:09:06 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
756<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #2#7</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #2#7">combine #2#7</a></div></div>Remapping chain ID &#x27;A&#x27; in PSI_6yez_A_B_for_docking_hike6_0.pdb #7 to &#x27;F&#x27;<br>
757<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #2#7</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #2#7">combine #2#7</a></div></div>Remapping chain ID &#x27;A&#x27; in PSI_6yez_A_B_for_docking_hike6_0.pdb #7 to &#x27;F&#x27;<br>
758<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/F">select #8/F</a></div></div>1916 atoms, 1915 bonds, 479 residues, 1 model selected<br>
759<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/F:GLY</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/F:GLY">select #8/F:GLY</a></div></div>392 atoms, 350 bonds, 98 residues, 1 model selected<br>
760<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> sequence GGG</div><div class="cxcmd_as_cmd"><a href="cxcmd:select sequence GGG">select sequence GGG</a></div></div>768 atoms, 735 bonds, 192 residues, 3 models selected<br>
761<div class="cxcmd"><a href="help:user/commands/select.html">select</a> sequence GGG|sequence <span style="color:white; background-color:crimson;">GGGGG</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><a href="help:user/commands/select.html">select</a> sequence GGG <span style="color:white; background-color:crimson;">| GGGGG</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> sequence GGGGG</div><div class="cxcmd_as_cmd"><a href="cxcmd:select sequence GGGGG">select sequence GGGGG</a></div></div>480 atoms, 471 bonds, 120 residues, 3 models selected<br>
762<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #8/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #8/F">sequence chain #8/F</a></div></div>Alignment identifier is 8/F<br>
763<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/F:181-185,221-250,432-436</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/F:181-185,221-250,432-436">select #8/F:181-185,221-250,432-436</a></div></div>160 atoms, 157 bonds, 40 residues, 1 model selected<br>
764<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> sequence GGG</div><div class="cxcmd_as_cmd"><a href="cxcmd:select sequence GGG">select sequence GGG</a></div></div>768 atoms, 735 bonds, 192 residues, 3 models selected<br>
765<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #8-9</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #8-9">close #8-9</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #7">close #7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
766<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
767<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:FES</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:FES">select #2/N:FES</a></div></div>4 atoms, 4 bonds, 1 residue, 1 model selected<br>
768<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 4 atom styles<br>
769<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 4 atom styles<br>
770<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:FES :&lt;2 &amp;/N:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:FES :&lt;2 &amp;/N:CYS">select #2/N:FES :&lt;2 &amp;/N:CYS</a></div></div>Nothing selected<br>
771<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:FES :&lt;2.5 &amp;/N:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:FES :&lt;2.5 &amp;/N:CYS">select #2/N:FES :&lt;2.5 &amp;/N:CYS</a></div></div>18 atoms, 15 bonds, 3 residues, 1 model selected<br>
772<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:FES :&lt;2.8 &amp;/N:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:FES :&lt;2.8 &amp;/N:CYS">select #2/N:FES :&lt;2.8 &amp;/N:CYS</a></div></div>24 atoms, 20 bonds, 4 residues, 1 model selected<br>
773<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N :&lt;4.5 &amp;#2/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N :&lt;4.5 &amp;#2/A-E">select #2/N :&lt;4.5 &amp;#2/A-E</a></div></div>106 atoms, 95 bonds, 12 residues, 1 model selected<br>
774<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 106 atom styles<br>
775<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;4.5 &amp;#2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;4.5 &amp;#2/N">select #2/A-E :&lt;4.5 &amp;#2/N</a></div></div>141 atoms, 134 bonds, 18 residues, 1 model selected<br>
776<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 141 atom styles<br>
777<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel dashes 6 intraMol false intraRes false reveal true retainCurrent true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel dashes 6 intraMol false intraRes false reveal true retainCurrent true log true">hbonds sel dashes 6 intraMol false intraRes false reveal true retainCurrent true log true</a></div></div><pre>Finding intermodel H-bonds
778Finding intramodel H-bonds
779Constraints relaxed by 0.4 angstroms and 20 degrees
780Models used:
781 1 AlphaFold A1Z1D6 PshB
782 2 6yez
783 3 AlphaFold Q8KCZ6 CbFdx
784 5 2fdn
785 6 PSI_IsiB_noFld.pdb
786
78761 H-bonds
788H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
789AlphaFold A1Z1D6 PshB #1/A TYR 3 OH 6yez #2/N ASP 26 OD2 no hydrogen 3.274 N/A
790AlphaFold A1Z1D6 PshB #1/A THR 6 OG1 6yez #2/N GLN 58 OE1 no hydrogen 2.570 N/A
791AlphaFold A1Z1D6 PshB #1/A CYS 12 SG 6yez #2/N GLY 61 O no hydrogen 3.429 N/A
792AlphaFold A1Z1D6 PshB #1/A CYS 20 SG 6yez #2/N SER 38 O no hydrogen 2.641 N/A
793AlphaFold A1Z1D6 PshB #1/A THR 33 N 6yez #2/N SER 45 O no hydrogen 2.919 N/A
794AlphaFold A1Z1D6 PshB #1/A THR 33 OG1 6yez #2/N SER 45 O no hydrogen 2.129 N/A
795AlphaFold A1Z1D6 PshB #1/A LYS 45 NZ 6yez #2/N ALA 41 O no hydrogen 3.560 N/A
7966yez #2/A ARG 42 NH1 6yez #2/N GLN 58 O no hydrogen 3.483 N/A
7976yez #2/A LYS 46 NZ 6yez #2/N GLY 61 O no hydrogen 3.235 N/A
7986yez #2/C LYS 35 NZ 6yez #2/N TYR 37 OH no hydrogen 2.696 N/A
7996yez #2/E ARG 106 NH2 6yez #2/N ASP 26 OD1 no hydrogen 3.124 N/A
8006yez #2/E THR 117 OG1 6yez #2/N ARG 40 O no hydrogen 3.442 N/A
8016yez #2/N ASP 26 N AlphaFold A1Z1D6 PshB #1/A TYR 3 OH no hydrogen 3.023 N/A
8026yez #2/N TYR 37 OH 2fdn #5/A HOH 179 O no hydrogen 1.912 N/A
8036yez #2/N CYS 39 SG AlphaFold Q8KCZ6 CbFdx #3/A GLU 16 O no hydrogen 3.985 N/A
8046yez #2/N ARG 40 NE 2fdn #5/A GLU 15 OE1 no hydrogen 1.468 N/A
8056yez #2/N ARG 40 NH1 AlphaFold Q8KCZ6 CbFdx #3/A ASN 39 O no hydrogen 3.073 N/A
8066yez #2/N ARG 40 NH2 AlphaFold Q8KCZ6 CbFdx #3/A ALA 45 O no hydrogen 3.441 N/A
8076yez #2/N SER 43 OG AlphaFold A1Z1D6 PshB #1/A CYS 19 O no hydrogen 3.491 N/A
8086yez #2/N CYS 44 SG AlphaFold A1Z1D6 PshB #1/A CYS 19 O no hydrogen 3.519 N/A
8096yez #2/N CYS 44 SG AlphaFold Q8KCZ6 CbFdx #3/A CYS 19 O no hydrogen 3.157 N/A
8106yez #2/N SER 45 OG 2fdn #5/A HOH 131 O no hydrogen 3.265 N/A
8116yez #2/N GLN 58 N 2fdn #5/A HOH 143 O no hydrogen 2.715 N/A
8126yez #2/N GLN 58 N 2fdn #5/A HOH 157 O no hydrogen 3.070 N/A
8136yez #2/N SER 59 N 2fdn #5/A HOH 169 O no hydrogen 2.977 N/A
8146yez #2/N THR 96 OG1 2fdn #5/A HOH 131 O no hydrogen 2.408 N/A
8156yez #2/N THR 96 OG1 2fdn #5/A HOH 147 O no hydrogen 3.427 N/A
816AlphaFold Q8KCZ6 CbFdx #3/A THR 6 OG1 6yez #2/N GLN 58 OE1 no hydrogen 2.737 N/A
817AlphaFold Q8KCZ6 CbFdx #3/A CYS 12 SG 6yez #2/N GLY 61 O no hydrogen 3.245 N/A
818AlphaFold Q8KCZ6 CbFdx #3/A ASP 34 N 6yez #2/N SER 45 O no hydrogen 2.864 N/A
819AlphaFold Q8KCZ6 CbFdx #3/A CYS 41 SG 6yez #2/N ARG 40 O no hydrogen 2.641 N/A
8202fdn #5/A SER 10 OG (alt loc A) 6yez #2/N TYR 37 O no hydrogen 0.740 N/A
8212fdn #5/A CYS 11 SG 6yez #2/N SER 43 OG no hydrogen 3.518 N/A
8222fdn #5/A GLU 15 N 6yez #2/N ARG 40 O 2fdn #5/A GLU 15 H 2.748 2.059
8232fdn #5/A SER 25 OG (alt loc B) 6yez #2/N TYR 37 OH no hydrogen 2.248 N/A
8242fdn #5/A TYR 30 OH 6yez #2/N SER 38 O 2fdn #5/A TYR 30 HH 3.238 2.616
8252fdn #5/A CYS 47 SG 6yez #2/N CYS 44 O no hydrogen 1.073 N/A
8262fdn #5/A HOH 114 O 6yez #2/N ILE 69 O no hydrogen 2.944 N/A
8272fdn #5/A HOH 115 O 6yez #2/N ALA 41 O no hydrogen 2.833 N/A
8282fdn #5/A HOH 118 O 6yez #2/N PHE 63 O no hydrogen 2.570 N/A
8292fdn #5/A HOH 119 O 6yez #2/N GLN 58 O no hydrogen 2.512 N/A
8302fdn #5/A HOH 131 O 6yez #2/N SER 45 OG no hydrogen 3.265 N/A
8312fdn #5/A HOH 131 O 6yez #2/N THR 96 OG1 no hydrogen 2.408 N/A
8322fdn #5/A HOH 138 O 6yez #2/N TYR 37 O no hydrogen 3.553 N/A
8332fdn #5/A HOH 139 O 6yez #2/N GLY 61 O no hydrogen 1.926 N/A
8342fdn #5/A HOH 141 O 6yez #2/N ARG 40 O no hydrogen 2.648 N/A
8352fdn #5/A HOH 147 O 6yez #2/N THR 96 OG1 no hydrogen 3.427 N/A
8362fdn #5/A HOH 148 O 6yez #2/N GLN 58 OE1 no hydrogen 2.593 N/A
8372fdn #5/A HOH 153 O 6yez #2/N GLN 58 O no hydrogen 1.710 N/A
8382fdn #5/A HOH 154 O 6yez #2/N SER 59 O no hydrogen 2.738 N/A
8392fdn #5/A HOH 155 O 6yez #2/N GLN 58 O no hydrogen 3.210 N/A
8402fdn #5/A HOH 159 O 6yez #2/N ASP 26 O no hydrogen 3.660 N/A
8412fdn #5/A HOH 161 O 6yez #2/N TYR 37 O no hydrogen 2.800 N/A
8422fdn #5/A HOH 171 O 6yez #2/N SER 38 O no hydrogen 2.044 N/A
8432fdn #5/A HOH 179 O 6yez #2/N TYR 37 OH no hydrogen 1.912 N/A
8442fdn #5/A HOH 186 O 6yez #2/N TYR 23 OH no hydrogen 2.883 N/A
8452fdn #5/A HOH 190 O 6yez #2/N GLN 58 OE1 no hydrogen 2.133 N/A
8462fdn #5/A HOH 190 O 6yez #2/N ILE 69 O no hydrogen 2.801 N/A
8472fdn #5/A HOH 194 O 6yez #2/N ILE 69 O no hydrogen 3.081 N/A
848PSI_IsiB_noFld.pdb #6/A LYS 28 NZ 6yez #2/N SER 59 O no hydrogen 2.762 N/A
849PSI_IsiB_noFld.pdb #6/A LYS 28 NZ 6yez #2/N GLY 61 O no hydrogen 3.493 N/A
850</pre><br/>61 hydrogen bonds found<br>
851<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel interModel false intraMol false intraRes false reveal true log true">hbonds sel interModel false intraMol false intraRes false reveal true log true</a></div></div><pre>Finding intramodel H-bonds
852Constraints relaxed by 0.4 angstroms and 20 degrees
853Models used:
854 2 6yez
855
8565 H-bonds
857H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8586yez #2/A ARG 42 NH1 6yez #2/N GLN 58 O no hydrogen 3.483 N/A
8596yez #2/A LYS 46 NZ 6yez #2/N GLY 61 O no hydrogen 3.235 N/A
8606yez #2/C LYS 35 NZ 6yez #2/N TYR 37 OH no hydrogen 2.696 N/A
8616yez #2/E ARG 106 NH2 6yez #2/N ASP 26 OD1 no hydrogen 3.124 N/A
8626yez #2/E THR 117 OG1 6yez #2/N ARG 40 O no hydrogen 3.442 N/A
863</pre><br/>5 hydrogen bonds found<br>
864<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;4.5 &amp;#2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;4.5 &amp;#2/N">select #2/A-E :&lt;4.5 &amp;#2/N</a></div></div>141 atoms, 134 bonds, 18 residues, 1 model selected<br>
865<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel interModel false intraModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel interModel false intraModel false intraMol false intraRes false reveal true log true">hbonds sel interModel false intraModel false intraMol false intraRes false reveal true log true</a></div></div><pre>Constraints relaxed by 0.4 angstroms and 20 degrees
866Models used:
867 2 6yez
868
8690 H-bonds
870H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
871</pre><br/>0 hydrogen bonds found<br>
872<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #7">close #7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel interModel false intraMol false intraRes false reveal true log true">hbonds sel interModel false intraMol false intraRes false reveal true log true</a></div></div><pre>Finding intramodel H-bonds
873Constraints relaxed by 0.4 angstroms and 20 degrees
874Models used:
875 2 6yez
876
8775 H-bonds
878H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8796yez #2/A ARG 42 NH1 6yez #2/N GLN 58 O no hydrogen 3.483 N/A
8806yez #2/A LYS 46 NZ 6yez #2/N GLY 61 O no hydrogen 3.235 N/A
8816yez #2/C LYS 35 NZ 6yez #2/N TYR 37 OH no hydrogen 2.696 N/A
8826yez #2/E ARG 106 NH2 6yez #2/N ASP 26 OD1 no hydrogen 3.124 N/A
8836yez #2/E THR 117 OG1 6yez #2/N ARG 40 O no hydrogen 3.442 N/A
884</pre><br/>5 hydrogen bonds found<br>
885<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Contacts">ui tool show Contacts</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E </div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E ">select #2/A-E </a></div></div>5656 atoms, 5816 bonds, 21 pseudobonds, 707 residues, 3 models selected<br>
886<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #2/N distanceOnly 4.5 resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #2/N distanceOnly 4.5 resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true">contacts sel restrict #2/N distanceOnly 4.5 resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true</a></div></div><pre>Ignore distances between atoms separated by 4 bonds or less
887Ignore distances between atoms in residues less than 5 apart in sequence
888Detect intra-residue distances: False
889Detect intra-molecule distances: False
890
89185 distances
892 atom1 atom2 distance
8936yez #2/C LYS 35 NZ 6yez #2/N TYR 37 OH 2.696
8946yez #2/E ARG 106 NH2 6yez #2/N ASP 26 OD1 3.124
8956yez #2/C GLN 16 NE2 6yez #2/N CYS 44 CB 3.133
8966yez #2/A LYS 46 NZ 6yez #2/N GLY 61 O 3.235
8976yez #2/C ILE 12 CD1 6yez #2/N CYS 39 CA 3.319
8986yez #2/C GLN 16 NE2 6yez #2/N CYS 44 CA 3.355
8996yez #2/E ARG 106 NH1 6yez #2/N TYR 23 CE2 3.379
9006yez #2/E THR 117 OG1 6yez #2/N ARG 40 O 3.442
9016yez #2/C LYS 35 CG 6yez #2/N TYR 37 OH 3.473
9026yez #2/A ARG 42 NH1 6yez #2/N GLN 58 O 3.483
9036yez #2/A ARG 42 NH1 6yez #2/N ILE 69 CG1 3.526
9046yez #2/C LYS 35 CD 6yez #2/N TYR 37 OH 3.585
9056yez #2/C LYS 35 CE 6yez #2/N TYR 37 OH 3.650
9066yez #2/A LYS 46 CE 6yez #2/N SER 59 O 3.708
9076yez #2/C ILE 12 CD1 6yez #2/N CYS 39 N 3.715
9086yez #2/C ILE 12 CD1 6yez #2/N SER 38 O 3.754
9096yez #2/C CYS 14 CA 6yez #2/N SER 38 OG 3.781
9106yez #2/A LYS 46 CD 6yez #2/N SER 59 O 3.788
9116yez #2/C ILE 12 CD1 6yez #2/N CYS 39 CB 3.788
9126yez #2/C GLN 16 NE2 6yez #2/N SER 45 N 3.796
9136yez #2/E ARG 70 CZ 6yez #2/N GLU 30 OE2 3.802
9146yez #2/A ARG 42 NH1 6yez #2/N ILE 69 CD1 3.805
9156yez #2/E THR 117 OG1 6yez #2/N ALA 41 CB 3.818
9166yez #2/A ARG 42 CZ 6yez #2/N ILE 69 CG1 3.820
9176yez #2/E ARG 70 NH1 6yez #2/N GLU 30 OE2 3.841
9186yez #2/C ILE 12 CD1 6yez #2/N SER 38 C 3.847
9196yez #2/C CYS 14 CB 6yez #2/N SER 38 OG 3.922
9206yez #2/C GLN 16 NE2 6yez #2/N SER 43 O 3.930
9216yez #2/A LYS 46 CG 6yez #2/N SER 59 OG 3.975
9226yez #2/A LYS 46 CB 6yez #2/N SER 59 OG 3.987
9236yez #2/A ARG 42 NE 6yez #2/N ILE 69 CG1 3.994
9246yez #2/E ARG 70 NE 6yez #2/N GLU 30 OE2 4.021
9256yez #2/E THR 117 OG1 6yez #2/N ALA 41 CA 4.021
9266yez #2/C LYS 35 NZ 6yez #2/N TYR 37 CZ 4.039
9276yez #2/C GLN 16 NE2 6yez #2/N CYS 44 C 4.040
9286yez #2/A LYS 46 CG 6yez #2/N SER 59 O 4.085
9296yez #2/C GLN 16 CD 6yez #2/N CYS 44 CB 4.085
9306yez #2/A ARG 42 CD 6yez #2/N GLU 70 OE1 4.097
9316yez #2/E THR 117 OG1 6yez #2/N ARG 40 C 4.100
9326yez #2/C GLN 16 OE1 6yez #2/N PHE 63 CE2 4.103
9336yez #2/C GLN 16 OE1 6yez #2/N PHE 63 CZ 4.120
9346yez #2/E ARG 106 CZ 6yez #2/N TYR 23 CE2 4.121
9356yez #2/C ARG 19 NH1 6yez #2/N THR 96 CG2 4.133
9366yez #2/C GLN 16 CG 6yez #2/N CYS 44 CB 4.147
9376yez #2/C PRO 59 CG 6yez #2/N CYS 39 CB 4.148
9386yez #2/C PRO 59 CB 6yez #2/N SER 43 OG 4.171
9396yez #2/E ARG 106 NH1 6yez #2/N TYR 23 CD2 4.173
9406yez #2/C LYS 35 CG 6yez #2/N TYR 37 CZ 4.175
9416yez #2/A LYS 46 NZ 6yez #2/N SER 59 O 4.182
9426yez #2/A ARG 42 NE 6yez #2/N ILE 69 CG2 4.190
9436yez #2/C LYS 35 CB 6yez #2/N TYR 37 OH 4.190
9446yez #2/C GLN 16 CD 6yez #2/N SER 43 O 4.191
9456yez #2/E ARG 106 CZ 6yez #2/N ASP 26 OD1 4.192
9466yez #2/C GLN 16 NE2 6yez #2/N PHE 63 CE2 4.196
9476yez #2/A ARG 42 NH1 6yez #2/N GLN 58 CB 4.208
9486yez #2/E ARG 70 NH2 6yez #2/N GLU 30 OE2 4.209
9496yez #2/C ILE 12 O 6yez #2/N SER 38 CB 4.235
9506yez #2/E ARG 106 NH1 6yez #2/N TYR 23 OH 4.249
9516yez #2/A LYS 46 CG 6yez #2/N SER 59 CA 4.265
9526yez #2/A LYS 46 CE 6yez #2/N GLY 61 O 4.269
9536yez #2/A LYS 46 CE 6yez #2/N GLN 58 O 4.274
9546yez #2/E ARG 106 NH1 6yez #2/N TYR 23 CZ 4.275
9556yez #2/C CYS 14 CA 6yez #2/N SER 38 CB 4.277
9566yez #2/E ARG 106 NH2 6yez #2/N TYR 23 CE2 4.281
9576yez #2/E ARG 106 NH2 6yez #2/N ASP 26 CG 4.311
9586yez #2/C GLN 16 CG 6yez #2/N SER 43 O 4.316
9596yez #2/C GLN 16 CD 6yez #2/N PHE 63 CE2 4.327
9606yez #2/C PRO 59 CB 6yez #2/N CYS 39 CB 4.328
9616yez #2/C GLN 16 CD 6yez #2/N CYS 44 CA 4.366
9626yez #2/A LYS 46 NZ 6yez #2/N GLY 61 C 4.370
9636yez #2/C ILE 12 CB 6yez #2/N SER 38 O 4.393
9646yez #2/A ARG 42 NE 6yez #2/N ILE 69 CB 4.406
9656yez #2/E THR 117 OG1 6yez #2/N ALA 41 N 4.411
9666yez #2/E ARG 70 NH2 6yez #2/N ASP 26 O 4.425
9676yez #2/C LYS 35 CB 6yez #2/N TYR 37 CZ 4.438
9686yez #2/E ARG 106 NH1 6yez #2/N ASP 26 OD1 4.440
9696yez #2/A ARG 42 NE 6yez #2/N GLU 70 OE1 4.443
9706yez #2/C LYS 35 CD 6yez #2/N TYR 37 CZ 4.447
9716yez #2/E THR 117 CB 6yez #2/N ARG 40 O 4.448
9726yez #2/C ILE 12 CD1 6yez #2/N CYS 39 C 4.449
9736yez #2/A ARG 42 NH1 6yez #2/N GLN 58 C 4.456
9746yez #2/C ILE 12 CG1 6yez #2/N SER 38 O 4.458
9756yez #2/E VAL 115 CG2 6yez #2/N ALA 41 CB 4.473
9766yez #2/A LYS 46 CE 6yez #2/N SER 59 CA 4.493
9776yez #2/A LYS 46 CE 6yez #2/N SER 59 C 4.500
978</pre><br/>85 distances<br>
979<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #2/N">sequence chain #2/N</a></div></div>Alignment identifier is 2/N<br>
980<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:23,26,30,37-45,58-63,96</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:23,26,30,37-45,58-63,96">select #2/N:23,26,30,37-45,58-63,96</a></div></div>142 atoms, 139 bonds, 19 residues, 1 model selected<br>
981<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 142 atom styles<br>
982<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 19 items<br>
983<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #2 atoms /N</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #2 atoms /N">split #2 atoms /N</a></div></div>Split 6yez (#2) into 2 models<br>
984<table border=1 cellpadding=4 cellspacing=0>
985 <thead>
986 <tr>
987 <th colspan="2">Chain information for 6yez 1 #2.1</th>
988 </tr>
989 <tr>
990 <th>Chain</th>
991 <th>Description</th>
992
993 </tr>
994 </thead>
995 <tbody>
996 <tr>
997 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.1/N:1-97">N</a></td>
998 <td><a title="Show sequence" href="cxcmd:sequence chain #2.1/N">No description available</a></td>
999
1000 </tr>
1001 </tbody>
1002</table><br/><table border=1 cellpadding=4 cellspacing=0>
1003 <thead>
1004 <tr>
1005 <th colspan="2">Chain information for 6yez 2 #2.2</th>
1006 </tr>
1007 <tr>
1008 <th>Chain</th>
1009 <th>Description</th>
1010
1011 </tr>
1012 </thead>
1013 <tbody>
1014 <tr>
1015 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2/A:16-729">A</a></td>
1016 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2/A">No description available</a></td>
1017
1018 </tr>
1019 <tr>
1020 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2/B:2-707">B</a></td>
1021 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2/B">No description available</a></td>
1022
1023 </tr>
1024 <tr>
1025 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2/C:2-81">C</a></td>
1026 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2/C">No description available</a></td>
1027
1028 </tr>
1029 <tr>
1030 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2/D:69-211">D</a></td>
1031 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2/D">No description available</a></td>
1032
1033 </tr>
1034 <tr>
1035 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2/E:64-129">E</a></td>
1036 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2/E">No description available</a></td>
1037
1038 </tr>
1039 </tbody>
1040</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #5:1-14</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #5:1-14">split #5:1-14</a></div></div>Did not split 2fdn, has only one piece<br>
1041<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-14</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-14">select #5:1-14</a></div></div>168 atoms, 168 bonds, 14 residues, 1 model selected<br>
1042<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-14,17-23,37-43</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-14,17-23,37-43">select #5:1-14,17-23,37-43</a></div></div>334 atoms, 333 bonds, 28 residues, 1 model selected<br>
1043<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-14,17-23,31-43</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-14,17-23,31-43">select #5:1-14,17-23,31-43</a></div></div>409 atoms, 408 bonds, 34 residues, 1 model selected<br>
1044<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-14,17-23,31-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-14,17-23,31-55">select #5:1-14,17-23,31-55</a></div></div>558 atoms, 559 bonds, 46 residues, 1 model selected<br>
1045<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel medium blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel medium blue">color sel medium blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;4.5 &amp;#5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;4.5 &amp;#5">select #2/A-E :&lt;4.5 &amp;#5</a></div></div>178 atoms, 150 bonds, 39 residues, 1 model selected<br>
1046<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;5 &amp;#5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;5 &amp;#5">select #2/A-E :&lt;5 &amp;#5</a></div></div>213 atoms, 181 bonds, 45 residues, 1 model selected<br>
1047<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;3 &amp;#5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;3 &amp;#5">select #2/A-E :&lt;3 &amp;#5</a></div></div>98 atoms, 86 bonds, 16 residues, 1 model selected<br>
1048<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;4 &amp;#5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;4 &amp;#5">select #2/A-E :&lt;4 &amp;#5</a></div></div>164 atoms, 140 bonds, 33 residues, 1 model selected<br>
1049<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;4 &amp;#5&amp;~:HOH</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;4 &amp;#5&amp;~:HOH">select #2/A-E :&lt;4 &amp;#5&amp;~:HOH</a></div></div>144 atoms, 140 bonds, 13 residues, 1 model selected<br>
1050<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;3 &amp;#5&amp;~:HOH</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;3 &amp;#5&amp;~:HOH">select #2/A-E :&lt;3 &amp;#5&amp;~:HOH</a></div></div>88 atoms, 86 bonds, 6 residues, 1 model selected<br>
1051<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;2 &amp;#5&amp;~:HOH</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;2 &amp;#5&amp;~:HOH">select #2/A-E :&lt;2 &amp;#5&amp;~:HOH</a></div></div>35 atoms, 33 bonds, 2 residues, 1 model selected<br>
1052<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;4 &amp;#5&amp;~:HOH</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;4 &amp;#5&amp;~:HOH">select #2/A-E :&lt;4 &amp;#5&amp;~:HOH</a></div></div>144 atoms, 140 bonds, 13 residues, 1 model selected<br>
1053<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Clashes</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Clashes">ui tool show Clashes</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true">clashes sel intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
1054H-bond overlap reduction: 0.4
1055Ignore clashes between atoms separated by 4 bonds or less
1056Detect intra-residue clashes: False
1057Detect intra-molecule clashes: True
1058
105910 clashes
1060 atom1 atom2 overlap distance
10612fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 O 1.079 2.041
10622fdn #5/A ILE 9 CD1 6yez 2 #2.2/C GLN 16 NE2 1.030 2.310
10632fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 O 1.019 1.401
10642fdn #5/A ILE 9 CD1 6yez 2 #2.2/C GLN 16 CG 0.900 2.680
10652fdn #5/A ILE 9 HD12 6yez 2 #2.2/C GLN 16 NE2 0.839 1.801
10662fdn #5/A CYS 11 HA 6yez 2 #2.2/C ILE 12 CD1 0.775 2.105
10672fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 0.738 2.382
10682fdn #5/A GLU 15 OE2 6yez 2 #2.2/E VAL 91 CG1 0.706 2.654
10692fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 0.661 1.979
10702fdn #5/A ILE 9 HD13 6yez 2 #2.2/C GLN 16 CG 0.632 2.248
1071</pre><br/>10 clashes<br>
1072<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5">select #5</a></div></div>762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected<br>
1073<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 151 items<br>
1074<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:12,14,16,91</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:12,14,16,91">select #5:12,14,16,91</a></div></div>31 atoms, 29 bonds, 3 residues, 1 model selected<br>
1075<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:9,11,15,49</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:9,11,15,49">select #5:9,11,15,49</a></div></div>60 atoms, 56 bonds, 4 residues, 1 model selected<br>
1076<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel orange</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel orange">color sel orange</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2 models">hide #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2 models">show #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2 models">hide #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2 models">show #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:FES@FE1,FE2,S1,S2:44@SG</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:FES@FE1,FE2,S1,S2:44@SG">select #2/N:FES@FE1,FE2,S1,S2:44@SG</a></div></div>5 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected<br>
1077<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N:FES@FE1,FE2,S1,S2:44@SG:39@SG:47@SG:77@SG</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N:FES@FE1,FE2,S1,S2:44@SG:39@SG:47@SG:77@SG">select #2/N:FES@FE1,FE2,S1,S2:44@SG:39@SG:47@SG:77@SG</a></div></div>8 atoms, 4 bonds, 4 pseudobonds, 5 residues, 2 models selected<br>
1078<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 8 atom styles<br>
1079<div class="cxcmd"><a href="help:user/commands/align.html">align</a> #5:61@FE2,FE3,S4,S1,S3,S2:11@SG:14@SG <span style="color:white; background-color:crimson;">toAtomsl #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG:77@SG</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #5:61@FE2,FE3,S4,S1,S3,S2:11@SG:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG:77@SG</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG:77@SG">align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG:77@SG</a></div></div>RMSD between 8 atom pairs is 0.719 angstroms<br>
1080<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #7">close #7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-E :&lt;4 &amp;#5&amp;~:HOH</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-E :&lt;4 &amp;#5&amp;~:HOH">select #2/A-E :&lt;4 &amp;#5&amp;~:HOH</a></div></div>120 atoms, 118 bonds, 10 residues, 1 model selected<br>
1081<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-55 :&lt;4&amp;#2/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-55 :&lt;4&amp;#2/A-E">select #5:1-55 :&lt;4&amp;#2/A-E</a></div></div>86 atoms, 80 bonds, 11 residues, 1 model selected<br>
1082<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true">clashes sel intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
1083H-bond overlap reduction: 0.4
1084Ignore clashes between atoms separated by 4 bonds or less
1085Detect intra-residue clashes: False
1086Detect intra-molecule clashes: True
1087
108831 clashes
1089 atom1 atom2 overlap distance
10906yez 2 #2.2/E ARG 106 CZ 2fdn #5/A HOH 183 O 2.185 0.885
10916yez 2 #2.2/C ARG 19 CZ 2fdn #5/A HOH 149 O 1.833 1.237
10926yez 2 #2.2/E ARG 106 NE 2fdn #5/A HOH 183 O 1.591 1.109
10936yez 2 #2.2/E VAL 91 O 2fdn #5/A HOH 182 O 1.380 1.100
10946yez 2 #2.2/E VAL 91 C 2fdn #5/A HOH 182 O 1.295 1.775
10956yez 2 #2.2/C GLN 16 NE2 2fdn #5/A VAL 49 HG11 1.244 1.396
10966yez 2 #2.2/C ARG 19 NH1 2fdn #5/A HOH 149 O 1.149 1.551
10976yez 2 #2.2/C CYS 14 O 2fdn #5/A ILE 9 HG22 1.100 1.320
10986yez 2 #2.2/C CYS 14 CB 2fdn #5/A ILE 9 HD11 1.095 1.785
10996yez 2 #2.2/C CYS 14 O 2fdn #5/A ILE 9 CG2 1.094 2.026
11006yez 2 #2.2/C CYS 14 CB 2fdn #5/A ILE 9 CD1 1.091 2.489
11016yez 2 #2.2/E ARG 106 CD 2fdn #5/A HOH 183 O 1.078 2.262
11026yez 2 #2.2/C ARG 19 NE 2fdn #5/A HOH 117 O 1.078 1.622
11036yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 HB 1.036 1.844
11046yez 2 #2.2/C GLN 16 NE2 2fdn #5/A VAL 49 CG1 1.032 2.308
11056yez 2 #2.2/E ARG 106 NH2 2fdn #5/A HOH 183 O 1.015 1.685
11066yez 2 #2.2/C ARG 19 NE 2fdn #5/A HOH 149 O 0.963 1.737
11076yez 2 #2.2/E VAL 91 CG1 2fdn #5/A HOH 182 O 0.944 2.396
11086yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 CB 0.919 2.661
11096yez 2 #2.2/E VAL 91 CA 2fdn #5/A HOH 182 O 0.915 2.425
11106yez 2 #2.2/C ILE 12 CD1 2fdn #5/A CYS 11 HA 0.873 2.007
11116yez 2 #2.2/C ARG 19 CD 2fdn #5/A HOH 149 O 0.871 2.469
11126yez 2 #2.2/E ARG 106 NH1 2fdn #5/A HOH 183 O 0.810 1.890
11136yez 2 #2.2/C ARG 19 CZ 2fdn #5/A HOH 117 O 0.807 2.263
11146yez 2 #2.2/C CYS 14 CB 2fdn #5/A ILE 9 CG1 0.774 2.806
11156yez 2 #2.2/C CYS 14 O 2fdn #5/A ILE 9 CB 0.742 2.378
11166yez 2 #2.2/C CYS 14 O 2fdn #5/A ILE 9 CD1 0.695 2.425
11176yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 CG1 0.683 2.897
11186yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 HD11 0.668 2.212
11196yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 CD1 0.667 2.913
11206yez 2 #2.2/C GLN 16 NE2 2fdn #5/A PRO 48 CG 0.613 2.727
1121</pre><br/>31 clashes<br>
1122<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #7">close #7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-55">select #5:1-55</a></div></div>652 atoms, 657 bonds, 55 residues, 1 model selected<br>
1123<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true">clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
1124H-bond overlap reduction: 0.4
1125Ignore clashes between atoms separated by 4 bonds or less
1126Detect intra-residue clashes: False
1127Detect intra-molecule clashes: True
1128
112916 clashes
1130 atom1 atom2 overlap distance
11312fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 1.244 1.396
11322fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 O 1.100 1.320
11332fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CB 1.095 1.785
11342fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 1.094 2.026
11352fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CB 1.091 2.489
11362fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CA 1.036 1.844
11372fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 NE2 1.032 2.308
11382fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CA 0.919 2.661
11392fdn #5/A CYS 11 HA 6yez 2 #2.2/C ILE 12 CD1 0.873 2.007
11402fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CB 0.774 2.806
11412fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 O 0.742 2.378
11422fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 O 0.695 2.425
11432fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CA 0.683 2.897
11442fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CA 0.668 2.212
11452fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CA 0.667 2.913
11462fdn #5/A PRO 48 CG 6yez 2 #2.2/C GLN 16 NE2 0.613 2.727
1147</pre><br/>16 clashes<br>
1148<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:9,11,48-49</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:9,11,48-49">select #5:9,11,48-49</a></div></div>59 atoms, 57 bonds, 4 residues, 1 model selected<br>
1149<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #5:61@FE2,FE3,S4,S1,S3,S2:11@SG,CB,CA:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG,CB,CA:77@SG</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG,CB,CA:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG,CB,CA:77@SG">align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG,CB,CA:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG,CB,CA:77@SG</a></div></div>RMSD between 10 atom pairs is 0.673 angstroms<br>
1150<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-55">select #5:1-55</a></div></div>652 atoms, 657 bonds, 55 residues, 1 model selected<br>
1151<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true">clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
1152H-bond overlap reduction: 0.4
1153Ignore clashes between atoms separated by 4 bonds or less
1154Detect intra-residue clashes: False
1155Detect intra-molecule clashes: True
1156
115715 clashes
1158 atom1 atom2 overlap distance
11592fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 1.558 1.082
11602fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CB 1.548 1.332
11612fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CB 1.462 2.118
11622fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 O 1.448 0.972
11632fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 NE2 1.337 2.003
11642fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 1.287 1.833
11652fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CA 1.254 1.626
11662fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CA 1.171 2.409
11672fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CB 1.000 2.580
11682fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CA 0.871 2.709
11692fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CA 0.845 2.035
11702fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CA 0.807 2.773
11712fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 SG 0.730 2.040
11722fdn #5/A CYS 11 HA 6yez 2 #2.2/C ILE 12 CD1 0.693 2.187
11732fdn #5/A PRO 48 HB2 6yez 2 #2.2/C GLN 16 CD 0.623 1.987
1174</pre><br/>15 clashes<br>
1175<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
1176<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 98 items<br>
1177<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2 models">hide #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #5:61@FE2,FE3,S4,S1,S3,S2:11@SG,CB,CA,C:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG,CB,CA,C:77@SG</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG,CB,CA,C:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG,CB,CA,C:77@SG">align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG,CB,CA,C:14@SG toAtoms #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG,CB,CA,C:77@SG</a></div></div>RMSD between 11 atom pairs is 0.654 angstroms<br>
1178<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-55">select #5:1-55</a></div></div>652 atoms, 657 bonds, 55 residues, 1 model selected<br>
1179<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true">clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
1180H-bond overlap reduction: 0.4
1181Ignore clashes between atoms separated by 4 bonds or less
1182Detect intra-residue clashes: False
1183Detect intra-molecule clashes: True
1184
11850 clashes
1186atom1 atom2 overlap distance
1187</pre><br/>No clashes<br>
1188<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2 models">show #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true">clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</a></div></div><font color="crimson"><b>No atoms match given atom specifier<br>
1189</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-55">select #5:1-55</a></div></div>652 atoms, 657 bonds, 55 residues, 1 model selected<br>
1190<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true">clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
1191H-bond overlap reduction: 0.4
1192Ignore clashes between atoms separated by 4 bonds or less
1193Detect intra-residue clashes: False
1194Detect intra-molecule clashes: True
1195
119614 clashes
1197 atom1 atom2 overlap distance
11982fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 1.670 0.970
11992fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CB 1.590 1.290
12002fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CB 1.488 2.092
12012fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 O 1.470 0.950
12022fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 NE2 1.451 1.889
12032fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 1.311 1.809
12042fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CA 1.236 1.644
12052fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CA 1.157 2.423
12062fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CB 0.994 2.586
12072fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CA 0.873 2.707
12082fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CA 0.853 2.027
12092fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CA 0.794 2.786
12102fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 SG 0.743 2.027
12112fdn #5/A CYS 11 HA 6yez 2 #2.2/C ILE 12 CD1 0.649 2.231
1212</pre><br/>14 clashes<br>
1213<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #5:11@CB,CA,C:14 toAtoms #2/N:39@CB,CA,C</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #5:11@CB,CA,C:14 toAtoms #2/N:39@CB,CA,C">align #5:11@CB,CA,C:14 toAtoms #2/N:39@CB,CA,C</a></div></div><font color="crimson"><b>Unequal number of atoms to pair, 13 and 3</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #5:11@CB,CA,C toAtoms #2/N:39@CB,CA,C</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #5:11@CB,CA,C toAtoms #2/N:39@CB,CA,C">align #5:11@CB,CA,C toAtoms #2/N:39@CB,CA,C</a></div></div>RMSD between 3 atom pairs is 0.032 angstroms<br>
1214<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:1-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:1-55">select #5:1-55</a></div></div>652 atoms, 657 bonds, 55 residues, 1 model selected<br>
1215<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true">clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
1216H-bond overlap reduction: 0.4
1217Ignore clashes between atoms separated by 4 bonds or less
1218Detect intra-residue clashes: False
1219Detect intra-molecule clashes: True
1220
122140 clashes
1222 atom1 atom2 overlap distance
12232fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 NE2 2.426 0.914
12242fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 2.354 0.766
12252fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 2.183 0.457
12262fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CA 2.131 0.749
12272fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CA 1.896 1.684
12282fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 CD 1.861 1.449
12292fdn #5/A ILE 9 HG23 6yez 2 #2.2/C CYS 14 O 1.757 0.663
12302fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 CD 1.639 0.971
12312fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 C 1.597 1.713
12322fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CB 1.539 2.041
12332fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CB 1.513 2.067
12342fdn #5/A VAL 49 CB 6yez 2 #2.2/C GLN 16 NE2 1.500 1.840
12352fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CB 1.492 2.088
12362fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 O 1.464 0.956
12372fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CB 1.369 1.511
12382fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 SG 1.353 1.417
12392fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CB 1.336 1.544
12402fdn #5/A VAL 49 HG12 6yez 2 #2.2/C GLN 16 NE2 1.275 1.365
12412fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 OE1 1.226 1.894
12422fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 CA 1.180 2.400
12432fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 C 1.152 2.158
12442fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 SG 1.135 2.335
12452fdn #5/A VAL 49 HG13 6yez 2 #2.2/C GLN 16 OE1 1.118 1.302
12462fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 O 1.081 2.039
12472fdn #5/A ILE 9 HG23 6yez 2 #2.2/C CYS 14 C 1.052 1.558
12482fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 C 1.047 1.563
12492fdn #5/A VAL 49 HG13 6yez 2 #2.2/C GLN 16 CD 1.029 1.581
12502fdn #5/A ILE 9 CD1 6yez 2 #2.2/C GLN 16 CG 1.005 2.575
12512fdn #5/A ILE 9 HD12 6yez 2 #2.2/C GLN 16 CG 0.986 1.894
12522fdn #5/A VAL 49 CG2 6yez 2 #2.2/C GLN 16 NE2 0.921 2.419
12532fdn #5/A VAL 49 HG13 6yez 2 #2.2/C GLN 16 NE2 0.893 1.747
12542fdn #5/A ILE 9 HG21 6yez 2 #2.2/C CYS 14 O 0.882 1.538
12552fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CA 0.881 2.699
12562fdn #5/A ILE 9 CA 6yez 2 #2.2/C CYS 14 CA 0.878 2.702
12572fdn #5/A ILE 9 HG13 6yez 2 #2.2/C CYS 14 CB 0.821 2.059
12582fdn #5/A VAL 49 HG12 6yez 2 #2.2/C GLN 16 CD 0.810 1.800
12592fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 C 0.800 1.810
12602fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 CG 0.772 2.808
12612fdn #5/A VAL 49 CA 6yez 2 #2.2/C GLN 16 NE2 0.683 2.657
12622fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 CG 0.683 2.197
1263</pre><br/>40 clashes<br>
1264<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:9,49</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:9,49">select #5:9,49</a></div></div>35 atoms, 33 bonds, 2 residues, 1 model selected<br>
1265<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:16</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:16">select #2/C:16</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
1266<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:16|#5:1-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:16|#5:1-55">select #2/C:16|#5:1-55</a></div></div>661 atoms, 665 bonds, 17 pseudobonds, 56 residues, 3 models selected<br>
1267<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:16/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:16/N">select #2/C:16/N</a></div></div>737 atoms, 748 bonds, 4 pseudobonds, 99 residues, 3 models selected<br>
1268<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel restrict both interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel restrict both interModel false intraMol false intraRes false reveal true log true">hbonds sel restrict both interModel false intraMol false intraRes false reveal true log true</a></div></div><pre>Finding intramodel H-bonds
1269Constraints relaxed by 0.4 angstroms and 20 degrees
1270Models used:
1271 2.1 6yez 1
1272 2.2 6yez 2
1273
12740 H-bonds
1275H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1276</pre><br/>0 hydrogen bonds found<br>
1277<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Contacts">ui tool show Contacts</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict both resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict both resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true">contacts sel restrict both resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
1278H-bond overlap reduction: 0.4
1279Ignore contacts between atoms separated by 4 bonds or less
1280Ignore contacts between atoms in residues less than 5 apart in sequence
1281Detect intra-residue contacts: False
1282Detect intra-molecule contacts: False
1283
128419 contacts
1285 atom1 atom2 overlap distance
12866yez 1 #2.1/N GLY 42 CA 6yez 1 #2.1/N FES 101 S2 0.389 3.261
12876yez 1 #2.1/N CYS 44 SG 6yez 1 #2.1/N FES 101 FE1 0.123 2.277
12886yez 1 #2.1/N FES 101 FE1 6yez 1 #2.1/N CYS 39 SG 0.081 2.319
12896yez 1 #2.1/N FES 101 FE2 6yez 1 #2.1/N CYS 47 SG 0.040 2.360
12906yez 1 #2.1/N CYS 44 O 6yez 1 #2.1/N FES 101 S2 -0.022 3.212
12916yez 1 #2.1/N LEU 75 CD1 6yez 1 #2.1/N FES 101 S2 -0.065 3.715
12926yez 1 #2.1/N CYS 44 N 6yez 1 #2.1/N FES 101 S2 -0.080 3.090
12936yez 1 #2.1/N GLY 42 C 6yez 1 #2.1/N FES 101 S2 -0.102 3.482
12946yez 1 #2.1/N CYS 44 CA 6yez 1 #2.1/N FES 101 S2 -0.180 3.830
12956yez 1 #2.1/N CYS 77 SG 6yez 1 #2.1/N FES 101 FE2 -0.190 2.590
12966yez 1 #2.1/N CYS 47 CB 6yez 1 #2.1/N FES 101 S1 -0.219 3.869
12976yez 1 #2.1/N SER 43 N 6yez 1 #2.1/N FES 101 S2 -0.245 3.255
12986yez 1 #2.1/N ARG 40 N 6yez 1 #2.1/N FES 101 S1 -0.246 3.256
12996yez 1 #2.1/N LEU 75 CD2 6yez 1 #2.1/N FES 101 S2 -0.266 3.916
13006yez 1 #2.1/N SER 38 N 6yez 1 #2.1/N FES 101 S1 -0.279 3.289
13016yez 1 #2.1/N TYR 37 CB 6yez 1 #2.1/N FES 101 S1 -0.280 3.930
13026yez 1 #2.1/N ARG 40 CA 6yez 1 #2.1/N FES 101 S1 -0.346 3.996
13036yez 1 #2.1/N FES 101 S1 6yez 1 #2.1/N TYR 37 CA -0.381 4.031
13046yez 1 #2.1/N FES 101 S2 6yez 1 #2.1/N CYS 39 SG -0.394 3.534
1305</pre><br/>19 contacts<br>
1306<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:16/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:16/N">select #2/C:16/N</a></div></div>737 atoms, 748 bonds, 23 pseudobonds, 99 residues, 4 models selected<br>
1307<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:16</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:16">select #2/C:16</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
1308<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #2/N resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #2/N resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true">contacts sel restrict #2/N resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
1309H-bond overlap reduction: 0.4
1310Ignore contacts between atoms separated by 4 bonds or less
1311Ignore contacts between atoms in residues less than 5 apart in sequence
1312Detect intra-residue contacts: False
1313Detect intra-molecule contacts: False
1314
13150 contacts
1316atom1 atom2 overlap distance
1317</pre><br/>No contacts<br>
1318<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:14</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:14">select #2/C:14</a></div></div>6 atoms, 5 bonds, 1 residue, 1 model selected<br>
1319<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #2/N resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #2/N resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true">contacts sel restrict #2/N resSeparation 5 interModel false intraMol false select true color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
1320H-bond overlap reduction: 0.4
1321Ignore contacts between atoms separated by 4 bonds or less
1322Ignore contacts between atoms in residues less than 5 apart in sequence
1323Detect intra-residue contacts: False
1324Detect intra-molecule contacts: False
1325
13260 contacts
1327atom1 atom2 overlap distance
1328</pre><br/>No contacts<br>
1329<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #8">close #8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:9,49</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:9,49">select #5:9,49</a></div></div>35 atoms, 33 bonds, 2 residues, 1 model selected<br>
1330<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
1331<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 728 atom styles<br>
1332<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Contacts">ui tool show Contacts</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #2/A-E resSeparation 5 interModel false intraMol false select true color #00f900 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #2/A-E resSeparation 5 interModel false intraMol false select true color #00f900 reveal true log true">contacts sel restrict #2/A-E resSeparation 5 interModel false intraMol false select true color #00f900 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
1333H-bond overlap reduction: 0.4
1334Ignore contacts between atoms separated by 4 bonds or less
1335Ignore contacts between atoms in residues less than 5 apart in sequence
1336Detect intra-residue contacts: False
1337Detect intra-molecule contacts: False
1338
13390 contacts
1340atom1 atom2 overlap distance
1341</pre><br/>No contacts<br>
1342<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #2/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #2/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true">contacts sel restrict #2/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true</a></div></div><font color="crimson"><b>No atoms match given atom specifier<br>
1343</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
1344<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #2/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #2/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true">contacts sel restrict #2/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
1345H-bond overlap reduction: 0.4
1346Ignore contacts between atoms separated by 4 bonds or less
1347Ignore contacts between atoms in residues less than 5 apart in sequence
1348Detect intra-residue contacts: False
1349Detect intra-molecule contacts: False
1350
13510 contacts
1352atom1 atom2 overlap distance
1353</pre><br/>No contacts<br>
1354<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N :&lt;4.5 &amp;#2/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N :&lt;4.5 &amp;#2/A-E">select #2/N :&lt;4.5 &amp;#2/A-E</a></div></div>106 atoms, 95 bonds, 12 residues, 1 model selected<br>
1355<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true">contacts sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true</a></div></div><pre>Ignore distances between atoms separated by 4 bonds or less
1356Ignore distances between atoms in residues less than 5 apart in sequence
1357Detect intra-residue distances: False
1358Detect intra-molecule distances: False
1359
136044 distances
1361 atom1 atom2 distance
13626yez 2 #2.2/C CYS 14 SG 6yez 2 #2.2/C SF4 3003 FE1 2.513
13636yez 2 #2.2/C LYS 35 NZ 6yez 2 #2.2/E ASP 94 OD1 2.817
13646yez 2 #2.2/C LYS 35 CE 6yez 2 #2.2/E ASP 94 OD1 3.169
13656yez 2 #2.2/C LYS 35 NZ 6yez 2 #2.2/E ASP 94 CB 3.301
13666yez 2 #2.2/C CYS 14 SG 6yez 2 #2.2/C SF4 3003 S2 3.328
13676yez 2 #2.2/C CYS 14 N 6yez 2 #2.2/C SF4 3003 S3 3.398
13686yez 2 #2.2/C LYS 35 NZ 6yez 2 #2.2/E ASP 94 CG 3.427
13696yez 2 #2.2/C CYS 14 CB 6yez 2 #2.2/C SF4 3003 FE1 3.477
13706yez 2 #2.2/C PRO 59 CD 6yez 2 #2.2/C SF4 3003 S2 3.547
13716yez 2 #2.2/C CYS 14 N 6yez 2 #2.2/C SF4 3003 FE1 3.558
13726yez 2 #2.2/C ILE 12 N 6yez 2 #2.2/C SF4 3003 S4 3.574
13736yez 2 #2.2/C ARG 19 CZ 6yez 2 #2.2/D GLU 176 CB 3.741
13746yez 2 #2.2/C PRO 59 CD 6yez 2 #2.2/C SF4 3003 FE1 3.759
13756yez 2 #2.2/C ARG 19 NH1 6yez 2 #2.2/D GLU 176 CG 3.791
13766yez 2 #2.2/C LYS 35 CE 6yez 2 #2.2/E ASP 94 CB 3.834
13776yez 2 #2.2/C PRO 59 O 6yez 2 #2.2/E VAL 115 CG1 3.837
13786yez 2 #2.2/C CYS 14 SG 6yez 2 #2.2/C SF4 3003 S3 3.855
13796yez 2 #2.2/C ARG 19 NH1 6yez 2 #2.2/D GLU 176 CB 3.861
13806yez 2 #2.2/C LYS 35 CE 6yez 2 #2.2/E ASP 94 CG 3.942
13816yez 2 #2.2/C ARG 19 CG 6yez 2 #2.2/D GLU 176 CB 3.953
13826yez 2 #2.2/C ARG 19 NH2 6yez 2 #2.2/D GLU 176 O 3.953
13836yez 2 #2.2/C PRO 59 O 6yez 2 #2.2/E VAL 115 CG2 3.956
13846yez 2 #2.2/C ARG 19 NH2 6yez 2 #2.2/D GLU 176 CB 3.961
13856yez 2 #2.2/C CYS 14 CA 6yez 2 #2.2/C SF4 3003 FE1 3.964
13866yez 2 #2.2/C ILE 12 CG1 6yez 2 #2.2/C SF4 3003 S4 3.982
13876yez 2 #2.2/C ARG 19 NE 6yez 2 #2.2/D GLU 176 CB 4.078
13886yez 2 #2.2/C LYS 35 CE 6yez 2 #2.2/E THR 99 CG2 4.085
13896yez 2 #2.2/C PRO 59 CD 6yez 2 #2.2/C SF4 3003 FE3 4.085
13906yez 2 #2.2/C PRO 59 CD 6yez 2 #2.2/C SF4 3003 S4 4.089
13916yez 2 #2.2/C ARG 19 CZ 6yez 2 #2.2/D GLU 176 CG 4.095
13926yez 2 #2.2/C CYS 14 C 6yez 2 #2.2/C SF4 3003 S3 4.143
13936yez 2 #2.2/C ILE 12 N 6yez 2 #2.2/C SF4 3003 FE2 4.195
13946yez 2 #2.2/C CYS 14 CA 6yez 2 #2.2/C SF4 3003 S3 4.198
13956yez 2 #2.2/C ARG 19 NH2 6yez 2 #2.2/D GLU 176 CG 4.263
13966yez 2 #2.2/C LYS 35 CG 6yez 2 #2.2/E ASP 94 OD1 4.284
13976yez 2 #2.2/C LYS 35 CD 6yez 2 #2.2/E ASP 94 OD1 4.295
13986yez 2 #2.2/C PRO 59 O 6yez 2 #2.2/E VAL 115 CB 4.335
13996yez 2 #2.2/C CYS 14 C 6yez 2 #2.2/C SF4 3003 FE1 4.384
14006yez 2 #2.2/C PRO 59 N 6yez 2 #2.2/C SF4 3003 S2 4.384
14016yez 2 #2.2/C CYS 14 SG 6yez 2 #2.2/C SF4 3003 FE4 4.408
14026yez 2 #2.2/C GLN 16 N 6yez 2 #2.2/C SF4 3003 S2 4.411
14036yez 2 #2.2/C ILE 12 CG1 6yez 2 #2.2/C SF4 3003 FE1 4.414
14046yez 2 #2.2/C PRO 59 CG 6yez 2 #2.2/C SF4 3003 FE1 4.463
14056yez 2 #2.2/C ILE 12 CG2 6yez 2 #2.2/E ASN 119 ND2 4.478
1406</pre><br/>44 distances<br>
1407<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
1408<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true">contacts sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true</a></div></div><pre>Ignore distances between atoms separated by 4 bonds or less
1409Ignore distances between atoms in residues less than 5 apart in sequence
1410Detect intra-residue distances: False
1411Detect intra-molecule distances: False
1412
14130 distances
1414atom1 atom2 distance
1415</pre><br/>No distances<br>
1416<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #8">close #8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #6</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #6">close #6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #3-4</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #3-4">close #3-4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #1">close #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 id 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 id 1">rename #2 id 1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1 id 2</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1 id 2">rename #1 id 2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #5 id 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #5 id 1">rename #5 id 1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #7 id 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #7 id 3">rename #7 id 3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #2.1#2.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #2.1#2.2">combine #2.1#2.2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/N">select #4/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
1417<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #4/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #4/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true">contacts sel restrict #4/A-E distanceOnly 4.5 resSeparation 5 intraMol false select true color #00f900 reveal true log true</a></div></div><pre>Ignore distances between atoms separated by 4 bonds or less
1418Ignore distances between atoms in residues less than 5 apart in sequence
1419Detect intra-residue distances: False
1420Detect intra-molecule distances: False
1421
142285 distances
1423 atom1 atom2 distance
1424combination #4/N TYR 37 OH combination #4/C LYS 35 NZ 2.696
1425combination #4/N ASP 26 OD1 combination #4/E ARG 106 NH2 3.124
1426combination #4/N CYS 44 CB combination #4/C GLN 16 NE2 3.133
1427combination #4/N GLY 61 O combination #4/A LYS 46 NZ 3.235
1428combination #4/N CYS 39 CA combination #4/C ILE 12 CD1 3.319
1429combination #4/N CYS 44 CA combination #4/C GLN 16 NE2 3.355
1430combination #4/N TYR 23 CE2 combination #4/E ARG 106 NH1 3.379
1431combination #4/N ARG 40 O combination #4/E THR 117 OG1 3.442
1432combination #4/N TYR 37 OH combination #4/C LYS 35 CG 3.473
1433combination #4/N GLN 58 O combination #4/A ARG 42 NH1 3.483
1434combination #4/N ILE 69 CG1 combination #4/A ARG 42 NH1 3.526
1435combination #4/N TYR 37 OH combination #4/C LYS 35 CD 3.585
1436combination #4/N TYR 37 OH combination #4/C LYS 35 CE 3.650
1437combination #4/N SER 59 O combination #4/A LYS 46 CE 3.708
1438combination #4/N CYS 39 N combination #4/C ILE 12 CD1 3.715
1439combination #4/N SER 38 O combination #4/C ILE 12 CD1 3.754
1440combination #4/N SER 38 OG combination #4/C CYS 14 CA 3.781
1441combination #4/N SER 59 O combination #4/A LYS 46 CD 3.788
1442combination #4/N CYS 39 CB combination #4/C ILE 12 CD1 3.788
1443combination #4/N SER 45 N combination #4/C GLN 16 NE2 3.796
1444combination #4/N GLU 30 OE2 combination #4/E ARG 70 CZ 3.802
1445combination #4/N ILE 69 CD1 combination #4/A ARG 42 NH1 3.805
1446combination #4/N ALA 41 CB combination #4/E THR 117 OG1 3.818
1447combination #4/N ILE 69 CG1 combination #4/A ARG 42 CZ 3.820
1448combination #4/N GLU 30 OE2 combination #4/E ARG 70 NH1 3.841
1449combination #4/N SER 38 C combination #4/C ILE 12 CD1 3.847
1450combination #4/N SER 38 OG combination #4/C CYS 14 CB 3.922
1451combination #4/N SER 43 O combination #4/C GLN 16 NE2 3.930
1452combination #4/N SER 59 OG combination #4/A LYS 46 CG 3.975
1453combination #4/N SER 59 OG combination #4/A LYS 46 CB 3.987
1454combination #4/N ILE 69 CG1 combination #4/A ARG 42 NE 3.994
1455combination #4/N GLU 30 OE2 combination #4/E ARG 70 NE 4.021
1456combination #4/N ALA 41 CA combination #4/E THR 117 OG1 4.021
1457combination #4/N TYR 37 CZ combination #4/C LYS 35 NZ 4.039
1458combination #4/N CYS 44 C combination #4/C GLN 16 NE2 4.040
1459combination #4/N SER 59 O combination #4/A LYS 46 CG 4.085
1460combination #4/N CYS 44 CB combination #4/C GLN 16 CD 4.085
1461combination #4/N GLU 70 OE1 combination #4/A ARG 42 CD 4.097
1462combination #4/N ARG 40 C combination #4/E THR 117 OG1 4.100
1463combination #4/N PHE 63 CE2 combination #4/C GLN 16 OE1 4.103
1464combination #4/N PHE 63 CZ combination #4/C GLN 16 OE1 4.120
1465combination #4/N TYR 23 CE2 combination #4/E ARG 106 CZ 4.121
1466combination #4/N THR 96 CG2 combination #4/C ARG 19 NH1 4.133
1467combination #4/N CYS 44 CB combination #4/C GLN 16 CG 4.147
1468combination #4/N CYS 39 CB combination #4/C PRO 59 CG 4.148
1469combination #4/N SER 43 OG combination #4/C PRO 59 CB 4.171
1470combination #4/N TYR 23 CD2 combination #4/E ARG 106 NH1 4.173
1471combination #4/N TYR 37 CZ combination #4/C LYS 35 CG 4.175
1472combination #4/N SER 59 O combination #4/A LYS 46 NZ 4.182
1473combination #4/N ILE 69 CG2 combination #4/A ARG 42 NE 4.190
1474combination #4/N TYR 37 OH combination #4/C LYS 35 CB 4.190
1475combination #4/N SER 43 O combination #4/C GLN 16 CD 4.191
1476combination #4/N ASP 26 OD1 combination #4/E ARG 106 CZ 4.192
1477combination #4/N PHE 63 CE2 combination #4/C GLN 16 NE2 4.196
1478combination #4/N GLN 58 CB combination #4/A ARG 42 NH1 4.208
1479combination #4/N GLU 30 OE2 combination #4/E ARG 70 NH2 4.209
1480combination #4/N SER 38 CB combination #4/C ILE 12 O 4.235
1481combination #4/N TYR 23 OH combination #4/E ARG 106 NH1 4.249
1482combination #4/N SER 59 CA combination #4/A LYS 46 CG 4.265
1483combination #4/N GLY 61 O combination #4/A LYS 46 CE 4.269
1484combination #4/N GLN 58 O combination #4/A LYS 46 CE 4.274
1485combination #4/N TYR 23 CZ combination #4/E ARG 106 NH1 4.275
1486combination #4/N SER 38 CB combination #4/C CYS 14 CA 4.277
1487combination #4/N TYR 23 CE2 combination #4/E ARG 106 NH2 4.281
1488combination #4/N ASP 26 CG combination #4/E ARG 106 NH2 4.311
1489combination #4/N SER 43 O combination #4/C GLN 16 CG 4.316
1490combination #4/N PHE 63 CE2 combination #4/C GLN 16 CD 4.327
1491combination #4/N CYS 39 CB combination #4/C PRO 59 CB 4.328
1492combination #4/N CYS 44 CA combination #4/C GLN 16 CD 4.366
1493combination #4/N GLY 61 C combination #4/A LYS 46 NZ 4.370
1494combination #4/N SER 38 O combination #4/C ILE 12 CB 4.393
1495combination #4/N ILE 69 CB combination #4/A ARG 42 NE 4.406
1496combination #4/N ALA 41 N combination #4/E THR 117 OG1 4.411
1497combination #4/N ASP 26 O combination #4/E ARG 70 NH2 4.425
1498combination #4/N TYR 37 CZ combination #4/C LYS 35 CB 4.438
1499combination #4/N ASP 26 OD1 combination #4/E ARG 106 NH1 4.440
1500combination #4/N GLU 70 OE1 combination #4/A ARG 42 NE 4.443
1501combination #4/N TYR 37 CZ combination #4/C LYS 35 CD 4.447
1502combination #4/N ARG 40 O combination #4/E THR 117 CB 4.448
1503combination #4/N CYS 39 C combination #4/C ILE 12 CD1 4.449
1504combination #4/N GLN 58 C combination #4/A ARG 42 NH1 4.456
1505combination #4/N SER 38 O combination #4/C ILE 12 CG1 4.458
1506combination #4/N ALA 41 CB combination #4/E VAL 115 CG2 4.473
1507combination #4/N SER 59 CA combination #4/A LYS 46 CE 4.493
1508combination #4/N SER 59 C combination #4/A LYS 46 CE 4.500
1509</pre><br/>85 distances<br>
1510<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #4/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #4/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true">contacts sel restrict #4/A-E resSeparation 5 intraMol false select true color #00f900 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
1511H-bond overlap reduction: 0.4
1512Ignore contacts between atoms separated by 4 bonds or less
1513Ignore contacts between atoms in residues less than 5 apart in sequence
1514Detect intra-residue contacts: False
1515Detect intra-molecule contacts: False
1516
151726 contacts
1518 atom1 atom2 overlap distance
1519combination #4/C ILE 12 CD1 combination #4/N CYS 39 CA 0.441 3.319
1520combination #4/C GLN 16 NE2 combination #4/N CYS 44 CB 0.387 3.133
1521combination #4/C LYS 35 NZ combination #4/E ASP 94 CB 0.219 3.301
1522combination #4/N CYS 44 CA combination #4/C GLN 16 NE2 0.165 3.355
1523combination #4/C LYS 35 CE combination #4/E ASP 94 OD1 0.131 3.169
1524combination #4/C LYS 35 NZ combination #4/E ASP 94 CG 0.093 3.427
1525combination #4/N TYR 23 CE2 combination #4/E ARG 106 NH1 0.021 3.379
1526combination #4/N TYR 37 OH combination #4/C LYS 35 NZ 0.004 2.696
1527combination #4/N ILE 69 CG1 combination #4/A ARG 42 NH1 -0.006 3.526
1528combination #4/C ILE 12 CD1 combination #4/N CYS 39 CB -0.028 3.788
1529combination #4/C LYS 35 CE combination #4/E ASP 94 CB -0.074 3.834
1530combination #4/N TYR 37 OH combination #4/C LYS 35 CG -0.133 3.473
1531combination #4/C LYS 35 NZ combination #4/E ASP 94 OD1 -0.157 2.817
1532combination #4/C LYS 35 CE combination #4/E ASP 94 CG -0.182 3.942
1533combination #4/C ILE 12 CD1 combination #4/N CYS 39 N -0.195 3.715
1534combination #4/N TYR 37 OH combination #4/C LYS 35 CD -0.245 3.585
1535combination #4/C ARG 19 NH1 combination #4/D GLU 176 CG -0.271 3.791
1536combination #4/A ARG 42 NH1 combination #4/N ILE 69 CD1 -0.285 3.805
1537combination #4/N TYR 37 OH combination #4/C LYS 35 CE -0.310 3.650
1538combination #4/C LYS 35 CE combination #4/E THR 99 CG2 -0.325 4.085
1539combination #4/N ILE 69 CG1 combination #4/A ARG 42 CZ -0.330 3.820
1540combination #4/C ILE 12 CG1 combination #4/C SF4 3003 S4 -0.332 3.982
1541combination #4/C ARG 19 NH1 combination #4/D GLU 176 CB -0.341 3.861
1542combination #4/N SER 38 C combination #4/C ILE 12 CD1 -0.357 3.847
1543combination #4/N CYS 44 CB combination #4/C GLN 16 CG -0.387 4.147
1544combination #4/N CYS 39 CB combination #4/C PRO 59 CG -0.388 4.148
1545</pre><br/>26 contacts<br>
1546<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/N">select #4/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
1547<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel restrict #4/A-E interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel restrict #4/A-E interModel false intraMol false intraRes false reveal true log true">hbonds sel restrict #4/A-E interModel false intraMol false intraRes false reveal true log true</a></div></div><pre>Finding intramodel H-bonds
1548Constraints relaxed by 0.4 angstroms and 20 degrees
1549Models used:
1550 4 combination
1551
15525 H-bonds
1553H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1554combination #4/A ARG 42 NH1 combination #4/N GLN 58 O no hydrogen 3.483 N/A
1555combination #4/A LYS 46 NZ combination #4/N GLY 61 O no hydrogen 3.235 N/A
1556combination #4/C LYS 35 NZ combination #4/N TYR 37 OH no hydrogen 2.696 N/A
1557combination #4/E ARG 106 NH2 combination #4/N ASP 26 OD1 no hydrogen 3.124 N/A
1558combination #4/E THR 117 OG1 combination #4/N ARG 40 O no hydrogen 3.442 N/A
1559</pre><br/>5 hydrogen bonds found<br>
1560<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117">select #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117</a></div></div>91 atoms, 82 bonds, 9 pseudobonds, 10 residues, 3 models selected<br>
1561<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.3 models">hide #4.3 models</a></div></div><div class="cxcmd"><a href="help:user/commands/select.html">select</a> <span style="color:white; background-color:crimson;">#4#2b&amp;protein</span></div><font color="crimson"><b>Expected an objects specifier or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4#2 &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4#2 &amp;protein">select #4#2 &amp;protein</a></div></div>12712 atoms, 13032 bonds, 72 pseudobonds, 1602 residues, 8 models selected<br>
1562<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel &amp; #!4 stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel &amp; #!4 stick">style sel &amp; #!4 stick</a></div></div>Changed 6356 atom styles<br>
1563<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel &amp; #!4 byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel &amp; #!4 byhetero">color sel &amp; #!4 byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117">select #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117</a></div></div>91 atoms, 82 bonds, 9 pseudobonds, 10 residues, 3 models selected<br>
1564<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:41-46</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:41-46">select #1:41-46</a></div></div>60 atoms, 59 bonds, 6 residues, 1 model selected<br>
1565<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime">color sel lime</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.3 models">show #4.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:HOH</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:HOH">select #1:HOH</a></div></div>94 atoms, 94 residues, 1 model selected<br>
1566<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.4 models">hide #2.2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:48-51</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:48-51">select #1:48-51</a></div></div>52 atoms, 52 bonds, 4 residues, 1 model selected<br>
1567<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime">color sel lime</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:41-43</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:41-43">select #1:41-43</a></div></div>27 atoms, 26 bonds, 3 residues, 1 model selected<br>
1568<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel medium blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel medium blue">color sel medium blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:9-10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:9-10">select #1:9-10</a></div></div>26 atoms, 25 bonds, 2 residues, 1 model selected<br>
1569<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime">color sel lime</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:15-17</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:15-17">select #1:15-17</a></div></div>39 atoms, 39 bonds, 3 residues, 1 model selected<br>
1570<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime">color sel lime</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:23-31</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:23-31">select #1:23-31</a></div></div>92 atoms, 92 bonds, 9 residues, 1 model selected<br>
1571<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime">color sel lime</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:3003 @&lt;12 &amp;#1:61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:3003 @&lt;12 &amp;#1:61">select #2/C:3003 @&lt;12 &amp;#1:61</a></div></div>6 atoms, 7 bonds, 1 residue, 1 model selected<br>
1572<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:3003 @&lt;10 &amp;#1:61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:3003 @&lt;10 &amp;#1:61">select #2/C:3003 @&lt;10 &amp;#1:61</a></div></div>2 atoms, 1 bond, 1 residue, 1 model selected<br>
1573<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:3003 @&lt;9 &amp;#1:61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:3003 @&lt;9 &amp;#1:61">select #2/C:3003 @&lt;9 &amp;#1:61</a></div></div>Nothing selected<br>
1574<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:3003 @&lt;9.5 &amp;#1:61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:3003 @&lt;9.5 &amp;#1:61">select #2/C:3003 @&lt;9.5 &amp;#1:61</a></div></div>1 atom, 1 residue, 1 model selected<br>
1575<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:61@S3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:61@S3">select #1:61@S3</a></div></div>1 atom, 1 residue, 1 model selected<br>
1576<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:61@S3 @&lt;9.5 &amp;#2/C:3003</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:61@S3 @&lt;9.5 &amp;#2/C:3003">select #1:61@S3 @&lt;9.5 &amp;#2/C:3003</a></div></div>1 atom, 1 residue, 1 model selected<br>
1577<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:61@S3|#2/C:3003@FE1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:61@S3|#2/C:3003@FE1">select #1:61@S3|#2/C:3003@FE1</a></div></div>2 atoms, 2 residues, 2 models selected<br>
1578<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Distances</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Distances">ui tool show Distances</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #2.2/C:3003@FE1 #1/A:61@S3</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #2.2/C:3003@FE1 #1/A:61@S3">distance #2.2/C:3003@FE1 #1/A:61@S3</a></div></div>Distance between 6yez 2 #2.2/C SF4 3003 FE1 and 2fdn #1/A SF4 61 S3: 9.093Å
1579<br>
1580<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> @@color=&quot;lime&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:select @@color=&quot;lime&quot;">select @@color=&quot;lime&quot;</a></div></div>93 atoms, 72 bonds, 21 residues, 1 model selected<br>
1581<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2">select #2</a></div></div>6384 atoms, 6556 bonds, 69 pseudobonds, 805 residues, 7 models selected<br>
1582<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/E">select #2/E</a></div></div>528 atoms, 540 bonds, 66 residues, 1 model selected<br>
1583<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 528 atom styles<br>
1584<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #1/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #1/A">sequence chain #1/A</a></div></div>Alignment identifier is 1/A<br>
1585<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> @@color=&quot;lime&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:select @@color=&quot;lime&quot;">select @@color=&quot;lime&quot;</a></div></div>93 atoms, 72 bonds, 21 residues, 1 model selected<br>
1586<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:1-8,11-14,18-22,32-43,47,52-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:1-8,11-14,18-22,32-43,47,52-55">select #1:1-8,11-14,18-22,32-43,47,52-55</a></div></div>410 atoms, 407 bonds, 34 residues, 1 model selected<br>
1587<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 6yez</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 6yez">open 6yez</a></div></div><i>6yez</i> title:<br><b>Plant PSI-ferredoxin-plastocyanin supercomplex</b> <a href="cxcmd:log metadata #6">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
1588 <thead>
1589 <tr>
1590 <th colspan="3">Chain information for 6yez #6</th>
1591 </tr>
1592 <tr>
1593 <th>Chain</th>
1594 <th>Description</th>
1595 <th>UniProt</th>
1596 </tr>
1597 </thead>
1598 <tbody>
1599 <tr>
1600 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/1:40-232">1</a></td>
1601 <td><a title="Show sequence" href="cxcmd:sequence chain #6/1">Lhca1</a></td>
1602 <td style="text-align:center"></td>
1603 </tr>
1604 <tr>
1605 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/2:58-265">2</a></td>
1606 <td><a title="Show sequence" href="cxcmd:sequence chain #6/2">Chlorophyll a-b binding protein, chloroplastic</a></td>
1607 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q41038 from uniprot associate #6/2">Q41038_PEA</a> <a title="Select sequence" href="cxcmd:select #6/2:58-265">58-265</a></td>
1608 </tr>
1609 <tr>
1610 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/3:55-275">3</a></td>
1611 <td><a title="Show sequence" href="cxcmd:sequence chain #6/3">Chlorophyll a-b binding protein 3, chloroplastic</a></td>
1612 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q32904 from uniprot associate #6/3">CB23_PEA</a> <a title="Select sequence" href="cxcmd:select #6/3:55-275">55-275</a></td>
1613 </tr>
1614 <tr>
1615 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/4:52-249">4</a></td>
1616 <td><a title="Show sequence" href="cxcmd:sequence chain #6/4">Chlorophyll a-b binding protein P4, chloroplastic</a></td>
1617 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q9SQL2 from uniprot associate #6/4">CB24_PEA</a> <a title="Select sequence" href="cxcmd:select #6/4:52-249">52-249</a></td>
1618 </tr>
1619 <tr>
1620 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/A:16-758">A</a></td>
1621 <td><a title="Show sequence" href="cxcmd:sequence chain #6/A">Photosystem I P700 chlorophyll a apoprotein A1</a></td>
1622 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open A0A0F6NFW5 from uniprot associate #6/A">A0A0F6NFW5_PEA</a> <a title="Select sequence" href="cxcmd:select #6/A:16-758">16-758</a></td>
1623 </tr>
1624 <tr>
1625 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/B:2-734">B</a></td>
1626 <td><a title="Show sequence" href="cxcmd:sequence chain #6/B">Photosystem I P700 chlorophyll a apoprotein A2</a></td>
1627 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open A0A0F6NGI2 from uniprot associate #6/B">A0A0F6NGI2_PEA</a> <a title="Select sequence" href="cxcmd:select #6/B:2-734">2-734</a></td>
1628 </tr>
1629 <tr>
1630 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/C:2-81">C</a></td>
1631 <td><a title="Show sequence" href="cxcmd:sequence chain #6/C">Photosystem I iron-sulfur center</a></td>
1632 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P10793 from uniprot associate #6/C">PSAC_PEA</a> <a title="Select sequence" href="cxcmd:select #6/C:2-81">2-81</a></td>
1633 </tr>
1634 <tr>
1635 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/D:69-211">D</a></td>
1636 <td><a title="Show sequence" href="cxcmd:sequence chain #6/D">PsaD</a></td>
1637 <td style="text-align:center"></td>
1638 </tr>
1639 <tr>
1640 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/E:64-129">E</a></td>
1641 <td><a title="Show sequence" href="cxcmd:sequence chain #6/E">PsaE</a></td>
1642 <td style="text-align:center"></td>
1643 </tr>
1644 <tr>
1645 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/F:78-231">F</a></td>
1646 <td><a title="Show sequence" href="cxcmd:sequence chain #6/F">PsaF</a></td>
1647 <td style="text-align:center"></td>
1648 </tr>
1649 <tr>
1650 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/G:58-154">G</a></td>
1651 <td><a title="Show sequence" href="cxcmd:sequence chain #6/G">PsaG</a></td>
1652 <td style="text-align:center"></td>
1653 </tr>
1654 <tr>
1655 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/H:48-140">H</a></td>
1656 <td><a title="Show sequence" href="cxcmd:sequence chain #6/H">PsaH</a></td>
1657 <td style="text-align:center"></td>
1658 </tr>
1659 <tr>
1660 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/I:2-32">I</a></td>
1661 <td><a title="Show sequence" href="cxcmd:sequence chain #6/I">Photosystem I reaction center subunit VIII</a></td>
1662 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P17227 from uniprot associate #6/I">PSAI_PEA</a> <a title="Select sequence" href="cxcmd:select #6/I:2-32">2-32</a></td>
1663 </tr>
1664 <tr>
1665 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/J:1-42">J</a></td>
1666 <td><a title="Show sequence" href="cxcmd:sequence chain #6/J">PsaJ</a></td>
1667 <td style="text-align:center"></td>
1668 </tr>
1669 <tr>
1670 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/K:46-126">K</a></td>
1671 <td><a title="Show sequence" href="cxcmd:sequence chain #6/K">Photosystem I reaction center subunit X psaK</a></td>
1672 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open E1C9L3 from uniprot associate #6/K">E1C9L3_PEA</a> <a title="Select sequence" href="cxcmd:select #6/K:46-126">46-126</a></td>
1673 </tr>
1674 <tr>
1675 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/L:54-212">L</a></td>
1676 <td><a title="Show sequence" href="cxcmd:sequence chain #6/L">PsaL</a></td>
1677 <td style="text-align:center"></td>
1678 </tr>
1679 <tr>
1680 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/N:1-97">N</a></td>
1681 <td><a title="Show sequence" href="cxcmd:sequence chain #6/N">Ferredoxin-1, chloroplastic</a></td>
1682 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P09911 from uniprot associate #6/N">FER1_PEA</a> <a title="Select sequence" href="cxcmd:select #6/N:1-97">1-97</a></td>
1683 </tr>
1684 <tr>
1685 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/P:1-99">P</a></td>
1686 <td><a title="Show sequence" href="cxcmd:sequence chain #6/P">Plastocyanin, chloroplastic</a></td>
1687 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P16002 from uniprot associate #6/P">PLAS_PEA</a> <a title="Select sequence" href="cxcmd:select #6/P:1-99">1-99</a></td>
1688 </tr>
1689 </tbody>
1690</table><br/><table border=1 cellpadding=4 cellspacing=0>
1691 <thead>
1692 <tr>
1693 <th>Non-standard residues in 6yez #6</th>
1694 </tr>
1695 </thead>
1696 <tbody>
1697 <tr>
1698 <td><a title="select residue" href="cxcmd:sel :3PH">3PH</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/3PH">1,2-diacyl-glycerol-3-Sn-phosphate</a> (phosphatidic acid)</td>
1699 </tr>
1700 <tr>
1701 <td><a title="select residue" href="cxcmd:sel :BCR">BCR</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/BCR">β-carotene</a></td>
1702 </tr>
1703 <tr>
1704 <td><a title="select residue" href="cxcmd:sel :C7Z">C7Z</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/C7Z">(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol</a></td>
1705 </tr>
1706 <tr>
1707 <td><a title="select residue" href="cxcmd:sel :CA">CA</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CA">calcium ion</a></td>
1708 </tr>
1709 <tr>
1710 <td><a title="select residue" href="cxcmd:sel :CHL">CHL</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CHL">chlorophyll B</a></td>
1711 </tr>
1712 <tr>
1713 <td><a title="select residue" href="cxcmd:sel :CL0">CL0</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CL0">chlorophyll A isomer</a></td>
1714 </tr>
1715 <tr>
1716 <td><a title="select residue" href="cxcmd:sel :CLA">CLA</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CLA">chlorophyll A</a></td>
1717 </tr>
1718 <tr>
1719 <td><a title="select residue" href="cxcmd:sel :CU">CU</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CU">copper (II) ion</a></td>
1720 </tr>
1721 <tr>
1722 <td><a title="select residue" href="cxcmd:sel :DGD">DGD</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/DGD">digalactosyl diacyl glycerol (DGDG)</a></td>
1723 </tr>
1724 <tr>
1725 <td><a title="select residue" href="cxcmd:sel :FES">FES</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/FES">FE2/S2 (inorganic) cluster</a></td>
1726 </tr>
1727 <tr>
1728 <td><a title="select residue" href="cxcmd:sel :LHG">LHG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LHG">1,2-dipalmitoyl-phosphatidyl-glycerole</a></td>
1729 </tr>
1730 <tr>
1731 <td><a title="select residue" href="cxcmd:sel :LMG">LMG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LMG">1,2-distearoyl-monogalactosyl-diglyceride</a></td>
1732 </tr>
1733 <tr>
1734 <td><a title="select residue" href="cxcmd:sel :LMT">LMT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LMT">dodecyl-β-D-maltoside</a></td>
1735 </tr>
1736 <tr>
1737 <td><a title="select residue" href="cxcmd:sel :LUT">LUT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LUT">(3R,3&#x27;R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3&#x27;-diol</a> ((3R,3&#x27;R)-β,β-carotene-3,3&#x27;-diol; lutein)</td>
1738 </tr>
1739 <tr>
1740 <td><a title="select residue" href="cxcmd:sel :PQN">PQN</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PQN">phylloquinone</a> (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)</td>
1741 </tr>
1742 <tr>
1743 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
1744 </tr>
1745 <tr>
1746 <td><a title="select residue" href="cxcmd:sel :XAT">XAT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/XAT">(3S,5R,6S,3&#x27;S,5&#x27;R,6&#x27;S)-5,6,5&#x27;,6&#x27;-diepoxy-5,6,5&#x27;,6&#x27;- tetrahydro-β,β-carotene-3,3&#x27;-diol</a> (violaxanthin)</td>
1747 </tr>
1748 </tbody>
1749</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #6">select add #6</a></div></div>39627 atoms, 41140 bonds, 678 pseudobonds, 3718 residues, 3 models selected<br>
1750<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #1">select add #1</a></div></div>39979 atoms, 41414 bonds, 686 pseudobonds, 3835 residues, 4 models selected<br>
1751<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #1">select subtract #1</a></div></div>39217 atoms, 40733 bonds, 678 pseudobonds, 3684 residues, 2 models selected<br>
1752<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/F-Z</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/F-Z">select #6/F-Z</a></div></div>8235 atoms, 8462 bonds, 68 pseudobonds, 894 residues, 2 models selected<br>
1753<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/F-Z/1-4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/F-Z/1-4">select #6/F-Z/1-4</a></div></div>18908 atoms, 19592 bonds, 309 pseudobonds, 1801 residues, 2 models selected<br>
1754<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/log.html#metadata">log metadata</a> #6</div><div class="cxcmd_as_cmd"><a href="cxcmd:log metadata #6">log metadata #6</a></div></div><table border=1 cellpadding=4 cellspacing=0>
1755 <thead>
1756 <tr>
1757 <th colspan="2">Metadata for 6yez #6</th>
1758 </tr>
1759 </thead>
1760 <tbody>
1761 <tr>
1762 <th>Title</th>
1763 <td>Plant PSI-ferredoxin-plastocyanin supercomplex</td>
1764 </tr>
1765 <tr>
1766 <th>Citation</th>
1767 <td>Caspy, I., Borovikova-Sheinker, A., Klaiman, D., Shkolnisky, Y., Nelson, N. (2020). The structure of a triple complex of plant photosystem I with ferredoxin and plastocyanin. <i>Nat.Plants</i>, <i>6</i>, 1300-1305. PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/33020607">33020607</a>. DOI: <a href="http://dx.doi.org/10.1038/s41477-020-00779-9">10.1038/s41477-020-00779-9</a></td>
1768 </tr>
1769 <tr>
1770 <th rowspan="17">Non-standard residues</th>
1771 <td><a title="select residue" href="cxcmd:sel :3PH">3PH</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/3PH">1,2-diacyl-glycerol-3-Sn-phosphate</a> (phosphatidic acid)</td>
1772 </tr>
1773 <tr>
1774 <td><a title="select residue" href="cxcmd:sel :BCR">BCR</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/BCR">β-carotene</a></td>
1775 </tr>
1776 <tr>
1777 <td><a title="select residue" href="cxcmd:sel :C7Z">C7Z</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/C7Z">(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol</a></td>
1778 </tr>
1779 <tr>
1780 <td><a title="select residue" href="cxcmd:sel :CA">CA</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CA">calcium ion</a></td>
1781 </tr>
1782 <tr>
1783 <td><a title="select residue" href="cxcmd:sel :CHL">CHL</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CHL">chlorophyll B</a></td>
1784 </tr>
1785 <tr>
1786 <td><a title="select residue" href="cxcmd:sel :CL0">CL0</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CL0">chlorophyll A isomer</a></td>
1787 </tr>
1788 <tr>
1789 <td><a title="select residue" href="cxcmd:sel :CLA">CLA</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CLA">chlorophyll A</a></td>
1790 </tr>
1791 <tr>
1792 <td><a title="select residue" href="cxcmd:sel :CU">CU</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CU">copper (II) ion</a></td>
1793 </tr>
1794 <tr>
1795 <td><a title="select residue" href="cxcmd:sel :DGD">DGD</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/DGD">digalactosyl diacyl glycerol (DGDG)</a></td>
1796 </tr>
1797 <tr>
1798 <td><a title="select residue" href="cxcmd:sel :FES">FES</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/FES">FE2/S2 (inorganic) cluster</a></td>
1799 </tr>
1800 <tr>
1801 <td><a title="select residue" href="cxcmd:sel :LHG">LHG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LHG">1,2-dipalmitoyl-phosphatidyl-glycerole</a></td>
1802 </tr>
1803 <tr>
1804 <td><a title="select residue" href="cxcmd:sel :LMG">LMG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LMG">1,2-distearoyl-monogalactosyl-diglyceride</a></td>
1805 </tr>
1806 <tr>
1807 <td><a title="select residue" href="cxcmd:sel :LMT">LMT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LMT">dodecyl-β-D-maltoside</a></td>
1808 </tr>
1809 <tr>
1810 <td><a title="select residue" href="cxcmd:sel :LUT">LUT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LUT">(3R,3&#x27;R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3&#x27;-diol</a> ((3R,3&#x27;R)-β,β-carotene-3,3&#x27;-diol; lutein)</td>
1811 </tr>
1812 <tr>
1813 <td><a title="select residue" href="cxcmd:sel :PQN">PQN</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PQN">phylloquinone</a> (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)</td>
1814 </tr>
1815 <tr>
1816 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
1817 </tr>
1818 <tr>
1819 <td><a title="select residue" href="cxcmd:sel :XAT">XAT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/XAT">(3S,5R,6S,3&#x27;S,5&#x27;R,6&#x27;S)-5,6,5&#x27;,6&#x27;-diepoxy-5,6,5&#x27;,6&#x27;- tetrahydro-β,β-carotene-3,3&#x27;-diol</a> (violaxanthin)</td>
1820 </tr>
1821 <tr>
1822 <th rowspan="2">Sources (natural)</th>
1823 <td><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3888">Pisum sativum</a> (garden pea)</td>
1824 </tr>
1825 <tr>
1826 <td><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3888">Pisum sativum</a> (pea)</td>
1827 </tr>
1828 <tr>
1829 <th>CryoEM Map</th>
1830 <td><a href="https://www.ebi.ac.uk/emdb/EMD-10798">EMDB 10798</a> &mdash; <a href="cxcmd:open 10798 from emdb">open map</a></td>
1831 </tr>
1832 <tr>
1833 <th>Experimental method</th>
1834 <td>Electron microscopy</td>
1835 </tr>
1836 <tr>
1837 <th>Resolution</th>
1838 <td>2.7Å</td>
1839 </tr>
1840 </tbody>
1841</table><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/F-Z/1-4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/F-Z/1-4">select #6/F-Z/1-4</a></div></div>18908 atoms, 19592 bonds, 309 pseudobonds, 1801 residues, 2 models selected<br>
1842<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#atoms">delete atoms</a> (#!6 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete atoms (#!6 &amp; sel)">delete atoms (#!6 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#bonds">delete bonds</a> (#!6 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete bonds (#!6 &amp; sel)">delete bonds (#!6 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #1#6</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #1#6">combine #1#6</a></div></div>Remapping chain ID &#x27;A&#x27; in 6yez #6 to &#x27;F&#x27;<br>
1843<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #7">close #7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/N">select #6/N</a></div></div>Nothing selected<br>
1844<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Change Chain IDs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Change Chain IDs&quot;">ui tool show &quot;Change Chain IDs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1">select #1</a></div></div>762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected<br>
1845<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Change Chain IDs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Change Chain IDs&quot;">ui tool show &quot;Change Chain IDs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel M</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel M">changechains sel M</a></div></div>Chain IDs of 151 residues changed<br>
1846<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #1#6</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #1#6">combine #1#6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/Bfdx_PSI_toDiffusion.pdb&quot; models #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/Bfdx_PSI_toDiffusion.pdb&quot; models #7">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/Bfdx_PSI_toDiffusion.pdb&quot; models #7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #7/A:700</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #7/A:700">combine #7/A:700</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #8">close #8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:700</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:700">select #7/A:700</a></div></div>14 atoms, 15 bonds, 1 residue, 1 model selected<br>
1847<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:740</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:740">select #7/A:740</a></div></div>8 atoms, 7 bonds, 1 residue, 1 model selected<br>
1848<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:759</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:759">select #7/A:759</a></div></div>Nothing selected<br>
1849<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:758</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:758">select #7/A:758</a></div></div>5 atoms, 4 bonds, 1 residue, 1 model selected<br>
1850<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:758/B:2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:758/B:2">select #7/A:758/B:2</a></div></div>10 atoms, 8 bonds, 2 residues, 1 model selected<br>
1851<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:758/B:724</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:758/B:724">select #2/A:758/B:724</a></div></div>Nothing selected<br>
1852<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:758/B:707</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:758/B:707">select #2/A:758/B:707</a></div></div>8 atoms, 7 bonds, 1 residue, 1 model selected<br>
1853<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:696/C:2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:696/C:2">select #2/B:696/C:2</a></div></div>15 atoms, 13 bonds, 2 residues, 1 model selected<br>
1854<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:696@C/C:2@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:696@C/C:2@N">select #2/B:696@C/C:2@N</a></div></div>2 atoms, 2 residues, 1 model selected<br>
1855<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:696@C/C:2@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:696@C/C:2@N">select #2/B:696@C/C:2@N</a></div></div>2 atoms, 2 residues, 1 model selected<br>
1856<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #2.2/B:696@C #2.2/C:2@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #2.2/B:696@C #2.2/C:2@N">distance #2.2/B:696@C #2.2/C:2@N</a></div></div>Distance between 6yez 2 #2.2/B LYS 696 C and /C SER 2 N: 16.567Å
1857<br>
1858<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/D:59@N/C:81@C</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/D:59@N/C:81@C">select #2/D:59@N/C:81@C</a></div></div>1 atom, 1 residue, 1 model selected<br>
1859<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/D:69@N/C:81@C</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/D:69@N/C:81@C">select #2/D:69@N/C:81@C</a></div></div>2 atoms, 2 residues, 1 model selected<br>
1860<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #2.2/C:81@C #2.2/D:69@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #2.2/C:81@C #2.2/D:69@N">distance #2.2/C:81@C #2.2/D:69@N</a></div></div>Distance between 6yez 2 #2.2/C TYR 81 C and /D GLY 69 N: 36.658Å
1861<br>
1862<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/E:64@N/D:211@C</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/E:64@N/D:211@C">select #2/E:64@N/D:211@C</a></div></div>2 atoms, 2 residues, 1 model selected<br>
1863<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #2.2/E:64@N #2.2/D:211@C</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #2.2/E:64@N #2.2/D:211@C">distance #2.2/E:64@N #2.2/D:211@C</a></div></div>Distance between 6yez 2 #2.2/E PRO 64 N and /D LEU 211 C: 36.932Å
1864<br>
1865<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge_0.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge_0.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge_0.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
1866 <thead>
1867 <tr>
1868 <th colspan="2">Chain information for PSI_stromal_ridge_0.pdb #8</th>
1869 </tr>
1870 <tr>
1871 <th>Chain</th>
1872 <th>Description</th>
1873
1874 </tr>
1875 </thead>
1876 <tbody>
1877 <tr>
1878 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #8/A:1-829">A</a></td>
1879 <td><a title="Show sequence" href="cxcmd:sequence chain #8/A">No description available</a></td>
1880
1881 </tr>
1882 </tbody>
1883</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #8 to #2.2 showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #8 to #2.2 showAlignment true">matchmaker #8 to #2.2 showAlignment true</a></div></div>
1884 <table border=1 cellpadding=4 cellspacing=0>
1885 <tr>
1886 <th colspan="2">Parameters</th>
1887 </tr>
1888 <tr>
1889 <td>Chain pairing</td>
1890 <td>bb</td>
1891 </tr>
1892 <tr>
1893 <td>Alignment algorithm</td>
1894 <td>Needleman-Wunsch</td>
1895 </tr>
1896 <tr>
1897 <td>Similarity matrix</td>
1898 <td>BLOSUM-62</td>
1899 </tr>
1900
1901 <tr>
1902 <td>SS fraction</td>
1903 <td>0.3</td>
1904 </tr>
1905 <tr>
1906 <td>Gap open (HH/SS/other)</td>
1907 <td>18/18/6</td>
1908 </tr>
1909 <tr>
1910 <td>Gap extend</td>
1911 <td>1</td>
1912 </tr>
1913 <tr>
1914 <td>SS matrix</td>
1915 <td>
1916 <table>
1917 <tr>
1918 <th></th> <th>H</th> <th>S</th> <th>O</th>
1919 </tr>
1920 <tr>
1921 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
1922 </tr>
1923 <tr>
1924 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
1925 </tr>
1926 <tr>
1927 <th>O</th> <td></td> <td></td> <td align="right">4</td>
1928 </tr>
1929 </table>
1930 </td>
1931 </tr>
1932
1933 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
1934 </table>
1935 <br/>Matchmaker 6yez 2, chain A (#2.2) with PSI_stromal_ridge_0.pdb, chain A (#8), sequence alignment score = 924.3<br>
1936Alignment identifier is 1<br>
1937Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
1938Hiding conservation header for alignment 1<br>
1939Chains used in RMSD evaluation for alignment 1: 6yez 2 #2.2/A, PSI_stromal_ridge_0.pdb #8/A<br>
1940Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
1941RMSD between 203 pruned atom pairs is 0.259 angstroms; (across all 203 pairs: 0.259)<br>
1942<br>
1943<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#header">sequence header</a> consensus show</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence header consensus show">sequence header consensus show</a></div></div>Showing consensus header (&quot;seq_consensus&quot; residue attribute) for alignment 1<br>
1944<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:59</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:59">select #8/A:59</a></div></div>4 atoms, 3 bonds, 1 residue, 1 model selected<br>
1945<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:59-62</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:59-62">select #8/A:59-62</a></div></div>16 atoms, 15 bonds, 4 residues, 1 model selected<br>
1946<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8:59-62</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8:59-62">select #8:59-62</a></div></div>16 atoms, 15 bonds, 4 residues, 1 model selected<br>
1947<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8:58-63</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8:58-63">select #8:58-63</a></div></div>24 atoms, 23 bonds, 6 residues, 1 model selected<br>
1948<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:192</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:192">select #2/A:192</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
1949<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 9 atom styles<br>
1950<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Build Structure&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Build Structure&quot;">ui tool show &quot;Build Structure&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #8">combine #8</a></div></div>Associated copy of PSI_stromal_ridge_0.pdb chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
1951Chains used in RMSD evaluation for alignment 1: 6yez 2 #2.2/A, PSI_stromal_ridge_0.pdb #8/A, copy of PSI_stromal_ridge_0.pdb #9/A<br>
1952<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #9/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #9/A">sequence chain #9/A</a></div></div>Alignment identifier is 9/A<br>
1953<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9 sequence GGGG</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9 sequence GGGG">select #9 sequence GGGG</a></div></div>676 atoms, 663 bonds, 169 residues, 1 model selected<br>
1954<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9:59-62,73-76,117-120,147-150,185-192,228-257,301-304,320-323,365-368,398-401,443-470,551-586,729-763</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9:59-62,73-76,117-120,147-150,185-192,228-257,301-304,320-323,365-368,398-401,443-470,551-586,729-763">select #9:59-62,73-76,117-120,147-150,185-192,228-257,301-304,320-323,365-368,398-401,443-470,551-586,729-763</a></div></div>676 atoms, 663 bonds, 169 residues, 1 model selected<br>
1955<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.2">select add #2.2</a></div></div>6332 atoms, 6479 bonds, 68 pseudobonds, 876 residues, 6 models selected<br>
1956<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 6332 atom styles<br>
1957<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2">select add #2</a></div></div>7060 atoms, 7219 bonds, 72 pseudobonds, 974 residues, 9 models selected<br>
1958<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2">select subtract #2</a></div></div>676 atoms, 663 bonds, 169 residues, 1 model selected<br>
1959<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2 models">hide #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #9 atoms :59-62 atoms :73-76 atoms :117-120 atoms :147-150 atoms :185-192 atoms :228-257 atoms :301-304 atoms :320-323 atoms :365-368 atoms :398-401 atoms :443-470 atoms :551-586 atoms :729-763</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #9 atoms :59-62 atoms :73-76 atoms :117-120 atoms :147-150 atoms :185-192 atoms :228-257 atoms :301-304 atoms :320-323 atoms :365-368 atoms :398-401 atoms :443-470 atoms :551-586 atoms :729-763">split #9 atoms :59-62 atoms :73-76 atoms :117-120 atoms :147-150 atoms :185-192 atoms :228-257 atoms :301-304 atoms :320-323 atoms :365-368 atoms :398-401 atoms :443-470 atoms :551-586 atoms :729-763</a></div></div>Split copy of PSI_stromal_ridge_0.pdb (#9) into 14 models<br>
1960<table border=1 cellpadding=4 cellspacing=0>
1961 <thead>
1962 <tr>
1963 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 1 #9.1</th>
1964 </tr>
1965 <tr>
1966 <th>Chain</th>
1967 <th>Description</th>
1968
1969 </tr>
1970 </thead>
1971 <tbody>
1972 <tr>
1973 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.1/A:59-62">A</a></td>
1974 <td><a title="Show sequence" href="cxcmd:sequence chain #9.1/A">No description available</a></td>
1975
1976 </tr>
1977 </tbody>
1978</table><br/><table border=1 cellpadding=4 cellspacing=0>
1979 <thead>
1980 <tr>
1981 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 2 #9.2</th>
1982 </tr>
1983 <tr>
1984 <th>Chain</th>
1985 <th>Description</th>
1986
1987 </tr>
1988 </thead>
1989 <tbody>
1990 <tr>
1991 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.2/A:73-76">A</a></td>
1992 <td><a title="Show sequence" href="cxcmd:sequence chain #9.2/A">No description available</a></td>
1993
1994 </tr>
1995 </tbody>
1996</table><br/><table border=1 cellpadding=4 cellspacing=0>
1997 <thead>
1998 <tr>
1999 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 3 #9.3</th>
2000 </tr>
2001 <tr>
2002 <th>Chain</th>
2003 <th>Description</th>
2004
2005 </tr>
2006 </thead>
2007 <tbody>
2008 <tr>
2009 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.3/A:117-120">A</a></td>
2010 <td><a title="Show sequence" href="cxcmd:sequence chain #9.3/A">No description available</a></td>
2011
2012 </tr>
2013 </tbody>
2014</table><br/><table border=1 cellpadding=4 cellspacing=0>
2015 <thead>
2016 <tr>
2017 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 4 #9.4</th>
2018 </tr>
2019 <tr>
2020 <th>Chain</th>
2021 <th>Description</th>
2022
2023 </tr>
2024 </thead>
2025 <tbody>
2026 <tr>
2027 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.4/A:147-150">A</a></td>
2028 <td><a title="Show sequence" href="cxcmd:sequence chain #9.4/A">No description available</a></td>
2029
2030 </tr>
2031 </tbody>
2032</table><br/><table border=1 cellpadding=4 cellspacing=0>
2033 <thead>
2034 <tr>
2035 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 5 #9.5</th>
2036 </tr>
2037 <tr>
2038 <th>Chain</th>
2039 <th>Description</th>
2040
2041 </tr>
2042 </thead>
2043 <tbody>
2044 <tr>
2045 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.5/A:185-192">A</a></td>
2046 <td><a title="Show sequence" href="cxcmd:sequence chain #9.5/A">No description available</a></td>
2047
2048 </tr>
2049 </tbody>
2050</table><br/><table border=1 cellpadding=4 cellspacing=0>
2051 <thead>
2052 <tr>
2053 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 6 #9.6</th>
2054 </tr>
2055 <tr>
2056 <th>Chain</th>
2057 <th>Description</th>
2058
2059 </tr>
2060 </thead>
2061 <tbody>
2062 <tr>
2063 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.6/A:228-257">A</a></td>
2064 <td><a title="Show sequence" href="cxcmd:sequence chain #9.6/A">No description available</a></td>
2065
2066 </tr>
2067 </tbody>
2068</table><br/><table border=1 cellpadding=4 cellspacing=0>
2069 <thead>
2070 <tr>
2071 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 7 #9.7</th>
2072 </tr>
2073 <tr>
2074 <th>Chain</th>
2075 <th>Description</th>
2076
2077 </tr>
2078 </thead>
2079 <tbody>
2080 <tr>
2081 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.7/A:301-304">A</a></td>
2082 <td><a title="Show sequence" href="cxcmd:sequence chain #9.7/A">No description available</a></td>
2083
2084 </tr>
2085 </tbody>
2086</table><br/><table border=1 cellpadding=4 cellspacing=0>
2087 <thead>
2088 <tr>
2089 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 8 #9.8</th>
2090 </tr>
2091 <tr>
2092 <th>Chain</th>
2093 <th>Description</th>
2094
2095 </tr>
2096 </thead>
2097 <tbody>
2098 <tr>
2099 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.8/A:320-323">A</a></td>
2100 <td><a title="Show sequence" href="cxcmd:sequence chain #9.8/A">No description available</a></td>
2101
2102 </tr>
2103 </tbody>
2104</table><br/><table border=1 cellpadding=4 cellspacing=0>
2105 <thead>
2106 <tr>
2107 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 9 #9.9</th>
2108 </tr>
2109 <tr>
2110 <th>Chain</th>
2111 <th>Description</th>
2112
2113 </tr>
2114 </thead>
2115 <tbody>
2116 <tr>
2117 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.9/A:365-368">A</a></td>
2118 <td><a title="Show sequence" href="cxcmd:sequence chain #9.9/A">No description available</a></td>
2119
2120 </tr>
2121 </tbody>
2122</table><br/><table border=1 cellpadding=4 cellspacing=0>
2123 <thead>
2124 <tr>
2125 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 10 #9.10</th>
2126 </tr>
2127 <tr>
2128 <th>Chain</th>
2129 <th>Description</th>
2130
2131 </tr>
2132 </thead>
2133 <tbody>
2134 <tr>
2135 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.10/A:398-401">A</a></td>
2136 <td><a title="Show sequence" href="cxcmd:sequence chain #9.10/A">No description available</a></td>
2137
2138 </tr>
2139 </tbody>
2140</table><br/><table border=1 cellpadding=4 cellspacing=0>
2141 <thead>
2142 <tr>
2143 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 11 #9.11</th>
2144 </tr>
2145 <tr>
2146 <th>Chain</th>
2147 <th>Description</th>
2148
2149 </tr>
2150 </thead>
2151 <tbody>
2152 <tr>
2153 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.11/A:443-470">A</a></td>
2154 <td><a title="Show sequence" href="cxcmd:sequence chain #9.11/A">No description available</a></td>
2155
2156 </tr>
2157 </tbody>
2158</table><br/><table border=1 cellpadding=4 cellspacing=0>
2159 <thead>
2160 <tr>
2161 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 12 #9.12</th>
2162 </tr>
2163 <tr>
2164 <th>Chain</th>
2165 <th>Description</th>
2166
2167 </tr>
2168 </thead>
2169 <tbody>
2170 <tr>
2171 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.12/A:551-586">A</a></td>
2172 <td><a title="Show sequence" href="cxcmd:sequence chain #9.12/A">No description available</a></td>
2173
2174 </tr>
2175 </tbody>
2176</table><br/><table border=1 cellpadding=4 cellspacing=0>
2177 <thead>
2178 <tr>
2179 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 13 #9.13</th>
2180 </tr>
2181 <tr>
2182 <th>Chain</th>
2183 <th>Description</th>
2184
2185 </tr>
2186 </thead>
2187 <tbody>
2188 <tr>
2189 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.13/A:729-763">A</a></td>
2190 <td><a title="Show sequence" href="cxcmd:sequence chain #9.13/A">No description available</a></td>
2191
2192 </tr>
2193 </tbody>
2194</table><br/><table border=1 cellpadding=4 cellspacing=0>
2195 <thead>
2196 <tr>
2197 <th colspan="2">Chain information for copy of PSI_stromal_ridge_0.pdb 14 #9.14</th>
2198 </tr>
2199 <tr>
2200 <th>Chain</th>
2201 <th>Description</th>
2202
2203 </tr>
2204 </thead>
2205 <tbody>
2206 <tr>
2207 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9.14/A:1-829">A</a></td>
2208 <td><a title="Show sequence" href="cxcmd:sequence chain #9.14/A">No description available</a></td>
2209
2210 </tr>
2211 </tbody>
2212</table><br/>Associated copy of PSI_stromal_ridge_0.pdb 6 (9.6) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2213Associated copy of PSI_stromal_ridge_0.pdb 11 (9.11) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2214Associated copy of PSI_stromal_ridge_0.pdb 12 (9.12) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2215Associated copy of PSI_stromal_ridge_0.pdb 13 (9.13) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2216Associated copy of PSI_stromal_ridge_0.pdb 14 (9.14) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2217Chains used in RMSD evaluation for alignment 1: 6yez 2 #2.2/A, PSI_stromal_ridge_0.pdb #8/A, copy of PSI_stromal_ridge_0.pdb 6 #9.6/A, copy of PSI_stromal_ridge_0.pdb 11 #9.11/A, copy of PSI_stromal_ridge_0.pdb 12 #9.12/A, copy of PSI_stromal_ridge_0.pdb 13 #9.13/A, copy of PSI_stromal_ridge_0.pdb 14 #9.14/A<br>
2218<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.14 models">hide #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2 models">show #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #9">select add #9</a></div></div>3316 atoms, 3289 bonds, 829 residues, 15 models selected<br>
2219<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #9.14</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #9.14">select subtract #9.14</a></div></div>676 atoms, 663 bonds, 169 residues, 14 models selected<br>
2220<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #9">select add #9</a></div></div>3316 atoms, 3289 bonds, 829 residues, 15 models selected<br>
2221<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #9">select subtract #9</a></div></div>Nothing selected<br>
2222<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.13 models">hide #9.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.12 models">hide #9.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.11 models">hide #9.11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.10 models">hide #9.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.9 models">hide #9.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.8 models">hide #9.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.7 models">hide #9.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.6 models">hide #9.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.5 models">hide #9.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.4 models">hide #9.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.3 models">hide #9.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.2 models">hide #9.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Add Hydrogens&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Add Hydrogens&quot;">ui tool show &quot;Add Hydrogens&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Build Structure&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Build Structure&quot;">ui tool show &quot;Build Structure&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sat May 18 14:49:43 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
2223<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9.1:58@C:59@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9.1:58@C:59@N">select #9.1:58@C:59@N</a></div></div>1 atom, 1 residue, 1 model selected<br>
2224<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.14 models">show #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html#~bond">~bond</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:~bond sel">~bond sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:73@C#9.1:59@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:73@C#9.1:59@N">select #2/A:73@C#9.1:59@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2225<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move small</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move small">build join peptide sel length 1.33 omega 180 phi -120 move small</a></div></div><font color="crimson"><b>No chain-terminal carbons in atoms<br>
2226</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html#~bond">~bond</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:~bond sel">~bond sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:73@C#9.1:59@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:73@C#9.1:59@N">select #2.2/A:73@C#9.1:59@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2227<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move small</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move small">build join peptide sel length 1.33 omega 180 phi -120 move small</a></div></div><font color="crimson"><b>No chain-terminal carbons in atoms<br>
2228</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.14 models">hide #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.14 models">show #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.14 models">hide #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.14 models">show #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.14 models">hide #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.14 models">show #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.14 models">hide #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.14 models">show #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.14 models">hide #9.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #2.2 atoms /A:1-73</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #2.2 atoms /A:1-73">split #2.2 atoms /A:1-73</a></div></div>Split 6yez 2 (#2.2) into 2 models<br>
2229<table border=1 cellpadding=4 cellspacing=0>
2230 <thead>
2231 <tr>
2232 <th colspan="2">Chain information for 6yez 2 1 #2.2.1</th>
2233 </tr>
2234 <tr>
2235 <th>Chain</th>
2236 <th>Description</th>
2237
2238 </tr>
2239 </thead>
2240 <tbody>
2241 <tr>
2242 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1/A:16-73">A</a></td>
2243 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1/A">No description available</a></td>
2244
2245 </tr>
2246 </tbody>
2247</table><br/><table border=1 cellpadding=4 cellspacing=0>
2248 <thead>
2249 <tr>
2250 <th colspan="2">Chain information for 6yez 2 2 #2.2.2</th>
2251 </tr>
2252 <tr>
2253 <th>Chain</th>
2254 <th>Description</th>
2255
2256 </tr>
2257 </thead>
2258 <tbody>
2259 <tr>
2260 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.2/A:191-729">A</a></td>
2261 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.2/A">No description available</a></td>
2262
2263 </tr>
2264 <tr>
2265 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.2/B:2-707">B</a></td>
2266 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.2/B">No description available</a></td>
2267
2268 </tr>
2269 <tr>
2270 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.2/C:2-81">C</a></td>
2271 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.2/C">No description available</a></td>
2272
2273 </tr>
2274 <tr>
2275 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.2/D:69-211">D</a></td>
2276 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.2/D">No description available</a></td>
2277
2278 </tr>
2279 <tr>
2280 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.2/E:64-129">E</a></td>
2281 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.2/E">No description available</a></td>
2282
2283 </tr>
2284 </tbody>
2285</table><br/>Associated 6yez 2 1 (2.2.1) chain A to 6yez 2, chain A with 0 mismatches<br>
2286Associated 6yez 2 2 (2.2.2) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2287Associated 6yez 2 2 (2.2.2) chain D to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2288Associated 6yez 2 2 (2.2.2) chain C to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2289Associated 6yez 2 2 (2.2.2) chain E to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2290<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2.2 models">hide #!2.2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2.1/A:73</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2.1/A:73">select #2.2.1/A:73</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
2291<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2.1/A:73@C#9.1:59@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2.1/A:73@C#9.1:59@N">select #2.2.1/A:73@C#9.1:59@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2292<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move small</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move small">build join peptide sel length 1.33 omega 180 phi -120 move small</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:132-135 toAtoms #8:59-63 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:132-135 toAtoms #8:59-63 matchAtomNames true move residues">align #2.2.1/A:132-135 toAtoms #8:59-63 matchAtomNames true move residues</a></div></div>Pairing dropped 0 atoms and 4 reference atoms<br>
2293RMSD between 16 atom pairs is 0.000 angstroms<br>
2294<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1 models">hide #2.2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2.2 models">show #!2.2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1 models">show #2.2.1 models</a></div></div><div class="cxcmd"><a href="help:user/commands/align.html">align</a> #2.2.2/A:191</div><font color="crimson"><b>Missing required &quot;to_atoms&quot; argument</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2.2/A:191</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2.2/A:191">select #2.2.2/A:191</a></div></div>7 atoms, 7 bonds, 1 residue, 1 model selected<br>
2295<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2.2/A:191@N#2.2.1/A:135@C</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2.2/A:191@N#2.2.1/A:135@C">select #2.2.2/A:191@N#2.2.1/A:135@C</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2296<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Build Structure&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Build Structure&quot;">ui tool show &quot;Build Structure&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2.1/A:191</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2.1/A:191">select #2.2.1/A:191</a></div></div>7 atoms, 7 bonds, 1 residue, 1 model selected<br>
2297<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><a href="help:user/commands/select.html">select</a> <span style="color:white; background-color:crimson;">#4/A:191-*</span></div><font color="crimson"><b>Expected an objects specifier or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:191-707/B-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:191-707/B-E">select #4/A:191-707/B-E</a></div></div>5003 atoms, 5138 bonds, 26 pseudobonds, 626 residues, 4 models selected<br>
2298<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2.1/A:191-707/B-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2.1/A:191-707/B-E">select #2.2.1/A:191-707/B-E</a></div></div>5003 atoms, 5138 bonds, 60 pseudobonds, 626 residues, 4 models selected<br>
2299<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><a href="help:user/commands/select.html">select</a> #2.2.1/A:191-707/B-E <span style="color:white; background-color:crimson;">to #4/A:191-707/B-E matchA t matchN t move res</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:191-707/B-E toAtoms #4/A:191-707/B-E matchAtomNames true matchNumbering true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:191-707/B-E toAtoms #4/A:191-707/B-E matchAtomNames true matchNumbering true move residues">align #2.2.1/A:191-707/B-E toAtoms #4/A:191-707/B-E matchAtomNames true matchNumbering true move residues</a></div></div>RMSD between 5003 atom pairs is 0.000 angstroms<br>
2300<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:708-729,3001 toAtoms #4/A:708-729,3001 matchAtomNames true matchNumbering true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:708-729,3001 toAtoms #4/A:708-729,3001 matchAtomNames true matchNumbering true move residues">align #2.2.1/A:708-729,3001 toAtoms #4/A:708-729,3001 matchAtomNames true matchNumbering true move residues</a></div></div>RMSD between 179 atom pairs is 0.000 angstroms<br>
2301<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2 models">hide #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2 models">show #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2.1 models">hide #!2.2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2.1 models">show #!2.2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2.1 models">hide #!2.2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2.1 models">show #!2.2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2.1/A:315-354,417-442,562-595,695-729/B:2-44,162-176,291-331,392-420,535-575,665-696/C/D/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2.1/A:315-354,417-442,562-595,695-729/B:2-44,162-176,291-331,392-420,535-575,665-696/C/D/E">select #2.2.1/A:315-354,417-442,562-595,695-729/B:2-44,162-176,291-331,392-420,535-575,665-696/C/D/E</a></div></div>5004 atoms, 5140 bonds, 59 pseudobonds, 627 residues, 4 models selected<br>
2302<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #2.2.1 atoms /A:315-354 atoms /A:417-442 atoms /A:562-595 atoms /A:695-729 atoms /B:2-44 atoms /B:162-176 atoms /B:291-331 atoms /B:392-420 atoms /B:535-575 atoms /B:665-696 atoms /C atoms /D atoms /E</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #2.2.1 atoms /A:315-354 atoms /A:417-442 atoms /A:562-595 atoms /A:695-729 atoms /B:2-44 atoms /B:162-176 atoms /B:291-331 atoms /B:392-420 atoms /B:535-575 atoms /B:665-696 atoms /C atoms /D atoms /E">split #2.2.1 atoms /A:315-354 atoms /A:417-442 atoms /A:562-595 atoms /A:695-729 atoms /B:2-44 atoms /B:162-176 atoms /B:291-331 atoms /B:392-420 atoms /B:535-575 atoms /B:665-696 atoms /C atoms /D atoms /E</a></div></div>Split 6yez 2 1 (#2.2.1) into 14 models<br>
2303<table border=1 cellpadding=4 cellspacing=0>
2304 <thead>
2305 <tr>
2306 <th colspan="2">Chain information for 6yez 2 1 1 #2.2.1.1</th>
2307 </tr>
2308 <tr>
2309 <th>Chain</th>
2310 <th>Description</th>
2311
2312 </tr>
2313 </thead>
2314 <tbody>
2315 <tr>
2316 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.1/A:315-354">A</a></td>
2317 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.1/A">No description available</a></td>
2318
2319 </tr>
2320 </tbody>
2321</table><br/><table border=1 cellpadding=4 cellspacing=0>
2322 <thead>
2323 <tr>
2324 <th colspan="2">Chain information for 6yez 2 1 2 #2.2.1.2</th>
2325 </tr>
2326 <tr>
2327 <th>Chain</th>
2328 <th>Description</th>
2329
2330 </tr>
2331 </thead>
2332 <tbody>
2333 <tr>
2334 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.2/A:417-442">A</a></td>
2335 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.2/A">No description available</a></td>
2336
2337 </tr>
2338 </tbody>
2339</table><br/><table border=1 cellpadding=4 cellspacing=0>
2340 <thead>
2341 <tr>
2342 <th colspan="2">Chain information for 6yez 2 1 3 #2.2.1.3</th>
2343 </tr>
2344 <tr>
2345 <th>Chain</th>
2346 <th>Description</th>
2347
2348 </tr>
2349 </thead>
2350 <tbody>
2351 <tr>
2352 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.3/A:562-595">A</a></td>
2353 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.3/A">No description available</a></td>
2354
2355 </tr>
2356 </tbody>
2357</table><br/><table border=1 cellpadding=4 cellspacing=0>
2358 <thead>
2359 <tr>
2360 <th colspan="2">Chain information for 6yez 2 1 4 #2.2.1.4</th>
2361 </tr>
2362 <tr>
2363 <th>Chain</th>
2364 <th>Description</th>
2365
2366 </tr>
2367 </thead>
2368 <tbody>
2369 <tr>
2370 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.4/A:695-729">A</a></td>
2371 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.4/A">No description available</a></td>
2372
2373 </tr>
2374 </tbody>
2375</table><br/><table border=1 cellpadding=4 cellspacing=0>
2376 <thead>
2377 <tr>
2378 <th colspan="2">Chain information for 6yez 2 1 5 #2.2.1.5</th>
2379 </tr>
2380 <tr>
2381 <th>Chain</th>
2382 <th>Description</th>
2383
2384 </tr>
2385 </thead>
2386 <tbody>
2387 <tr>
2388 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.5/B:2-44">B</a></td>
2389 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.5/B">No description available</a></td>
2390
2391 </tr>
2392 </tbody>
2393</table><br/><table border=1 cellpadding=4 cellspacing=0>
2394 <thead>
2395 <tr>
2396 <th colspan="2">Chain information for 6yez 2 1 6 #2.2.1.6</th>
2397 </tr>
2398 <tr>
2399 <th>Chain</th>
2400 <th>Description</th>
2401
2402 </tr>
2403 </thead>
2404 <tbody>
2405 <tr>
2406 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.6/B:162-176">B</a></td>
2407 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.6/B">No description available</a></td>
2408
2409 </tr>
2410 </tbody>
2411</table><br/><table border=1 cellpadding=4 cellspacing=0>
2412 <thead>
2413 <tr>
2414 <th colspan="2">Chain information for 6yez 2 1 7 #2.2.1.7</th>
2415 </tr>
2416 <tr>
2417 <th>Chain</th>
2418 <th>Description</th>
2419
2420 </tr>
2421 </thead>
2422 <tbody>
2423 <tr>
2424 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.7/B:291-331">B</a></td>
2425 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.7/B">No description available</a></td>
2426
2427 </tr>
2428 </tbody>
2429</table><br/><table border=1 cellpadding=4 cellspacing=0>
2430 <thead>
2431 <tr>
2432 <th colspan="2">Chain information for 6yez 2 1 8 #2.2.1.8</th>
2433 </tr>
2434 <tr>
2435 <th>Chain</th>
2436 <th>Description</th>
2437
2438 </tr>
2439 </thead>
2440 <tbody>
2441 <tr>
2442 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.8/B:392-420">B</a></td>
2443 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.8/B">No description available</a></td>
2444
2445 </tr>
2446 </tbody>
2447</table><br/><table border=1 cellpadding=4 cellspacing=0>
2448 <thead>
2449 <tr>
2450 <th colspan="2">Chain information for 6yez 2 1 9 #2.2.1.9</th>
2451 </tr>
2452 <tr>
2453 <th>Chain</th>
2454 <th>Description</th>
2455
2456 </tr>
2457 </thead>
2458 <tbody>
2459 <tr>
2460 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.9/B:535-575">B</a></td>
2461 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.9/B">No description available</a></td>
2462
2463 </tr>
2464 </tbody>
2465</table><br/><table border=1 cellpadding=4 cellspacing=0>
2466 <thead>
2467 <tr>
2468 <th colspan="2">Chain information for 6yez 2 1 10 #2.2.1.10</th>
2469 </tr>
2470 <tr>
2471 <th>Chain</th>
2472 <th>Description</th>
2473
2474 </tr>
2475 </thead>
2476 <tbody>
2477 <tr>
2478 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.10/B:665-696">B</a></td>
2479 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.10/B">No description available</a></td>
2480
2481 </tr>
2482 </tbody>
2483</table><br/><table border=1 cellpadding=4 cellspacing=0>
2484 <thead>
2485 <tr>
2486 <th colspan="2">Chain information for 6yez 2 1 11 #2.2.1.11</th>
2487 </tr>
2488 <tr>
2489 <th>Chain</th>
2490 <th>Description</th>
2491
2492 </tr>
2493 </thead>
2494 <tbody>
2495 <tr>
2496 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.11/C:2-81">C</a></td>
2497 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.11/C">No description available</a></td>
2498
2499 </tr>
2500 </tbody>
2501</table><br/><table border=1 cellpadding=4 cellspacing=0>
2502 <thead>
2503 <tr>
2504 <th colspan="2">Chain information for 6yez 2 1 12 #2.2.1.12</th>
2505 </tr>
2506 <tr>
2507 <th>Chain</th>
2508 <th>Description</th>
2509
2510 </tr>
2511 </thead>
2512 <tbody>
2513 <tr>
2514 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.12/D:69-211">D</a></td>
2515 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.12/D">No description available</a></td>
2516
2517 </tr>
2518 </tbody>
2519</table><br/><table border=1 cellpadding=4 cellspacing=0>
2520 <thead>
2521 <tr>
2522 <th colspan="2">Chain information for 6yez 2 1 13 #2.2.1.13</th>
2523 </tr>
2524 <tr>
2525 <th>Chain</th>
2526 <th>Description</th>
2527
2528 </tr>
2529 </thead>
2530 <tbody>
2531 <tr>
2532 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.13/E:64-129">E</a></td>
2533 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.13/E">No description available</a></td>
2534
2535 </tr>
2536 </tbody>
2537</table><br/><table border=1 cellpadding=4 cellspacing=0>
2538 <thead>
2539 <tr>
2540 <th colspan="2">Chain information for 6yez 2 1 14 #2.2.1.14</th>
2541 </tr>
2542 <tr>
2543 <th>Chain</th>
2544 <th>Description</th>
2545
2546 </tr>
2547 </thead>
2548 <tbody>
2549 <tr>
2550 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.14/A:16-200">A</a></td>
2551 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.14/A">No description available</a></td>
2552
2553 </tr>
2554 <tr>
2555 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2.1.14/B:697-707">B</a></td>
2556 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2.1.14/B">No description available</a></td>
2557
2558 </tr>
2559 </tbody>
2560</table><br/>Associated 6yez 2 1 1 (2.2.1.1) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2561Associated 6yez 2 1 2 (2.2.1.2) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2562Associated 6yez 2 1 3 (2.2.1.3) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2563Associated 6yez 2 1 4 (2.2.1.4) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2564Associated 6yez 2 1 5 (2.2.1.5) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2565Associated 6yez 2 1 6 (2.2.1.6) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2566Associated 6yez 2 1 7 (2.2.1.7) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2567Associated 6yez 2 1 8 (2.2.1.8) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2568Associated 6yez 2 1 9 (2.2.1.9) chain B to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2569Associated 6yez 2 1 11 (2.2.1.11) chain C to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2570Associated 6yez 2 1 12 (2.2.1.12) chain D to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2571Associated 6yez 2 1 13 (2.2.1.13) chain E to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2572Associated 6yez 2 1 14 (2.2.1.14) chain A to PSI_stromal_ridge_0.pdb, chain A with 0 mismatches<br>
2573Associated 6yez 2 1 14 (2.2.1.14) chain B to 6yez 2, chain A with 1 mismatch<br>
2574<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.14 models">hide #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.14 models">show #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.14 models">hide #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.14 models">show #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.13 models">hide #2.2.1.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.13 models">show #2.2.1.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.1 models">hide #2.2.1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.1 models">show #2.2.1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.1 models">hide #2.2.1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.1 models">show #2.2.1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2.1 models">hide #!2.2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2.1 models">show #!2.2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.1 models">hide #2.2.1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.1 models">show #2.2.1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.2 models">show #9.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:200@C#9.2:73@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:200@C#9.2:73@N">select #2.2/A:200@C#9.2:73@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2575<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:273-276 toAtoms #8:73-76 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:273-276 toAtoms #8:73-76 matchAtomNames true move residues">align #2.2.1/A:273-276 toAtoms #8:73-76 matchAtomNames true move residues</a></div></div>RMSD between 16 atom pairs is 0.000 angstroms<br>
2576<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:276@C:315@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:276@C:315@N">select #2.2/A:276@C:315@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2577<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:315-354 toAtoms #4/A:315-354 matchAtomNames true matchNumbering true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:315-354 toAtoms #4/A:315-354 matchAtomNames true matchNumbering true move residues">align #2.2.1/A:315-354 toAtoms #4/A:315-354 matchAtomNames true matchNumbering true move residues</a></div></div>RMSD between 322 atom pairs is 0.000 angstroms<br>
2578<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:276-315</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:276-315">select #2.2/A:276-315</a></div></div>14 atoms, 14 bonds, 2 residues, 1 model selected<br>
2579<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:72-315</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:72-315">select #2.2/A:72-315</a></div></div>149 atoms, 153 bonds, 21 residues, 1 model selected<br>
2580<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.3 models">show #9.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:354@C#9.3:117@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:354@C#9.3:117@N">select #2.2/A:354@C#9.3:117@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2581<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:117-120 toAtoms #8:117-120 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:117-120 toAtoms #8:117-120 matchAtomNames true move residues">align #2.2.1/A:117-120 toAtoms #8:117-120 matchAtomNames true move residues</a></div></div>RMSD between 16 atom pairs is 0.000 angstroms<br>
2582<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#up">select up</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select up">select up</a></div></div>14 atoms, 15 bonds, 1 residue, 1 model selected<br>
2583<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#down">select down</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select down">select down</a></div></div>1 atom, 1 residue, 1 model selected<br>
2584<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:120@C#2.2:417@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:120@C#2.2:417@N">select #2.2/A:120@C#2.2:417@N</a></div></div>3 atoms, 3 residues, 3 models selected<br>
2585<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.8 models">hide #2.2.1.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.8 models">show #2.2.1.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.8 models">hide #2.2.1.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.8 models">show #2.2.1.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.2 models">hide #2.2.1.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.2 models">show #2.2.1.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:120@C#2.2:417@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:120@C#2.2:417@N">select #2.2/A:120@C#2.2:417@N</a></div></div>3 atoms, 3 residues, 3 models selected<br>
2586<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:417-442 toAtoms #4/A:417-442 matchAtomNames true matchNumbering true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:417-442 toAtoms #4/A:417-442 matchAtomNames true matchNumbering true move residues">align #2.2.1/A:417-442 toAtoms #4/A:417-442 matchAtomNames true matchNumbering true move residues</a></div></div>RMSD between 228 atom pairs is 0.000 angstroms<br>
2587<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2.1/A:417-442</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2.1/A:417-442">select #2.2.1/A:417-442</a></div></div>228 atoms, 232 bonds, 26 residues, 1 model selected<br>
2588<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2.1/A:72-442</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2.1/A:72-442">select #2.2.1/A:72-442</a></div></div>705 atoms, 725 bonds, 90 residues, 1 model selected<br>
2589<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.4 models">show #9.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:442@C#9.4:147@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:442@C#9.4:147@N">select #2.2/A:442@C#9.4:147@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2590<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:147-150 toAtoms #8:147-150 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:147-150 toAtoms #8:147-150 matchAtomNames true move residues">align #2.2.1/A:147-150 toAtoms #8:147-150 matchAtomNames true move residues</a></div></div>RMSD between 16 atom pairs is 0.000 angstroms<br>
2591<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:150@C#2.2:562@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:150@C#2.2:562@N">select #2.2/A:150@C#2.2:562@N</a></div></div>3 atoms, 3 residues, 3 models selected<br>
2592<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:562-595 toAtoms #4/A:562-595 matchAtomNames true matchNumbering true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:562-595 toAtoms #4/A:562-595 matchAtomNames true matchNumbering true move residues">align #2.2.1/A:562-595 toAtoms #4/A:562-595 matchAtomNames true matchNumbering true move residues</a></div></div>RMSD between 257 atom pairs is 0.000 angstroms<br>
2593<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.5 models">show #9.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:595@C#9.5:185@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:595@C#9.5:185@N">select #2.2/A:595@C#9.5:185@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2594<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:780-787 toAtoms #8:185-192 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:780-787 toAtoms #8:185-192 matchAtomNames true move residues">align #2.2.1/A:780-787 toAtoms #8:185-192 matchAtomNames true move residues</a></div></div>RMSD between 32 atom pairs is 0.000 angstroms<br>
2595<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:787@C#2.2:695@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:787@C#2.2:695@N">select #2.2/A:787@C#2.2:695@N</a></div></div>3 atoms, 3 residues, 3 models selected<br>
2596<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:695-729 toAtoms #4/A:695-729 matchAtomNames true matchNumbering true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:695-729 toAtoms #4/A:695-729 matchAtomNames true matchNumbering true move residues">align #2.2.1/A:695-729 toAtoms #4/A:695-729 matchAtomNames true matchNumbering true move residues</a></div></div>RMSD between 279 atom pairs is 0.000 angstroms<br>
2597<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.14 models">hide #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.14 models">show #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.14 models">hide #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.14 models">show #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A">select #2.2/A</a></div></div>1753 atoms, 1810 bonds, 228 residues, 1 model selected<br>
2598<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.6 models">show #9.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:729@C#9.6:228@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:729@C#9.6:228@N">select #2.2/A:729@C#9.6:228@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2599<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:228-257 toAtoms #8:228-257 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:228-257 toAtoms #8:228-257 matchAtomNames true move residues">align #2.2.1/A:228-257 toAtoms #8:228-257 matchAtomNames true move residues</a></div></div>RMSD between 120 atom pairs is 0.000 angstroms<br>
2600<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:257@C#2.2/B:2@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:257@C#2.2/B:2@N">select #2.2/A:257@C#2.2/B:2@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2601<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true matchNumbering true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true matchNumbering true move residues">align #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true matchNumbering true move residues</a></div></div>Pairing dropped 356 atoms and 356 reference atoms<br>
2602<font color="crimson"><b>No atoms paired for alignment</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true move residues">align #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true move residues</a></div></div>RMSD between 356 atom pairs is 0.000 angstroms<br>
2603<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.7 models">show #9.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.7 models">hide #9.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.7 models">show #9.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:831@C#9.7:301@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:831@C#9.7:301@N">select #2.2/A:831@C#9.7:301@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2604<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:301-304 toAtoms #8:301-304 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:301-304 toAtoms #8:301-304 matchAtomNames true move residues">align #2.2.1/A:301-304 toAtoms #8:301-304 matchAtomNames true move residues</a></div></div>RMSD between 16 atom pairs is 0.000 angstroms<br>
2605<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:304@C#2.2/B:162@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:304@C#2.2/B:162@N">select #2.2/A:304@C#2.2/B:162@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2606<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:162-176 toAtoms #4/B:162-176 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:162-176 toAtoms #4/B:162-176 matchAtomNames true move residues">align #2.2.1/A:162-176 toAtoms #4/B:162-176 matchAtomNames true move residues</a></div></div>RMSD between 124 atom pairs is 0.000 angstroms<br>
2607<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.8 models">show #9.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:176@C#9.8:320@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:176@C#9.8:320@N">select #2.2/A:176@C#9.8:320@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2608<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:1151-1154 toAtoms #8:320-323 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:1151-1154 toAtoms #8:320-323 matchAtomNames true move residues">align #2.2.1/A:1151-1154 toAtoms #8:320-323 matchAtomNames true move residues</a></div></div>RMSD between 16 atom pairs is 0.000 angstroms<br>
2609<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:1154@C#2.2/B:291@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:1154@C#2.2/B:291@N">select #2.2/A:1154@C#2.2/B:291@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2610<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:1445-1485 toAtoms #4/B:291-331 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:1445-1485 toAtoms #4/B:291-331 matchAtomNames true move residues">align #2.2.1/A:1445-1485 toAtoms #4/B:291-331 matchAtomNames true move residues</a></div></div>RMSD between 324 atom pairs is 0.000 angstroms<br>
2611<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.9 models">show #9.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.9 models">hide #9.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.9 models">show #9.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:1485@C#9.9:365@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:1485@C#9.9:365@N">select #2.2/A:1485@C#9.9:365@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2612<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:365-368 toAtoms #8:365-368 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:365-368 toAtoms #8:365-368 matchAtomNames true move residues">align #2.2.1/A:365-368 toAtoms #8:365-368 matchAtomNames true move residues</a></div></div>RMSD between 16 atom pairs is 0.000 angstroms<br>
2613<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:368@C#2.2/B:392@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:368@C#2.2/B:392@N">select #2.2/A:368@C#2.2/B:392@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2614<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:1877-1905 toAtoms #4/B:392-420 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:1877-1905 toAtoms #4/B:392-420 matchAtomNames true move residues">align #2.2.1/A:1877-1905 toAtoms #4/B:392-420 matchAtomNames true move residues</a></div></div>RMSD between 242 atom pairs is 0.000 angstroms<br>
2615<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.10 models">show #9.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:1905@C#9.10:398@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:1905@C#9.10:398@N">select #2.2/A:1905@C#9.10:398@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2616<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:398-401 toAtoms #8:398-401 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:398-401 toAtoms #8:398-401 matchAtomNames true move residues">align #2.2.1/A:398-401 toAtoms #8:398-401 matchAtomNames true move residues</a></div></div>RMSD between 16 atom pairs is 0.000 angstroms<br>
2617<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:401@C#2.2/B:535@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:401@C#2.2/B:535@N">select #2.2/A:401@C#2.2/B:535@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2618<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:2440-2480 toAtoms #4/B:535-575 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:2440-2480 toAtoms #4/B:535-575 matchAtomNames true move residues">align #2.2.1/A:2440-2480 toAtoms #4/B:535-575 matchAtomNames true move residues</a></div></div>RMSD between 299 atom pairs is 0.000 angstroms<br>
2619<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.11 models">show #9.11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:2480@C#9.11:443@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:2480@C#9.11:443@N">select #2.2/A:2480@C#9.11:443@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2620<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:2480@C#9.11:443@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:2480@C#9.11:443@N">select #2.2/A:2480@C#9.11:443@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2621<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A">select #2.2/A</a></div></div>3282 atoms, 3377 bonds, 443 residues, 1 model selected<br>
2622<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.14 models">hide #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.14 models">show #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.14 models">hide #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.14 models">show #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.10 models">hide #2.2.1.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.10 models">show #2.2.1.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.14 models">hide #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.14 models">show #2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:2480@C#9.11:443@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:2480@C#9.11:443@N">select #2.2/A:2480@C#9.11:443@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2623<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:443-470 toAtoms #8:443-470 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:443-470 toAtoms #8:443-470 matchAtomNames true move residues">align #2.2.1/A:443-470 toAtoms #8:443-470 matchAtomNames true move residues</a></div></div>RMSD between 112 atom pairs is 0.000 angstroms<br>
2624<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.12 models">show #9.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.12 models">hide #9.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:470@C#2.2/C:2@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:470@C#2.2/C:2@N">select #2.2/A:470@C#2.2/C:2@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2625<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:2482-2561 toAtoms #4/C:2-81 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:2482-2561 toAtoms #4/C:2-81 matchAtomNames true move residues">align #2.2.1/A:2482-2561 toAtoms #4/C:2-81 matchAtomNames true move residues</a></div></div>RMSD between 612 atom pairs is 0.000 angstroms<br>
2626<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:3002-3003 toAtoms #4/C:3002-3003 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:3002-3003 toAtoms #4/C:3002-3003 matchAtomNames true move residues">align #2.2.1/A:3002-3003 toAtoms #4/C:3002-3003 matchAtomNames true move residues</a></div></div>RMSD between 16 atom pairs is 0.000 angstroms<br>
2627<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.12 models">show #9.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:2561@C#9.11:551@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:2561@C#9.11:551@N">select #2.2/A:2561@C#9.11:551@N</a></div></div>1 atom, 1 residue, 1 model selected<br>
2628<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><font color="crimson"><b>No nitrogens in specified atoms<br>
2629</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:2561@C#9.12:551@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:2561@C#9.12:551@N">select #2.2/A:2561@C#9.12:551@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2630<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:3112-3147 toAtoms #8:551-586 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:3112-3147 toAtoms #8:551-586 matchAtomNames true move residues">align #2.2.1/A:3112-3147 toAtoms #8:551-586 matchAtomNames true move residues</a></div></div>RMSD between 144 atom pairs is 0.000 angstroms<br>
2631<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.10 models">hide #2.2.1.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.12 models">hide #2.2.1.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.12 models">show #2.2.1.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.12 models">hide #2.2.1.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.12 models">show #2.2.1.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.12 models">hide #2.2.1.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.12 models">show #2.2.1.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.12 models">hide #2.2.1.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.13 models">hide #2.2.1.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2.1.14 models">hide #!2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2.1.14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2.1.14 models">show #!2.2.1.14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.13 models">show #9.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.13 models">hide #9.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.13 models">show #9.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.13 models">hide #9.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.13 models">show #9.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9.13 models">hide #9.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.13 models">show #2.2.1.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.13 models">hide #2.2.1.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.12 models">show #2.2.1.12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/D:69</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/D:69">select #2/D:69</a></div></div>4 atoms, 3 bonds, 1 residue, 1 model selected<br>
2632<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.2/A:3147@C#2.2/D:69@N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.2/A:3147@C#2.2/D:69@N">select #2.2/A:3147@C#2.2/D:69@N</a></div></div>2 atoms, 2 residues, 2 models selected<br>
2633<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/build.html#join-peptide">build join peptide</a> sel length 1.33 omega 180 phi -120 move N</div><div class="cxcmd_as_cmd"><a href="cxcmd:build join peptide sel length 1.33 omega 180 phi -120 move N">build join peptide sel length 1.33 omega 180 phi -120 move N</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #2.2.1/A:3216-3358 toAtoms #4/D:69-211 matchAtomNames true move residues</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #2.2.1/A:3216-3358 toAtoms #4/D:69-211 matchAtomNames true move residues">align #2.2.1/A:3216-3358 toAtoms #4/D:69-211 matchAtomNames true move residues</a></div></div>RMSD between 1132 atom pairs is 0.000 angstroms<br>
2634<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.10 models">show #2.2.1.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1.10 models">hide #2.2.1.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.2.1.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.2.1.10 models">show #2.2.1.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #9.13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #9.13 models">show #9.13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain for interface design.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sat May 18 17:13:54 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
2635<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #2.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #2.2">close #2.2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #6</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #6">close #6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #8#9</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #8#9">close #8#9</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #7">close #7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #3">close #3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #5">close #5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #2">close #2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb&quot; format pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb&quot; format pdb">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb&quot; format pdb</a></div></div>
2636<table border=1 cellpadding=4 cellspacing=0>
2637 <thead>
2638 <tr>
2639 <th colspan="2">Summary of feedback from opening /Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb</th>
2640 </tr>
2641 </thead>
2642 <tbody>
2643 <tr>
2644 <td><i>warnings</i></td> <td style="background-color:#ffb961">Ignored bad PDB record found on line 34701<br>SEQRES *** A 830<br><br>Ignored bad PDB record found on line 34702<br>SEQRES *** A 830<br><br>Ignored bad PDB record found on line 34703<br>SEQRES *** A 830<br><br>Ignored bad PDB record found on line 34704<br>SEQRES *** A 830<br><br>Ignored bad PDB record found on line 34705<br>SEQRES *** A 830<br><br>92885266 messages similar to the above omitted</td> </tr>
2645 </tbody>
2646</table><br/><table border=1 cellpadding=4 cellspacing=0>
2647 <thead>
2648 <tr>
2649 <th colspan="2">Chain information for SingleChainStromalRidge_PetF_Fdn.pdb #2</th>
2650 </tr>
2651 <tr>
2652 <th>Chain</th>
2653 <th>Description</th>
2654
2655 </tr>
2656 </thead>
2657 <tbody>
2658 <tr>
2659 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/A:1-830">A</a></td>
2660 <td><a title="Show sequence" href="cxcmd:sequence chain #2/A">No description available</a></td>
2661
2662 </tr>
2663 <tr>
2664 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/M:1-55">M</a></td>
2665 <td><a title="Show sequence" href="cxcmd:sequence chain #2/M">No description available</a></td>
2666
2667 </tr>
2668 <tr>
2669 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/N:1-97">N</a></td>
2670 <td><a title="Show sequence" href="cxcmd:sequence chain #2/N">No description available</a></td>
2671
2672 </tr>
2673 </tbody>
2674</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user/tools/modelpanel.html</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user/tools/modelpanel.html">help help:user/tools/modelpanel.html</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb&quot; models #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb&quot; models #2">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge/SingleChainStromalRidge_PetF_Fdn.pdb&quot; models #2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
2675<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2">select #2</a></div></div>7455 atoms, 7544 bonds, 23 pseudobonds, 1082 residues, 3 models selected<br>
2676<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel bychain</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel bychain">color sel bychain</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:FES,SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:FES,SF4">select #2:FES,SF4</a></div></div>44 atoms, 64 bonds, 6 residues, 1 model selected<br>
2677<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2">select #2</a></div></div>7455 atoms, 7544 bonds, 23 pseudobonds, 1082 residues, 3 models selected<br>
2678<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:FES,SF4,CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:FES,SF4,CYS">select #2:FES,SF4,CYS</a></div></div>238 atoms, 231 bonds, 19 pseudobonds, 33 residues, 2 models selected<br>
2679<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v2.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sat May 18 22:45:24 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
2680<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #2">close #2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #4/A">sequence chain #4/A</a></div></div>Alignment identifier is 4/A<br>
2681<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:729">select #4/A:729</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
2682<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:729">select #4/A:729</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
2683<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #4 id 2</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #4 id 2">rename #4 id 2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-73,191-200,315-354,417-442,562-595,695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-73,191-200,315-354,417-442,562-595,695-729">select #2/A:16-73,191-200,315-354,417-442,562-595,695-729</a></div></div>1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected<br>
2684<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-73</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-73">select #2/A:16-73</a></div></div>474 atoms, 490 bonds, 58 residues, 1 model selected<br>
2685<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Renumber Residues&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Renumber Residues&quot;">ui tool show &quot;Renumber Residues&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/A:16-73 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/A:16-73 start 1">renumber #2/A:16-73 start 1</a></div></div>58 residues renumbered<br>
2686<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:191</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:191">select #2/A:191</a></div></div>7 atoms, 7 bonds, 1 residue, 1 model selected<br>
2687<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:191</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:191">select #2/A:191</a></div></div>7 atoms, 7 bonds, 1 residue, 1 model selected<br>
2688<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:191-200</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:191-200">select #2/A:191-200</a></div></div>89 atoms, 92 bonds, 10 residues, 1 model selected<br>
2689<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/A:191-200 start 63</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/A:191-200 start 63">renumber #2/A:191-200 start 63</a></div></div>10 residues renumbered<br>
2690<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:315-354</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:315-354">select #2/A:315-354</a></div></div>322 atoms, 333 bonds, 40 residues, 1 model selected<br>
2691<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/A:315-354 start 77</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/A:315-354 start 77">renumber #2/A:315-354 start 77</a></div></div>40 residues renumbered<br>
2692<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:417-442</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:417-442">select #2/A:417-442</a></div></div>228 atoms, 232 bonds, 26 residues, 1 model selected<br>
2693<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/A:417-442 start 121</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/A:417-442 start 121">renumber #2/A:417-442 start 121</a></div></div>26 residues renumbered<br>
2694<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:562-595</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:562-595">select #2/A:562-595</a></div></div>257 atoms, 264 bonds, 34 residues, 1 model selected<br>
2695<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/A:562-595 start 151</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/A:562-595 start 151">renumber #2/A:562-595 start 151</a></div></div>34 residues renumbered<br>
2696<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:695-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:695-729">select #2/A:695-729</a></div></div>279 atoms, 286 bonds, 35 residues, 1 model selected<br>
2697<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/A:695-729 start 193</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/A:695-729 start 193">renumber #2/A:695-729 start 193</a></div></div>35 residues renumbered<br>
2698<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain v3.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #2/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #2/B">sequence chain #2/B</a></div></div>Alignment identifier is 2/B<br>
2699<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44,162-176,291-331,392-420,535-575,665-696/A:227</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44,162-176,291-331,392-420,535-575,665-696/A:227">select #2/B:2-44,162-176,291-331,392-420,535-575,665-696/A:227</a></div></div>1639 atoms, 1681 bonds, 5 pseudobonds, 202 residues, 2 models selected<br>
2700<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44/A:227</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44/A:227">select #2/B:2-44/A:227</a></div></div>365 atoms, 374 bonds, 44 residues, 1 model selected<br>
2701<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge_0.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge_0.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI_stromal_ridge_0.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
2702 <thead>
2703 <tr>
2704 <th colspan="2">Chain information for PSI_stromal_ridge_0.pdb #3</th>
2705 </tr>
2706 <tr>
2707 <th>Chain</th>
2708 <th>Description</th>
2709
2710 </tr>
2711 </thead>
2712 <tbody>
2713 <tr>
2714 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3/A:1-829">A</a></td>
2715 <td><a title="Show sequence" href="cxcmd:sequence chain #3/A">No description available</a></td>
2716
2717 </tr>
2718 </tbody>
2719</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #3 to #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #3 to #2">matchmaker #3 to #2</a></div></div>
2720 <table border=1 cellpadding=4 cellspacing=0>
2721 <tr>
2722 <th colspan="2">Parameters</th>
2723 </tr>
2724 <tr>
2725 <td>Chain pairing</td>
2726 <td>bb</td>
2727 </tr>
2728 <tr>
2729 <td>Alignment algorithm</td>
2730 <td>Needleman-Wunsch</td>
2731 </tr>
2732 <tr>
2733 <td>Similarity matrix</td>
2734 <td>BLOSUM-62</td>
2735 </tr>
2736
2737 <tr>
2738 <td>SS fraction</td>
2739 <td>0.3</td>
2740 </tr>
2741 <tr>
2742 <td>Gap open (HH/SS/other)</td>
2743 <td>18/18/6</td>
2744 </tr>
2745 <tr>
2746 <td>Gap extend</td>
2747 <td>1</td>
2748 </tr>
2749 <tr>
2750 <td>SS matrix</td>
2751 <td>
2752 <table>
2753 <tr>
2754 <th></th> <th>H</th> <th>S</th> <th>O</th>
2755 </tr>
2756 <tr>
2757 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
2758 </tr>
2759 <tr>
2760 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
2761 </tr>
2762 <tr>
2763 <th>O</th> <td></td> <td></td> <td align="right">4</td>
2764 </tr>
2765 </table>
2766 </td>
2767 </tr>
2768
2769 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
2770 </table>
2771 <br/>Matchmaker combination, chain A (#2) with PSI_stromal_ridge_0.pdb, chain A (#3), sequence alignment score = 924.3<br>
2772RMSD between 203 pruned atom pairs is 0.259 angstroms; (across all 203 pairs: 0.259)<br>
2773<br>
2774<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44/A:227</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44/A:227">select #2/B:2-44/A:227</a></div></div>365 atoms, 374 bonds, 44 residues, 1 model selected<br>
2775<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44">select #2/B:2-44</a></div></div>356 atoms, 366 bonds, 43 residues, 1 model selected<br>
2776<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:2-44 start 258</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:2-44 start 258">renumber #2/B:2-44 start 258</a></div></div><font color="crimson"><b>Proposed renumbering conflicts with existing residue combination #2/B TYR 291<br>
2777</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44,162-176,291-331,392-420,535-575,665-696</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44,162-176,291-331,392-420,535-575,665-696">select #2/B:2-44,162-176,291-331,392-420,535-575,665-696</a></div></div>1630 atoms, 1673 bonds, 5 pseudobonds, 201 residues, 2 models selected<br>
2778<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44,162-176,291-331,392-420,535-575,665-696</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44,162-176,291-331,392-420,535-575,665-696">select #2/B:2-44,162-176,291-331,392-420,535-575,665-696</a></div></div>1630 atoms, 1673 bonds, 5 pseudobonds, 201 residues, 2 models selected<br>
2779<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:2-696 start 1002</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:2-696 start 1002">renumber #2/B:2-696 start 1002</a></div></div>201 residues renumbered<br>
2780<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:697</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:697">select #2/B:697</a></div></div>7 atoms, 7 bonds, 1 residue, 1 model selected<br>
2781<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:697-707</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:697-707">select #2/B:697-707</a></div></div>81 atoms, 81 bonds, 11 residues, 1 model selected<br>
2782<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:697-707 start 1697</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:697-707 start 1697">renumber #2/B:697-707 start 1697</a></div></div>11 residues renumbered<br>
2783<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3 sequence GGGG</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3 sequence GGGG">select #3 sequence GGGG</a></div></div>676 atoms, 663 bonds, 169 residues, 1 model selected<br>
2784<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1002-1044</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1002-1044">select #2/B:1002-1044</a></div></div>356 atoms, 366 bonds, 43 residues, 1 model selected<br>
2785<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:1002-1044 start 258</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:1002-1044 start 258">renumber #2/B:1002-1044 start 258</a></div></div>43 residues renumbered<br>
2786<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1162-1176</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1162-1176">select #2/B:1162-1176</a></div></div>124 atoms, 127 bonds, 15 residues, 1 model selected<br>
2787<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:300</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:300">select #2/B:300</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
2788<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:300-1162</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:300-1162">select #2/B:300-1162</a></div></div>18 atoms, 16 bonds, 1 pseudobond, 2 residues, 2 models selected<br>
2789<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1162-1176</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1162-1176">select #2/B:1162-1176</a></div></div>124 atoms, 127 bonds, 15 residues, 1 model selected<br>
2790<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:1162-1176 start 305</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:1162-1176 start 305">renumber #2/B:1162-1176 start 305</a></div></div>15 residues renumbered<br>
2791<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:319</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:319">select #2/B:319</a></div></div>8 atoms, 7 bonds, 1 residue, 1 model selected<br>
2792<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:319-1291</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:319-1291">select #2/B:319-1291</a></div></div>20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected<br>
2793<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1291-1331</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1291-1331">select #2/B:1291-1331</a></div></div>324 atoms, 333 bonds, 41 residues, 1 model selected<br>
2794<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N">select #2/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
2795<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_0.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_1.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_2.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_0.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_1.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_2.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_0.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_1.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_2.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
2796 <thead>
2797 <tr>
2798 <th colspan="2">Chain information for PSI_fdn_0.pdb #4</th>
2799 </tr>
2800 <tr>
2801 <th>Chain</th>
2802 <th>Description</th>
2803
2804 </tr>
2805 </thead>
2806 <tbody>
2807 <tr>
2808 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4/A:1-889">A</a></td>
2809 <td><a title="Show sequence" href="cxcmd:sequence chain #4/A">No description available</a></td>
2810
2811 </tr>
2812 </tbody>
2813</table><br/><table border=1 cellpadding=4 cellspacing=0>
2814 <thead>
2815 <tr>
2816 <th colspan="2">Chain information for PSI_fdn_1.pdb #5</th>
2817 </tr>
2818 <tr>
2819 <th>Chain</th>
2820 <th>Description</th>
2821
2822 </tr>
2823 </thead>
2824 <tbody>
2825 <tr>
2826 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/A:1-889">A</a></td>
2827 <td><a title="Show sequence" href="cxcmd:sequence chain #5/A">No description available</a></td>
2828
2829 </tr>
2830 </tbody>
2831</table><br/><table border=1 cellpadding=4 cellspacing=0>
2832 <thead>
2833 <tr>
2834 <th colspan="2">Chain information for PSI_fdn_2.pdb #6</th>
2835 </tr>
2836 <tr>
2837 <th>Chain</th>
2838 <th>Description</th>
2839
2840 </tr>
2841 </thead>
2842 <tbody>
2843 <tr>
2844 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/A:1-889">A</a></td>
2845 <td><a title="Show sequence" href="cxcmd:sequence chain #6/A">No description available</a></td>
2846
2847 </tr>
2848 </tbody>
2849</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #4-6 to #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #4-6 to #1">matchmaker #4-6 to #1</a></div></div>
2850 <table border=1 cellpadding=4 cellspacing=0>
2851 <tr>
2852 <th colspan="2">Parameters</th>
2853 </tr>
2854 <tr>
2855 <td>Chain pairing</td>
2856 <td>bb</td>
2857 </tr>
2858 <tr>
2859 <td>Alignment algorithm</td>
2860 <td>Needleman-Wunsch</td>
2861 </tr>
2862 <tr>
2863 <td>Similarity matrix</td>
2864 <td>BLOSUM-62</td>
2865 </tr>
2866
2867 <tr>
2868 <td>SS fraction</td>
2869 <td>0.3</td>
2870 </tr>
2871 <tr>
2872 <td>Gap open (HH/SS/other)</td>
2873 <td>18/18/6</td>
2874 </tr>
2875 <tr>
2876 <td>Gap extend</td>
2877 <td>1</td>
2878 </tr>
2879 <tr>
2880 <td>SS matrix</td>
2881 <td>
2882 <table>
2883 <tr>
2884 <th></th> <th>H</th> <th>S</th> <th>O</th>
2885 </tr>
2886 <tr>
2887 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
2888 </tr>
2889 <tr>
2890 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
2891 </tr>
2892 <tr>
2893 <th>O</th> <td></td> <td></td> <td align="right">4</td>
2894 </tr>
2895 </table>
2896 </td>
2897 </tr>
2898
2899 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
2900 </table>
2901 <br/>Matchmaker 2fdn, chain M (#1) with PSI_fdn_0.pdb, chain A (#4), sequence alignment score = 139.6<br>
2902RMSD between 46 pruned atom pairs is 0.501 angstroms; (across all 53 pairs: 2.902)<br>
2903<br>
2904Matchmaker 2fdn, chain M (#1) with PSI_fdn_1.pdb, chain A (#5), sequence alignment score = 147.1<br>
2905RMSD between 47 pruned atom pairs is 0.590 angstroms; (across all 53 pairs: 2.756)<br>
2906<br>
2907Matchmaker 2fdn, chain M (#1) with PSI_fdn_2.pdb, chain A (#6), sequence alignment score = 135.4<br>
2908RMSD between 44 pruned atom pairs is 0.540 angstroms; (across all 48 pairs: 2.878)<br>
2909<br>
2910<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4-6/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4-6/A">select #4-6/A</a></div></div>10668 atoms, 10665 bonds, 2667 residues, 3 models selected<br>
2911<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4-6:1-831</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4-6:1-831">select #4-6:1-831</a></div></div>9972 atoms, 9969 bonds, 2493 residues, 3 models selected<br>
2912<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn large target.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn large target.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn large target.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #4-6</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #4-6">close #4-6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1291-1331</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1291-1331">select #2/B:1291-1331</a></div></div>324 atoms, 333 bonds, 41 residues, 1 model selected<br>
2913<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:319</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:319">select #2/B:319</a></div></div>8 atoms, 7 bonds, 1 residue, 1 model selected<br>
2914<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:319-1291</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:319-1291">select #2/B:319-1291</a></div></div>20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected<br>
2915<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1291-1331</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1291-1331">select #2/B:1291-1331</a></div></div>324 atoms, 333 bonds, 41 residues, 1 model selected<br>
2916<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:1291-1331 start 305</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:1291-1331 start 305">renumber #2/B:1291-1331 start 305</a></div></div><font color="crimson"><b>Proposed renumbering conflicts with existing residue combination #2/B LYS 305<br>
2917</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:305</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:305">select #2/B:305</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
2918<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:2-44,162-176,291-331,392-420,535-575,665-696</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:2-44,162-176,291-331,392-420,535-575,665-696">select #2/B:2-44,162-176,291-331,392-420,535-575,665-696</a></div></div>208 atoms, 211 bonds, 1 pseudobond, 25 residues, 2 models selected<br>
2919<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1291-1331</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1291-1331">select #2/B:1291-1331</a></div></div>324 atoms, 333 bonds, 41 residues, 1 model selected<br>
2920<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:1291-1331 start 324</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:1291-1331 start 324">renumber #2/B:1291-1331 start 324</a></div></div>41 residues renumbered<br>
2921<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1392-1420</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1392-1420">select #2/B:1392-1420</a></div></div>242 atoms, 246 bonds, 29 residues, 1 model selected<br>
2922<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:364</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:364">select #2/B:364</a></div></div>10 atoms, 10 bonds, 1 residue, 1 model selected<br>
2923<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:364-1392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:364-1392">select #2/B:364-1392</a></div></div>18 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected<br>
2924<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1392-1420</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1392-1420">select #2/B:1392-1420</a></div></div>242 atoms, 246 bonds, 29 residues, 1 model selected<br>
2925<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:364</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:364">select #2/B:364</a></div></div>10 atoms, 10 bonds, 1 residue, 1 model selected<br>
2926<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:364-1392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:364-1392">select #2/B:364-1392</a></div></div>18 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected<br>
2927<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1392-1420</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1392-1420">select #2/B:1392-1420</a></div></div>242 atoms, 246 bonds, 29 residues, 1 model selected<br>
2928<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:1392-1420 start 369</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:1392-1420 start 369">renumber #2/B:1392-1420 start 369</a></div></div>29 residues renumbered<br>
2929<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:397</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:397">select #2/B:397</a></div></div>6 atoms, 5 bonds, 1 residue, 1 model selected<br>
2930<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:397-1535</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:397-1535">select #2/B:397-1535</a></div></div>13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected<br>
2931<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1535-1575</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1535-1575">select #2/B:1535-1575</a></div></div>299 atoms, 306 bonds, 41 residues, 1 model selected<br>
2932<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:1535-1575 start 402</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:1535-1575 start 402">renumber #2/B:1535-1575 start 402</a></div></div>41 residues renumbered<br>
2933<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1665-1696</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1665-1696">select #2/B:1665-1696</a></div></div>285 atoms, 295 bonds, 32 residues, 1 model selected<br>
2934<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:442</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:442">select #2/B:442</a></div></div>5 atoms, 4 bonds, 1 residue, 1 model selected<br>
2935<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:442-1665</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:442-1665">select #2/B:442-1665</a></div></div>13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected<br>
2936<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1665-1696</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1665-1696">select #2/B:1665-1696</a></div></div>285 atoms, 295 bonds, 32 residues, 1 model selected<br>
2937<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1665-170</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1665-170">select #2/B:1665-170</a></div></div>Nothing selected<br>
2938<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show cartoons">show cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:1665-1707</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:1665-1707">select #2/B:1665-1707</a></div></div>366 atoms, 377 bonds, 43 residues, 1 model selected<br>
2939<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/B:1665-1707 start 451</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/B:1665-1707 start 451">renumber #2/B:1665-1707 start 451</a></div></div>43 residues renumbered<br>
2940<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B">select #2/B</a></div></div>1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected<br>
2941<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B">select #2/B</a></div></div>1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected<br>
2942<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C">select #2/C</a></div></div>628 atoms, 649 bonds, 8 pseudobonds, 82 residues, 3 models selected<br>
2943<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C">select #2/C</a></div></div>628 atoms, 649 bonds, 8 pseudobonds, 82 residues, 3 models selected<br>
2944<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:2-81</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:2-81">select #2/C:2-81</a></div></div>612 atoms, 625 bonds, 80 residues, 1 model selected<br>
2945<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:2">select #2/C:2</a></div></div>6 atoms, 5 bonds, 1 residue, 1 model selected<br>
2946<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/C:2 start 471</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/C:2 start 471">renumber #2/C:2 start 471</a></div></div>1 residues renumbered<br>
2947<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #2/C</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #2/C">sequence chain #2/C</a></div></div>Alignment identifier is 2/C<br>
2948<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C:2-81</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C:2-81">select #2/C:2-81</a></div></div>606 atoms, 619 bonds, 79 residues, 1 model selected<br>
2949<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/C:3-81 start 472</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/C:3-81 start 472">renumber #2/C:3-81 start 472</a></div></div>79 residues renumbered<br>
2950<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/D</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/D">select #2/D</a></div></div>1132 atoms, 1163 bonds, 143 residues, 1 model selected<br>
2951<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/D</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/D">select #2/D</a></div></div>1132 atoms, 1163 bonds, 143 residues, 1 model selected<br>
2952<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/D start 587</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/D start 587">renumber #2/D start 587</a></div></div>143 residues renumbered<br>
2953<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/E">select #2/E</a></div></div>528 atoms, 540 bonds, 66 residues, 1 model selected<br>
2954<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #2/E start 764</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #2/E start 764">renumber #2/E start 764</a></div></div>66 residues renumbered<br>
2955<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn large target reunumbered.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn large target reunumbered.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn large target reunumbered.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #2/D</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #2/D">sequence chain #2/D</a></div></div>Alignment identifier is 2/D<br>
2956<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #2/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #2/E">sequence chain #2/E</a></div></div>Alignment identifier is 2/E<br>
2957<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/D</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/D">select #2/D</a></div></div>1132 atoms, 1163 bonds, 143 residues, 1 model selected<br>
2958<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/D:701-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/D:701-729">select #2/D:701-729</a></div></div>224 atoms, 228 bonds, 29 residues, 1 model selected<br>
2959<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B">select #2/B</a></div></div>1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected<br>
2960<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:1-15</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:1-15">select #2/A:1-15</a></div></div>119 atoms, 120 bonds, 15 residues, 1 model selected<br>
2961<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:1-15,63-115</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:1-15,63-115">select #2/A:1-15,63-115</a></div></div>516 atoms, 529 bonds, 1 pseudobond, 64 residues, 2 models selected<br>
2962<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:1-15,63-146</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:1-15,63-146">select #2/A:1-15,63-146</a></div></div>758 atoms, 777 bonds, 2 pseudobonds, 91 residues, 2 models selected<br>
2963<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:1-15,63-146/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:1-15,63-146/C/D:587-700/E">select #2/A:1-15,63-146/C/D:587-700/E</a></div></div>2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected<br>
2964<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Change Chain IDs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Change Chain IDs&quot;">ui tool show &quot;Change Chain IDs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel A</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel A">changechains sel A</a></div></div><font color="crimson"><b>Cannot reassign chain ID to only part of polymeric chain (combination #2/A)<br>
2965</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #2">combine #2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #4 &quot;Stromal ridge small&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #4 &quot;Stromal ridge small&quot;">rename #4 &quot;Stromal ridge small&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:1-15,63-146/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:1-15,63-146/C/D:587-700/E">select #2/A:1-15,63-146/C/D:587-700/E</a></div></div>2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected<br>
2966<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-15,63-146/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-15,63-146/C/D:587-700/E">select #4/A:1-15,63-146/C/D:587-700/E</a></div></div>2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected<br>
2967<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:1-15,63-146/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:1-15,63-146/C/D:587-700/E">select #2/A:1-15,63-146/C/D:587-700/E</a></div></div>2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected<br>
2968<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-62,147/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-62,147/C/D:587-700/E">select #2/A:16-62,147/C/D:587-700/E</a></div></div>2419 atoms, 2492 bonds, 17 pseudobonds, 305 residues, 3 models selected<br>
2969<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-62,147-227/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-62,147-227/C/D:587-700/E">select #2/A:16-62,147-227/C/D:587-700/E</a></div></div>2955 atoms, 3042 bonds, 18 pseudobonds, 374 residues, 4 models selected<br>
2970<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:16-62,147-227,3001/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:16-62,147-227,3001/C/D:587-700/E">select #2/A:16-62,147-227,3001/C/D:587-700/E</a></div></div>2963 atoms, 3054 bonds, 20 pseudobonds, 375 residues, 4 models selected<br>
2971<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-15,63-146/B/D:701-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-15,63-146/B/D:701-729">select #4/A:1-15,63-146/B/D:701-729</a></div></div>2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected<br>
2972<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-15,63-146/B/D:701-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-15,63-146/B/D:701-729">select #4/A:1-15,63-146/B/D:701-729</a></div></div>2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected<br>
2973<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-15,63-146/B/D:701-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-15,63-146/B/D:701-729">select #4/A:1-15,63-146/B/D:701-729</a></div></div>2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected<br>
2974<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-15,63-146/D:701-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-15,63-146/D:701-729">select #4/A:1-15,63-146/D:701-729</a></div></div>982 atoms, 1005 bonds, 2 pseudobonds, 120 residues, 2 models selected<br>
2975<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-12,46-146/D:701-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-12,46-146/D:701-729">select #4/A:1-12,46-146/D:701-729</a></div></div>1065 atoms, 1090 bonds, 3 pseudobonds, 130 residues, 2 models selected<br>
2976<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-12,55-146/D:701-729</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-12,55-146/D:701-729">select #4/A:1-12,55-146/D:701-729</a></div></div>994 atoms, 1016 bonds, 3 pseudobonds, 121 residues, 2 models selected<br>
2977<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B">select #4/B</a></div></div>1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected<br>
2978<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B &amp;~:425-436</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B &amp;~:425-436">select #4/B &amp;~:425-436</a></div></div>1635 atoms, 1676 bonds, 5 pseudobonds, 200 residues, 2 models selected<br>
2979<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:16-54,151-227,3001/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:16-54,151-227,3001/C/D:587-700/E">select #4/A:16-54,151-227,3001/C/D:587-700/E</a></div></div>2929 atoms, 3020 bonds, 20 pseudobonds, 371 residues, 4 models selected<br>
2980<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E">select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</a></div></div>3005 atoms, 3097 bonds, 22 pseudobonds, 383 residues, 4 models selected<br>
2981<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #4 enclose #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #4 enclose #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E">surface #4 enclose #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
2982Coulombic values for Stromal ridge small_A SES surface #4.5: minimum, -23.39, mean -1.01, maximum 11.65<br>
2983Coulombic values for Stromal ridge small_B SES surface #4.6: minimum, -18.54, mean 0.17, maximum 12.46<br>
2984Coulombic values for Stromal ridge small_C SES surface #4.7: minimum, -12.54, mean -0.30, maximum 9.66<br>
2985Coulombic values for Stromal ridge small_D SES surface #4.8: minimum, -11.89, mean 1.48, maximum 14.01<br>
2986Coulombic values for Stromal ridge small_E SES surface #4.9: minimum, -13.21, mean 1.18, maximum 10.80<br>
2987<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #4.5-9</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #4.5-9">close #4.5-9</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.4">select add #4.4</a></div></div>3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected<br>
2988<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #4.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #4.4">select subtract #4.4</a></div></div>3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected<br>
2989<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.4">select add #4.4</a></div></div>3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected<br>
2990<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #4.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #4.4">select subtract #4.4</a></div></div>3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected<br>
2991<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.4">select add #4.4</a></div></div>3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected<br>
2992<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #4.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #4.4">close #4.4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/M</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/M">select #4/M</a></div></div>Nothing selected<br>
2993<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/N</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/N">select #4/N</a></div></div>728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected<br>
2994<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4 &amp;@@display</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4 &amp;@@display">select #4 &amp;@@display</a></div></div>184 atoms, 176 bonds, 15 pseudobonds, 24 residues, 3 models selected<br>
2995<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4 &amp;@@~display</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4 &amp;@@~display">select #4 &amp;@@~display</a></div></div>184 atoms, 176 bonds, 15 pseudobonds, 24 residues, 3 models selected<br>
2996<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4 &amp;~@@display</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4 &amp;~@@display">select #4 &amp;~@@display</a></div></div>6200 atoms, 6338 bonds, 4 pseudobonds, 784 residues, 2 models selected<br>
2997<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E">select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</a></div></div>3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected<br>
2998<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4 </div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4 ">select #4 </a></div></div>6384 atoms, 6556 bonds, 46 pseudobonds, 805 residues, 4 models selected<br>
2999<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Change Chain IDs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Change Chain IDs&quot;">ui tool show &quot;Change Chain IDs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel A</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel A">changechains sel A</a></div></div><font color="crimson"><b>Proposed chain ID change would produce multiple residues with the samechain-ID/number/insertion-code combo (A/477/)<br>
3000</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B">select #4/B</a></div></div>1711 atoms, 1755 bonds, 212 residues, 1 model selected<br>
3001<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:402-442</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:402-442">select #4/B:402-442</a></div></div>299 atoms, 306 bonds, 41 residues, 1 model selected<br>
3002<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:402-442</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:402-442">select #4/A:402-442</a></div></div>Nothing selected<br>
3003<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/C:402-442</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/C:402-442">select #4/C:402-442</a></div></div>Nothing selected<br>
3004<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/D:402-442</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/D:402-442">select #4/D:402-442</a></div></div>Nothing selected<br>
3005<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/E:402-442</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/E:402-442">select #4/E:402-442</a></div></div>Nothing selected<br>
3006<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E">select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</a></div></div>3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected<br>
3007<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4&amp;~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4&amp;~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E">select #4&amp;~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</a></div></div>3379 atoms, 3454 bonds, 4 pseudobonds, 422 residues, 2 models selected<br>
3008<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4&amp;~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4&amp;~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E">select #4&amp;~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E</a></div></div>3379 atoms, 3454 bonds, 4 pseudobonds, 422 residues, 2 models selected<br>
3009<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#atoms">delete atoms</a> (#!4 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete atoms (#!4 &amp; sel)">delete atoms (#!4 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#bonds">delete bonds</a> (#!4 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete bonds (#!4 &amp; sel)">delete bonds (#!4 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4">select #4</a></div></div>3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected<br>
3010<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Change Chain IDs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Change Chain IDs&quot;">ui tool show &quot;Change Chain IDs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel A</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel A">changechains sel A</a></div></div>Chain IDs of 274 residues changed<br>
3011<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel A</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel A">changechains sel A</a></div></div>Chain IDs of 0 residues changed<br>
3012<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A">select #4/A</a></div></div>3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected<br>
3013<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4#5</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4#5">combine #4#5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #5 &quot;Stromal ridge and 2fdn&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #5 &quot;Stromal ridge and 2fdn&quot;">rename #5 &quot;Stromal ridge and 2fdn&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A &amp;protein">select #5/A &amp;protein</a></div></div>2981 atoms, 3061 bonds, 9 pseudobonds, 380 residues, 2 models selected<br>
3014<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27, 31, 504, 807,818, 481, 485, 528</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27, 31, 504, 807,818, 481, 485, 528">select #5/A:27, 31, 504, 807,818, 481, 485, 528</a></div></div>72 atoms, 66 bonds, 8 residues, 1 model selected<br>
3015<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:27, 31, 504, 807,818, 481, 485, 528</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:27, 31, 504, 807,818, 481, 485, 528">select #2/A:27, 31, 504, 807,818, 481, 485, 528</a></div></div>20 atoms, 18 bonds, 2 residues, 1 model selected<br>
3016<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI fdn small target.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sun May 19 17:29:55 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
3017<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #3">close #3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 &quot;PSI chains&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 &quot;PSI chains&quot;">rename #2 &quot;PSI chains&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/M</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/M">select #5/M</a></div></div>Nothing selected<br>
3018<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #2">split #2</a></div></div>Split PSI chains (#2) into 6 models<br>
3019<table border=1 cellpadding=4 cellspacing=0>
3020 <thead>
3021 <tr>
3022 <th colspan="2">Chain information for PSI chains A #2.1</th>
3023 </tr>
3024 <tr>
3025 <th>Chain</th>
3026 <th>Description</th>
3027
3028 </tr>
3029 </thead>
3030 <tbody>
3031 <tr>
3032 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.1/A:1-227">A</a></td>
3033 <td><a title="Show sequence" href="cxcmd:sequence chain #2.1/A">No description available</a></td>
3034
3035 </tr>
3036 </tbody>
3037</table><br/><table border=1 cellpadding=4 cellspacing=0>
3038 <thead>
3039 <tr>
3040 <th colspan="2">Chain information for PSI chains B #2.2</th>
3041 </tr>
3042 <tr>
3043 <th>Chain</th>
3044 <th>Description</th>
3045
3046 </tr>
3047 </thead>
3048 <tbody>
3049 <tr>
3050 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.2/B:258-493">B</a></td>
3051 <td><a title="Show sequence" href="cxcmd:sequence chain #2.2/B">No description available</a></td>
3052
3053 </tr>
3054 </tbody>
3055</table><br/><table border=1 cellpadding=4 cellspacing=0>
3056 <thead>
3057 <tr>
3058 <th colspan="2">Chain information for PSI chains C #2.3</th>
3059 </tr>
3060 <tr>
3061 <th>Chain</th>
3062 <th>Description</th>
3063
3064 </tr>
3065 </thead>
3066 <tbody>
3067 <tr>
3068 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.3/C:471-550">C</a></td>
3069 <td><a title="Show sequence" href="cxcmd:sequence chain #2.3/C">No description available</a></td>
3070
3071 </tr>
3072 </tbody>
3073</table><br/><table border=1 cellpadding=4 cellspacing=0>
3074 <thead>
3075 <tr>
3076 <th colspan="2">Chain information for PSI chains D #2.4</th>
3077 </tr>
3078 <tr>
3079 <th>Chain</th>
3080 <th>Description</th>
3081
3082 </tr>
3083 </thead>
3084 <tbody>
3085 <tr>
3086 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.4/D:587-729">D</a></td>
3087 <td><a title="Show sequence" href="cxcmd:sequence chain #2.4/D">No description available</a></td>
3088
3089 </tr>
3090 </tbody>
3091</table><br/><table border=1 cellpadding=4 cellspacing=0>
3092 <thead>
3093 <tr>
3094 <th colspan="2">Chain information for PSI chains E #2.5</th>
3095 </tr>
3096 <tr>
3097 <th>Chain</th>
3098 <th>Description</th>
3099
3100 </tr>
3101 </thead>
3102 <tbody>
3103 <tr>
3104 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.5/E:764-829">E</a></td>
3105 <td><a title="Show sequence" href="cxcmd:sequence chain #2.5/E">No description available</a></td>
3106
3107 </tr>
3108 </tbody>
3109</table><br/><table border=1 cellpadding=4 cellspacing=0>
3110 <thead>
3111 <tr>
3112 <th colspan="2">Chain information for PSI chains N #2.6</th>
3113 </tr>
3114 <tr>
3115 <th>Chain</th>
3116 <th>Description</th>
3117
3118 </tr>
3119 </thead>
3120 <tbody>
3121 <tr>
3122 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.6/N:1-97">N</a></td>
3123 <td><a title="Show sequence" href="cxcmd:sequence chain #2.6/N">No description available</a></td>
3124
3125 </tr>
3126 </tbody>
3127</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2 models">hide #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.3 models">hide #!2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.4 models">hide #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 &quot;PSI 6yez chains&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 &quot;PSI 6yez chains&quot;">rename #2 &quot;PSI 6yez chains&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #5/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #5/B">split #5/B</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/B">select #5/B</a></div></div>Nothing selected<br>
3128<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #4">close #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #5 id 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #5 id 3">rename #5 id 3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design7.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design6.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design5.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design4.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design3.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design2.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design1.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design0.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design7.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design6.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design5.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design4.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design3.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design2.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design1.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design0.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design7.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design6.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design5.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design4.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design3.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design2.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design1.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/best_design0.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
3129 <thead>
3130 <tr>
3131 <th colspan="2">Chain information for best.pdb #4</th>
3132 </tr>
3133 <tr>
3134 <th>Chain</th>
3135 <th>Description</th>
3136
3137 </tr>
3138 </thead>
3139 <tbody>
3140 <tr>
3141 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4/A:1-814">A</a></td>
3142 <td><a title="Show sequence" href="cxcmd:sequence chain #4/A">No description available</a></td>
3143
3144 </tr>
3145 <tr>
3146 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4/B:1-54">B</a></td>
3147 <td><a title="Show sequence" href="cxcmd:sequence chain #4/B">No description available</a></td>
3148
3149 </tr>
3150 </tbody>
3151</table><br/><table border=1 cellpadding=4 cellspacing=0>
3152 <thead>
3153 <tr>
3154 <th colspan="2">Chain information for best_design7.pdb #5</th>
3155 </tr>
3156 <tr>
3157 <th>Chain</th>
3158 <th>Description</th>
3159
3160 </tr>
3161 </thead>
3162 <tbody>
3163 <tr>
3164 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/A:1-814">A</a></td>
3165 <td><a title="Show sequence" href="cxcmd:sequence chain #5/A">No description available</a></td>
3166
3167 </tr>
3168 <tr>
3169 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/B:1-54">B</a></td>
3170 <td><a title="Show sequence" href="cxcmd:sequence chain #5/B">No description available</a></td>
3171
3172 </tr>
3173 </tbody>
3174</table><br/><table border=1 cellpadding=4 cellspacing=0>
3175 <thead>
3176 <tr>
3177 <th colspan="2">Chain information for best_design6.pdb #6</th>
3178 </tr>
3179 <tr>
3180 <th>Chain</th>
3181 <th>Description</th>
3182
3183 </tr>
3184 </thead>
3185 <tbody>
3186 <tr>
3187 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/A:1-814">A</a></td>
3188 <td><a title="Show sequence" href="cxcmd:sequence chain #6/A">No description available</a></td>
3189
3190 </tr>
3191 <tr>
3192 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/B:1-54">B</a></td>
3193 <td><a title="Show sequence" href="cxcmd:sequence chain #6/B">No description available</a></td>
3194
3195 </tr>
3196 </tbody>
3197</table><br/><table border=1 cellpadding=4 cellspacing=0>
3198 <thead>
3199 <tr>
3200 <th colspan="2">Chain information for best_design5.pdb #7</th>
3201 </tr>
3202 <tr>
3203 <th>Chain</th>
3204 <th>Description</th>
3205
3206 </tr>
3207 </thead>
3208 <tbody>
3209 <tr>
3210 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #7/A:1-814">A</a></td>
3211 <td><a title="Show sequence" href="cxcmd:sequence chain #7/A">No description available</a></td>
3212
3213 </tr>
3214 <tr>
3215 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #7/B:1-54">B</a></td>
3216 <td><a title="Show sequence" href="cxcmd:sequence chain #7/B">No description available</a></td>
3217
3218 </tr>
3219 </tbody>
3220</table><br/><table border=1 cellpadding=4 cellspacing=0>
3221 <thead>
3222 <tr>
3223 <th colspan="2">Chain information for best_design4.pdb #8</th>
3224 </tr>
3225 <tr>
3226 <th>Chain</th>
3227 <th>Description</th>
3228
3229 </tr>
3230 </thead>
3231 <tbody>
3232 <tr>
3233 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #8/A:1-814">A</a></td>
3234 <td><a title="Show sequence" href="cxcmd:sequence chain #8/A">No description available</a></td>
3235
3236 </tr>
3237 <tr>
3238 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #8/B:1-54">B</a></td>
3239 <td><a title="Show sequence" href="cxcmd:sequence chain #8/B">No description available</a></td>
3240
3241 </tr>
3242 </tbody>
3243</table><br/><table border=1 cellpadding=4 cellspacing=0>
3244 <thead>
3245 <tr>
3246 <th colspan="2">Chain information for best_design3.pdb #9</th>
3247 </tr>
3248 <tr>
3249 <th>Chain</th>
3250 <th>Description</th>
3251
3252 </tr>
3253 </thead>
3254 <tbody>
3255 <tr>
3256 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9/A:1-814">A</a></td>
3257 <td><a title="Show sequence" href="cxcmd:sequence chain #9/A">No description available</a></td>
3258
3259 </tr>
3260 <tr>
3261 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9/B:1-54">B</a></td>
3262 <td><a title="Show sequence" href="cxcmd:sequence chain #9/B">No description available</a></td>
3263
3264 </tr>
3265 </tbody>
3266</table><br/><table border=1 cellpadding=4 cellspacing=0>
3267 <thead>
3268 <tr>
3269 <th colspan="2">Chain information for best_design2.pdb #10</th>
3270 </tr>
3271 <tr>
3272 <th>Chain</th>
3273 <th>Description</th>
3274
3275 </tr>
3276 </thead>
3277 <tbody>
3278 <tr>
3279 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10/A:1-814">A</a></td>
3280 <td><a title="Show sequence" href="cxcmd:sequence chain #10/A">No description available</a></td>
3281
3282 </tr>
3283 <tr>
3284 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10/B:1-54">B</a></td>
3285 <td><a title="Show sequence" href="cxcmd:sequence chain #10/B">No description available</a></td>
3286
3287 </tr>
3288 </tbody>
3289</table><br/><table border=1 cellpadding=4 cellspacing=0>
3290 <thead>
3291 <tr>
3292 <th colspan="2">Chain information for best_design1.pdb #11</th>
3293 </tr>
3294 <tr>
3295 <th>Chain</th>
3296 <th>Description</th>
3297
3298 </tr>
3299 </thead>
3300 <tbody>
3301 <tr>
3302 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #11/A:1-814">A</a></td>
3303 <td><a title="Show sequence" href="cxcmd:sequence chain #11/A">No description available</a></td>
3304
3305 </tr>
3306 <tr>
3307 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #11/B:1-54">B</a></td>
3308 <td><a title="Show sequence" href="cxcmd:sequence chain #11/B">No description available</a></td>
3309
3310 </tr>
3311 </tbody>
3312</table><br/><table border=1 cellpadding=4 cellspacing=0>
3313 <thead>
3314 <tr>
3315 <th colspan="2">Chain information for best_design0.pdb #12</th>
3316 </tr>
3317 <tr>
3318 <th>Chain</th>
3319 <th>Description</th>
3320
3321 </tr>
3322 </thead>
3323 <tbody>
3324 <tr>
3325 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #12/A:1-814">A</a></td>
3326 <td><a title="Show sequence" href="cxcmd:sequence chain #12/A">No description available</a></td>
3327
3328 </tr>
3329 <tr>
3330 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #12/B:1-54">B</a></td>
3331 <td><a title="Show sequence" href="cxcmd:sequence chain #12/B">No description available</a></td>
3332
3333 </tr>
3334 </tbody>
3335</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 &quot;Stromal ridge target&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 &quot;Stromal ridge target&quot;">rename #3 &quot;Stromal ridge target&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!4-12 to #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!4-12 to #3">matchmaker #!4-12 to #3</a></div></div>
3336 <table border=1 cellpadding=4 cellspacing=0>
3337 <tr>
3338 <th colspan="2">Parameters</th>
3339 </tr>
3340 <tr>
3341 <td>Chain pairing</td>
3342 <td>bb</td>
3343 </tr>
3344 <tr>
3345 <td>Alignment algorithm</td>
3346 <td>Needleman-Wunsch</td>
3347 </tr>
3348 <tr>
3349 <td>Similarity matrix</td>
3350 <td>BLOSUM-62</td>
3351 </tr>
3352
3353 <tr>
3354 <td>SS fraction</td>
3355 <td>0.3</td>
3356 </tr>
3357 <tr>
3358 <td>Gap open (HH/SS/other)</td>
3359 <td>18/18/6</td>
3360 </tr>
3361 <tr>
3362 <td>Gap extend</td>
3363 <td>1</td>
3364 </tr>
3365 <tr>
3366 <td>SS matrix</td>
3367 <td>
3368 <table>
3369 <tr>
3370 <th></th> <th>H</th> <th>S</th> <th>O</th>
3371 </tr>
3372 <tr>
3373 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
3374 </tr>
3375 <tr>
3376 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
3377 </tr>
3378 <tr>
3379 <th>O</th> <td></td> <td></td> <td align="right">4</td>
3380 </tr>
3381 </table>
3382 </td>
3383 </tr>
3384
3385 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
3386 </table>
3387 <br/>Matchmaker Stromal ridge target, chain A (#3) with best.pdb, chain A (#4), sequence alignment score = 561.8<br>
3388RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs: 0.365)<br>
3389<br>
3390Matchmaker Stromal ridge target, chain A (#3) with best_design7.pdb, chain A (#5), sequence alignment score = 561.8<br>
3391RMSD between 114 pruned atom pairs is 0.362 angstroms; (across all 114 pairs: 0.362)<br>
3392<br>
3393Matchmaker Stromal ridge target, chain A (#3) with best_design6.pdb, chain A (#6), sequence alignment score = 561.8<br>
3394RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs: 0.365)<br>
3395<br>
3396Matchmaker Stromal ridge target, chain A (#3) with best_design5.pdb, chain A (#7), sequence alignment score = 561.8<br>
3397RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs: 0.366)<br>
3398<br>
3399Matchmaker Stromal ridge target, chain A (#3) with best_design4.pdb, chain A (#8), sequence alignment score = 561.8<br>
3400RMSD between 114 pruned atom pairs is 0.367 angstroms; (across all 114 pairs: 0.367)<br>
3401<br>
3402Matchmaker Stromal ridge target, chain A (#3) with best_design3.pdb, chain A (#9), sequence alignment score = 561.8<br>
3403RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs: 0.366)<br>
3404<br>
3405Matchmaker Stromal ridge target, chain A (#3) with best_design2.pdb, chain A (#10), sequence alignment score = 561.8<br>
3406RMSD between 114 pruned atom pairs is 0.364 angstroms; (across all 114 pairs: 0.364)<br>
3407<br>
3408Matchmaker Stromal ridge target, chain A (#3) with best_design1.pdb, chain A (#11), sequence alignment score = 561.8<br>
3409RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs: 0.365)<br>
3410<br>
3411Matchmaker Stromal ridge target, chain A (#3) with best_design0.pdb, chain A (#12), sequence alignment score = 561.8<br>
3412RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs: 0.366)<br>
3413<br>
3414<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:8-11,14-18,38-41,44-48</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:8-11,14-18,38-41,44-48">select #4/B:8-11,14-18,38-41,44-48</a></div></div>112 atoms, 108 bonds, 18 residues, 1 model selected<br>
3415<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
3416 <thead>
3417 <tr>
3418 <th colspan="2">Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #13</th>
3419 </tr>
3420 <tr>
3421 <th>Chain</th>
3422 <th>Description</th>
3423
3424 </tr>
3425 </thead>
3426 <tbody>
3427 <tr>
3428 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #13/A:1-54">A</a></td>
3429 <td><a title="Show sequence" href="cxcmd:sequence chain #13/A">No description available</a></td>
3430
3431 </tr>
3432 </tbody>
3433</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #13 to #4 showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #13 to #4 showAlignment true">matchmaker #13 to #4 showAlignment true</a></div></div>
3434 <table border=1 cellpadding=4 cellspacing=0>
3435 <tr>
3436 <th colspan="2">Parameters</th>
3437 </tr>
3438 <tr>
3439 <td>Chain pairing</td>
3440 <td>bb</td>
3441 </tr>
3442 <tr>
3443 <td>Alignment algorithm</td>
3444 <td>Needleman-Wunsch</td>
3445 </tr>
3446 <tr>
3447 <td>Similarity matrix</td>
3448 <td>BLOSUM-62</td>
3449 </tr>
3450
3451 <tr>
3452 <td>SS fraction</td>
3453 <td>0.3</td>
3454 </tr>
3455 <tr>
3456 <td>Gap open (HH/SS/other)</td>
3457 <td>18/18/6</td>
3458 </tr>
3459 <tr>
3460 <td>Gap extend</td>
3461 <td>1</td>
3462 </tr>
3463 <tr>
3464 <td>SS matrix</td>
3465 <td>
3466 <table>
3467 <tr>
3468 <th></th> <th>H</th> <th>S</th> <th>O</th>
3469 </tr>
3470 <tr>
3471 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
3472 </tr>
3473 <tr>
3474 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
3475 </tr>
3476 <tr>
3477 <th>O</th> <td></td> <td></td> <td align="right">4</td>
3478 </tr>
3479 </table>
3480 </td>
3481 </tr>
3482
3483 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
3484 </table>
3485 <br/>Matchmaker best.pdb, chain B (#4) with Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb, chain A (#13), sequence alignment score = 242.6<br>
3486Alignment identifier is 1<br>
3487Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
3488Hiding conservation header for alignment 1<br>
3489Chains used in RMSD evaluation for alignment 1: best.pdb #4/B, Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #13/A<br>
3490Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
3491RMSD between 36 pruned atom pairs is 0.894 angstroms; (across all 54 pairs: 2.833)<br>
3492<br>
3493<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#header">sequence header</a> consensus show</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence header consensus show">sequence header consensus show</a></div></div>Showing consensus header (&quot;seq_consensus&quot; residue attribute) for alignment 1<br>
3494<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #13 Best_alphafold2_rank5.pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #13 Best_alphafold2_rank5.pdb">rename #13 Best_alphafold2_rank5.pdb</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/Fdx_best_AF2/Fdx_mod_MPNN_620be_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
3495 <thead>
3496 <tr>
3497 <th colspan="2">Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb #14</th>
3498 </tr>
3499 <tr>
3500 <th>Chain</th>
3501 <th>Description</th>
3502
3503 </tr>
3504 </thead>
3505 <tbody>
3506 <tr>
3507 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #14/A:1-54">A</a></td>
3508 <td><a title="Show sequence" href="cxcmd:sequence chain #14/A">No description available</a></td>
3509
3510 </tr>
3511 </tbody>
3512</table><br/><table border=1 cellpadding=4 cellspacing=0>
3513 <thead>
3514 <tr>
3515 <th colspan="2">Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #15</th>
3516 </tr>
3517 <tr>
3518 <th>Chain</th>
3519 <th>Description</th>
3520
3521 </tr>
3522 </thead>
3523 <tbody>
3524 <tr>
3525 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #15/A:1-54">A</a></td>
3526 <td><a title="Show sequence" href="cxcmd:sequence chain #15/A">No description available</a></td>
3527
3528 </tr>
3529 </tbody>
3530</table><br/><table border=1 cellpadding=4 cellspacing=0>
3531 <thead>
3532 <tr>
3533 <th colspan="2">Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #16</th>
3534 </tr>
3535 <tr>
3536 <th>Chain</th>
3537 <th>Description</th>
3538
3539 </tr>
3540 </thead>
3541 <tbody>
3542 <tr>
3543 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #16/A:1-54">A</a></td>
3544 <td><a title="Show sequence" href="cxcmd:sequence chain #16/A">No description available</a></td>
3545
3546 </tr>
3547 </tbody>
3548</table><br/><table border=1 cellpadding=4 cellspacing=0>
3549 <thead>
3550 <tr>
3551 <th colspan="2">Chain information for Fdx_mod_MPNN_620be_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb #17</th>
3552 </tr>
3553 <tr>
3554 <th>Chain</th>
3555 <th>Description</th>
3556
3557 </tr>
3558 </thead>
3559 <tbody>
3560 <tr>
3561 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #17/A:1-54">A</a></td>
3562 <td><a title="Show sequence" href="cxcmd:sequence chain #17/A">No description available</a></td>
3563
3564 </tr>
3565 </tbody>
3566</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #14 Best_alphafold2_rank3.pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #14 Best_alphafold2_rank3.pdb">rename #14 Best_alphafold2_rank3.pdb</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #15 Best_alphafold2_rank1.pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #15 Best_alphafold2_rank1.pdb">rename #15 Best_alphafold2_rank1.pdb</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #16 Best_alphafold2_rank2.pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #16 Best_alphafold2_rank2.pdb">rename #16 Best_alphafold2_rank2.pdb</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #17 Best_alphafold2_rank4.pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #17 Best_alphafold2_rank4.pdb">rename #17 Best_alphafold2_rank4.pdb</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #13 id 18</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #13 id 18">rename #13 id 18</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #15 id 13</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #15 id 13">rename #15 id 13</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #14 id 15</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #14 id 15">rename #14 id 15</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #16 id 14</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #16 id 14">rename #16 id 14</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #18 id 17</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #18 id 17">rename #18 id 17</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #17.1 id 18</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #17.1 id 18">rename #17.1 id 18</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #17 id 16</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #17 id 16">rename #17 id 16</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #18 id 17</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #18 id 17">rename #18 id 17</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #13-17 to #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #13-17 to #4">matchmaker #13-17 to #4</a></div></div>
3567 <table border=1 cellpadding=4 cellspacing=0>
3568 <tr>
3569 <th colspan="2">Parameters</th>
3570 </tr>
3571 <tr>
3572 <td>Chain pairing</td>
3573 <td>bb</td>
3574 </tr>
3575 <tr>
3576 <td>Alignment algorithm</td>
3577 <td>Needleman-Wunsch</td>
3578 </tr>
3579 <tr>
3580 <td>Similarity matrix</td>
3581 <td>BLOSUM-62</td>
3582 </tr>
3583
3584 <tr>
3585 <td>SS fraction</td>
3586 <td>0.3</td>
3587 </tr>
3588 <tr>
3589 <td>Gap open (HH/SS/other)</td>
3590 <td>18/18/6</td>
3591 </tr>
3592 <tr>
3593 <td>Gap extend</td>
3594 <td>1</td>
3595 </tr>
3596 <tr>
3597 <td>SS matrix</td>
3598 <td>
3599 <table>
3600 <tr>
3601 <th></th> <th>H</th> <th>S</th> <th>O</th>
3602 </tr>
3603 <tr>
3604 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
3605 </tr>
3606 <tr>
3607 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
3608 </tr>
3609 <tr>
3610 <th>O</th> <td></td> <td></td> <td align="right">4</td>
3611 </tr>
3612 </table>
3613 </td>
3614 </tr>
3615
3616 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
3617 </table>
3618 <br/>Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank1.pdb, chain A (#13), sequence alignment score = 235.1<br>
3619RMSD between 34 pruned atom pairs is 0.831 angstroms; (across all 54 pairs: 3.025)<br>
3620<br>
3621Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank2.pdb, chain A (#14), sequence alignment score = 228.2<br>
3622RMSD between 32 pruned atom pairs is 0.678 angstroms; (across all 54 pairs: 3.041)<br>
3623<br>
3624Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank3.pdb, chain A (#15), sequence alignment score = 235.1<br>
3625RMSD between 32 pruned atom pairs is 0.771 angstroms; (across all 54 pairs: 3.139)<br>
3626<br>
3627Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank4.pdb, chain A (#16), sequence alignment score = 235.1<br>
3628RMSD between 34 pruned atom pairs is 0.832 angstroms; (across all 54 pairs: 3.177)<br>
3629<br>
3630Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank5.pdb, chain A (#17), sequence alignment score = 242.6<br>
3631RMSD between 36 pruned atom pairs is 0.894 angstroms; (across all 54 pairs: 2.833)<br>
3632<br>
3633<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #14 models">hide #14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #15 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #15 models">hide #15 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #16 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #16 models">hide #16 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #17 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #17 models">hide #17 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #13/B:8-11,14-18,38-41,44-48</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #13/B:8-11,14-18,38-41,44-48">select #13/B:8-11,14-18,38-41,44-48</a></div></div>Nothing selected<br>
3634<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #13/A:8-11,14-18,38-41,44-48</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #13/A:8-11,14-18,38-41,44-48">select #13/A:8-11,14-18,38-41,44-48</a></div></div>112 atoms, 108 bonds, 18 residues, 1 model selected<br>
3635<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #14 models">show #14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #15 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #15 models">show #15 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #16 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #16 models">show #16 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #17 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #17 models">show #17 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #17 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #17 models">hide #17 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #16 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #16 models">hide #16 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #15 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #15 models">hide #15 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #14 models">hide #14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sat Jun 1 14:26:44 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
3636<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #13 models">hide #13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><a href="help:user/commands/info.html">info</a> #3/A:16 <span style="color:white; background-color:crimson;">rescolor</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#rescolor">info rescolor</a> #3/A:16</div><div class="cxcmd_as_cmd"><a href="cxcmd:info rescolor #3/A:16">info rescolor #3/A:16</a></div></div>#3/A:16 color #b89a8c<br>
3637<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.6 models">hide #!2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2 models">show #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2 models">hide #!2.2 models</a></div></div><div class="cxcmd"><a href="help:user/commands/select.html">select</a> #3/A <span style="color:white; background-color:crimson;">&amp;@@color=#b89a8c</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><font color="crimson"><b>bad color: b89a8c: Invalid color name or specifier</b></font><br/><div class="cxcmd"><a href="help:user/commands/select.html">select</a> #3/A <span style="color:white; background-color:crimson;">&amp;@@color#b89a8c</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A &amp;@@color=&#x27;#b89a8c&#x27;</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A &amp;@@color=&#x27;#b89a8c&#x27;">select #3/A &amp;@@color=&#x27;#b89a8c&#x27;</a></div></div>518 atoms, 413 bonds, 104 residues, 1 model selected<br>
3638<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A &amp;@@color=&#x27;plum&#x27;</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A &amp;@@color=&#x27;plum&#x27;">select #3/A &amp;@@color=&#x27;plum&#x27;</a></div></div>Nothing selected<br>
3639<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#rescolor">info rescolor</a> #3/A:430</div><div class="cxcmd_as_cmd"><a href="cxcmd:info rescolor #3/A:430">info rescolor #3/A:430</a></div></div>#3/A:430 color #d9b3f5<br>
3640<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#rescolor">info rescolor</a> #3/A:804</div><div class="cxcmd_as_cmd"><a href="cxcmd:info rescolor #3/A:804">info rescolor #3/A:804</a></div></div>#3/A:804 color #ebe6fb<br>
3641<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#rescolor">info rescolor</a> #3/A:498</div><div class="cxcmd_as_cmd"><a href="cxcmd:info rescolor #3/A:498">info rescolor #3/A:498</a></div></div>#3/A:498 color #b88eb1<br>
3642<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#rescolor">info rescolor</a> #3/A:685</div><div class="cxcmd_as_cmd"><a href="cxcmd:info rescolor #3/A:685">info rescolor #3/A:685</a></div></div>#3/A:685 color #c8e69e<br>
3643<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A &amp;@@color=&#x27;#b89a8c&#x27;</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A &amp;@@color=&#x27;#b89a8c&#x27;">select #3/A &amp;@@color=&#x27;#b89a8c&#x27;</a></div></div>518 atoms, 413 bonds, 104 residues, 1 model selected<br>
3644<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#residues">info residues</a> sel attribute num</div><div class="cxcmd_as_cmd"><a href="cxcmd:info residues sel attribute num">info residues sel attribute num</a></div></div><br>
3645<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#residues">info residues</a> #3/A &amp;@@color=&#x27;#b89a8c&#x27; attribute num</div><div class="cxcmd_as_cmd"><a href="cxcmd:info residues #3/A &amp;@@color=&#x27;#b89a8c&#x27; attribute num">info residues #3/A &amp;@@color=&#x27;#b89a8c&#x27; attribute num</a></div></div><br>
3646<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#residues">info residues</a> #3/A &amp;@@color=&#x27;#b89a8c&#x27; attribute number</div><div class="cxcmd_as_cmd"><a href="cxcmd:info residues #3/A &amp;@@color=&#x27;#b89a8c&#x27; attribute number">info residues #3/A &amp;@@color=&#x27;#b89a8c&#x27; attribute number</a></div></div>residue id #3/A:16 number 16 index 15<br>
3647residue id #3/A:17 number 17 index 16<br>
3648residue id #3/A:18 number 18 index 17<br>
3649residue id #3/A:152 number 152 index 135<br>
3650residue id #3/A:153 number 153 index 136<br>
3651residue id #3/A:154 number 154 index 137<br>
3652residue id #3/A:155 number 155 index 138<br>
3653residue id #3/A:156 number 156 index 139<br>
3654residue id #3/A:157 number 157 index 140<br>
3655residue id #3/A:158 number 158 index 141<br>
3656residue id #3/A:159 number 159 index 142<br>
3657residue id #3/A:160 number 160 index 143<br>
3658residue id #3/A:161 number 161 index 144<br>
3659residue id #3/A:162 number 162 index 145<br>
3660residue id #3/A:163 number 163 index 146<br>
3661residue id #3/A:164 number 164 index 147<br>
3662residue id #3/A:165 number 165 index 148<br>
3663residue id #3/A:166 number 166 index 149<br>
3664residue id #3/A:52 number 52 index 51<br>
3665residue id #3/A:53 number 53 index 52<br>
3666residue id #3/A:54 number 54 index 53<br>
3667residue id #3/A:19 number 19 index 18<br>
3668residue id #3/A:20 number 20 index 19<br>
3669residue id #3/A:21 number 21 index 20<br>
3670residue id #3/A:22 number 22 index 21<br>
3671residue id #3/A:23 number 23 index 22<br>
3672residue id #3/A:24 number 24 index 23<br>
3673residue id #3/A:25 number 25 index 24<br>
3674residue id #3/A:26 number 26 index 25<br>
3675residue id #3/A:27 number 27 index 26<br>
3676residue id #3/A:28 number 28 index 27<br>
3677residue id #3/A:29 number 29 index 28<br>
3678residue id #3/A:30 number 30 index 29<br>
3679residue id #3/A:31 number 31 index 30<br>
3680residue id #3/A:32 number 32 index 31<br>
3681residue id #3/A:33 number 33 index 32<br>
3682residue id #3/A:34 number 34 index 33<br>
3683residue id #3/A:35 number 35 index 34<br>
3684residue id #3/A:36 number 36 index 35<br>
3685residue id #3/A:37 number 37 index 36<br>
3686residue id #3/A:38 number 38 index 37<br>
3687residue id #3/A:39 number 39 index 38<br>
3688residue id #3/A:40 number 40 index 39<br>
3689residue id #3/A:41 number 41 index 40<br>
3690residue id #3/A:42 number 42 index 41<br>
3691residue id #3/A:43 number 43 index 42<br>
3692residue id #3/A:44 number 44 index 43<br>
3693residue id #3/A:45 number 45 index 44<br>
3694residue id #3/A:46 number 46 index 45<br>
3695residue id #3/A:47 number 47 index 46<br>
3696residue id #3/A:48 number 48 index 47<br>
3697residue id #3/A:49 number 49 index 48<br>
3698residue id #3/A:50 number 50 index 49<br>
3699residue id #3/A:51 number 51 index 50<br>
3700residue id #3/A:209 number 209 index 184<br>
3701residue id #3/A:210 number 210 index 185<br>
3702residue id #3/A:211 number 211 index 186<br>
3703residue id #3/A:212 number 212 index 187<br>
3704residue id #3/A:213 number 213 index 188<br>
3705residue id #3/A:214 number 214 index 189<br>
3706residue id #3/A:215 number 215 index 190<br>
3707residue id #3/A:216 number 216 index 191<br>
3708residue id #3/A:217 number 217 index 192<br>
3709residue id #3/A:218 number 218 index 193<br>
3710residue id #3/A:219 number 219 index 194<br>
3711residue id #3/A:220 number 220 index 195<br>
3712residue id #3/A:221 number 221 index 196<br>
3713residue id #3/A:222 number 222 index 197<br>
3714residue id #3/A:223 number 223 index 198<br>
3715residue id #3/A:224 number 224 index 199<br>
3716residue id #3/A:225 number 225 index 200<br>
3717residue id #3/A:226 number 226 index 201<br>
3718residue id #3/A:167 number 167 index 150<br>
3719residue id #3/A:168 number 168 index 151<br>
3720residue id #3/A:169 number 169 index 152<br>
3721residue id #3/A:170 number 170 index 153<br>
3722residue id #3/A:171 number 171 index 154<br>
3723residue id #3/A:172 number 172 index 155<br>
3724residue id #3/A:173 number 173 index 156<br>
3725residue id #3/A:174 number 174 index 157<br>
3726residue id #3/A:175 number 175 index 158<br>
3727residue id #3/A:176 number 176 index 159<br>
3728residue id #3/A:177 number 177 index 160<br>
3729residue id #3/A:178 number 178 index 161<br>
3730residue id #3/A:179 number 179 index 162<br>
3731residue id #3/A:180 number 180 index 163<br>
3732residue id #3/A:181 number 181 index 164<br>
3733residue id #3/A:182 number 182 index 165<br>
3734residue id #3/A:183 number 183 index 166<br>
3735residue id #3/A:194 number 194 index 169<br>
3736residue id #3/A:195 number 195 index 170<br>
3737residue id #3/A:196 number 196 index 171<br>
3738residue id #3/A:197 number 197 index 172<br>
3739residue id #3/A:198 number 198 index 173<br>
3740residue id #3/A:199 number 199 index 174<br>
3741residue id #3/A:200 number 200 index 175<br>
3742residue id #3/A:201 number 201 index 176<br>
3743residue id #3/A:202 number 202 index 177<br>
3744residue id #3/A:203 number 203 index 178<br>
3745residue id #3/A:204 number 204 index 179<br>
3746residue id #3/A:205 number 205 index 180<br>
3747residue id #3/A:206 number 206 index 181<br>
3748residue id #3/A:207 number 207 index 182<br>
3749residue id #3/A:208 number 208 index 183<br>
3750<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#residues">info residues</a> sel attribute number</div><div class="cxcmd_as_cmd"><a href="cxcmd:info residues sel attribute number">info residues sel attribute number</a></div></div>residue id #3/A:16 number 16 index 15<br>
3751residue id #3/A:17 number 17 index 16<br>
3752residue id #3/A:18 number 18 index 17<br>
3753residue id #3/A:152 number 152 index 135<br>
3754residue id #3/A:153 number 153 index 136<br>
3755residue id #3/A:154 number 154 index 137<br>
3756residue id #3/A:155 number 155 index 138<br>
3757residue id #3/A:156 number 156 index 139<br>
3758residue id #3/A:157 number 157 index 140<br>
3759residue id #3/A:158 number 158 index 141<br>
3760residue id #3/A:159 number 159 index 142<br>
3761residue id #3/A:160 number 160 index 143<br>
3762residue id #3/A:161 number 161 index 144<br>
3763residue id #3/A:162 number 162 index 145<br>
3764residue id #3/A:163 number 163 index 146<br>
3765residue id #3/A:164 number 164 index 147<br>
3766residue id #3/A:165 number 165 index 148<br>
3767residue id #3/A:166 number 166 index 149<br>
3768residue id #3/A:52 number 52 index 51<br>
3769residue id #3/A:53 number 53 index 52<br>
3770residue id #3/A:54 number 54 index 53<br>
3771residue id #3/A:19 number 19 index 18<br>
3772residue id #3/A:20 number 20 index 19<br>
3773residue id #3/A:21 number 21 index 20<br>
3774residue id #3/A:22 number 22 index 21<br>
3775residue id #3/A:23 number 23 index 22<br>
3776residue id #3/A:24 number 24 index 23<br>
3777residue id #3/A:25 number 25 index 24<br>
3778residue id #3/A:26 number 26 index 25<br>
3779residue id #3/A:27 number 27 index 26<br>
3780residue id #3/A:28 number 28 index 27<br>
3781residue id #3/A:29 number 29 index 28<br>
3782residue id #3/A:30 number 30 index 29<br>
3783residue id #3/A:31 number 31 index 30<br>
3784residue id #3/A:32 number 32 index 31<br>
3785residue id #3/A:33 number 33 index 32<br>
3786residue id #3/A:34 number 34 index 33<br>
3787residue id #3/A:35 number 35 index 34<br>
3788residue id #3/A:36 number 36 index 35<br>
3789residue id #3/A:37 number 37 index 36<br>
3790residue id #3/A:38 number 38 index 37<br>
3791residue id #3/A:39 number 39 index 38<br>
3792residue id #3/A:40 number 40 index 39<br>
3793residue id #3/A:41 number 41 index 40<br>
3794residue id #3/A:42 number 42 index 41<br>
3795residue id #3/A:43 number 43 index 42<br>
3796residue id #3/A:44 number 44 index 43<br>
3797residue id #3/A:45 number 45 index 44<br>
3798residue id #3/A:46 number 46 index 45<br>
3799residue id #3/A:47 number 47 index 46<br>
3800residue id #3/A:48 number 48 index 47<br>
3801residue id #3/A:49 number 49 index 48<br>
3802residue id #3/A:50 number 50 index 49<br>
3803residue id #3/A:51 number 51 index 50<br>
3804residue id #3/A:209 number 209 index 184<br>
3805residue id #3/A:210 number 210 index 185<br>
3806residue id #3/A:211 number 211 index 186<br>
3807residue id #3/A:212 number 212 index 187<br>
3808residue id #3/A:213 number 213 index 188<br>
3809residue id #3/A:214 number 214 index 189<br>
3810residue id #3/A:215 number 215 index 190<br>
3811residue id #3/A:216 number 216 index 191<br>
3812residue id #3/A:217 number 217 index 192<br>
3813residue id #3/A:218 number 218 index 193<br>
3814residue id #3/A:219 number 219 index 194<br>
3815residue id #3/A:220 number 220 index 195<br>
3816residue id #3/A:221 number 221 index 196<br>
3817residue id #3/A:222 number 222 index 197<br>
3818residue id #3/A:223 number 223 index 198<br>
3819residue id #3/A:224 number 224 index 199<br>
3820residue id #3/A:225 number 225 index 200<br>
3821residue id #3/A:226 number 226 index 201<br>
3822residue id #3/A:167 number 167 index 150<br>
3823residue id #3/A:168 number 168 index 151<br>
3824residue id #3/A:169 number 169 index 152<br>
3825residue id #3/A:170 number 170 index 153<br>
3826residue id #3/A:171 number 171 index 154<br>
3827residue id #3/A:172 number 172 index 155<br>
3828residue id #3/A:173 number 173 index 156<br>
3829residue id #3/A:174 number 174 index 157<br>
3830residue id #3/A:175 number 175 index 158<br>
3831residue id #3/A:176 number 176 index 159<br>
3832residue id #3/A:177 number 177 index 160<br>
3833residue id #3/A:178 number 178 index 161<br>
3834residue id #3/A:179 number 179 index 162<br>
3835residue id #3/A:180 number 180 index 163<br>
3836residue id #3/A:181 number 181 index 164<br>
3837residue id #3/A:182 number 182 index 165<br>
3838residue id #3/A:183 number 183 index 166<br>
3839residue id #3/A:194 number 194 index 169<br>
3840residue id #3/A:195 number 195 index 170<br>
3841residue id #3/A:196 number 196 index 171<br>
3842residue id #3/A:197 number 197 index 172<br>
3843residue id #3/A:198 number 198 index 173<br>
3844residue id #3/A:199 number 199 index 174<br>
3845residue id #3/A:200 number 200 index 175<br>
3846residue id #3/A:201 number 201 index 176<br>
3847residue id #3/A:202 number 202 index 177<br>
3848residue id #3/A:203 number 203 index 178<br>
3849residue id #3/A:204 number 204 index 179<br>
3850residue id #3/A:205 number 205 index 180<br>
3851residue id #3/A:206 number 206 index 181<br>
3852residue id #3/A:207 number 207 index 182<br>
3853residue id #3/A:208 number 208 index 183<br>
3854<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#residues">info residues</a> #3/A &amp;@@color=&#x27;#b89a8c&#x27; attribute number</div><div class="cxcmd_as_cmd"><a href="cxcmd:info residues #3/A &amp;@@color=&#x27;#b89a8c&#x27; attribute number">info residues #3/A &amp;@@color=&#x27;#b89a8c&#x27; attribute number</a></div></div>residue id #3/A:16 number 16 index 15<br>
3855residue id #3/A:17 number 17 index 16<br>
3856residue id #3/A:18 number 18 index 17<br>
3857residue id #3/A:152 number 152 index 135<br>
3858residue id #3/A:153 number 153 index 136<br>
3859residue id #3/A:154 number 154 index 137<br>
3860residue id #3/A:155 number 155 index 138<br>
3861residue id #3/A:156 number 156 index 139<br>
3862residue id #3/A:157 number 157 index 140<br>
3863residue id #3/A:158 number 158 index 141<br>
3864residue id #3/A:159 number 159 index 142<br>
3865residue id #3/A:160 number 160 index 143<br>
3866residue id #3/A:161 number 161 index 144<br>
3867residue id #3/A:162 number 162 index 145<br>
3868residue id #3/A:163 number 163 index 146<br>
3869residue id #3/A:164 number 164 index 147<br>
3870residue id #3/A:165 number 165 index 148<br>
3871residue id #3/A:166 number 166 index 149<br>
3872residue id #3/A:52 number 52 index 51<br>
3873residue id #3/A:53 number 53 index 52<br>
3874residue id #3/A:54 number 54 index 53<br>
3875residue id #3/A:19 number 19 index 18<br>
3876residue id #3/A:20 number 20 index 19<br>
3877residue id #3/A:21 number 21 index 20<br>
3878residue id #3/A:22 number 22 index 21<br>
3879residue id #3/A:23 number 23 index 22<br>
3880residue id #3/A:24 number 24 index 23<br>
3881residue id #3/A:25 number 25 index 24<br>
3882residue id #3/A:26 number 26 index 25<br>
3883residue id #3/A:27 number 27 index 26<br>
3884residue id #3/A:28 number 28 index 27<br>
3885residue id #3/A:29 number 29 index 28<br>
3886residue id #3/A:30 number 30 index 29<br>
3887residue id #3/A:31 number 31 index 30<br>
3888residue id #3/A:32 number 32 index 31<br>
3889residue id #3/A:33 number 33 index 32<br>
3890residue id #3/A:34 number 34 index 33<br>
3891residue id #3/A:35 number 35 index 34<br>
3892residue id #3/A:36 number 36 index 35<br>
3893residue id #3/A:37 number 37 index 36<br>
3894residue id #3/A:38 number 38 index 37<br>
3895residue id #3/A:39 number 39 index 38<br>
3896residue id #3/A:40 number 40 index 39<br>
3897residue id #3/A:41 number 41 index 40<br>
3898residue id #3/A:42 number 42 index 41<br>
3899residue id #3/A:43 number 43 index 42<br>
3900residue id #3/A:44 number 44 index 43<br>
3901residue id #3/A:45 number 45 index 44<br>
3902residue id #3/A:46 number 46 index 45<br>
3903residue id #3/A:47 number 47 index 46<br>
3904residue id #3/A:48 number 48 index 47<br>
3905residue id #3/A:49 number 49 index 48<br>
3906residue id #3/A:50 number 50 index 49<br>
3907residue id #3/A:51 number 51 index 50<br>
3908residue id #3/A:209 number 209 index 184<br>
3909residue id #3/A:210 number 210 index 185<br>
3910residue id #3/A:211 number 211 index 186<br>
3911residue id #3/A:212 number 212 index 187<br>
3912residue id #3/A:213 number 213 index 188<br>
3913residue id #3/A:214 number 214 index 189<br>
3914residue id #3/A:215 number 215 index 190<br>
3915residue id #3/A:216 number 216 index 191<br>
3916residue id #3/A:217 number 217 index 192<br>
3917residue id #3/A:218 number 218 index 193<br>
3918residue id #3/A:219 number 219 index 194<br>
3919residue id #3/A:220 number 220 index 195<br>
3920residue id #3/A:221 number 221 index 196<br>
3921residue id #3/A:222 number 222 index 197<br>
3922residue id #3/A:223 number 223 index 198<br>
3923residue id #3/A:224 number 224 index 199<br>
3924residue id #3/A:225 number 225 index 200<br>
3925residue id #3/A:226 number 226 index 201<br>
3926residue id #3/A:167 number 167 index 150<br>
3927residue id #3/A:168 number 168 index 151<br>
3928residue id #3/A:169 number 169 index 152<br>
3929residue id #3/A:170 number 170 index 153<br>
3930residue id #3/A:171 number 171 index 154<br>
3931residue id #3/A:172 number 172 index 155<br>
3932residue id #3/A:173 number 173 index 156<br>
3933residue id #3/A:174 number 174 index 157<br>
3934residue id #3/A:175 number 175 index 158<br>
3935residue id #3/A:176 number 176 index 159<br>
3936residue id #3/A:177 number 177 index 160<br>
3937residue id #3/A:178 number 178 index 161<br>
3938residue id #3/A:179 number 179 index 162<br>
3939residue id #3/A:180 number 180 index 163<br>
3940residue id #3/A:181 number 181 index 164<br>
3941residue id #3/A:182 number 182 index 165<br>
3942residue id #3/A:183 number 183 index 166<br>
3943residue id #3/A:194 number 194 index 169<br>
3944residue id #3/A:195 number 195 index 170<br>
3945residue id #3/A:196 number 196 index 171<br>
3946residue id #3/A:197 number 197 index 172<br>
3947residue id #3/A:198 number 198 index 173<br>
3948residue id #3/A:199 number 199 index 174<br>
3949residue id #3/A:200 number 200 index 175<br>
3950residue id #3/A:201 number 201 index 176<br>
3951residue id #3/A:202 number 202 index 177<br>
3952residue id #3/A:203 number 203 index 178<br>
3953residue id #3/A:204 number 204 index 179<br>
3954residue id #3/A:205 number 205 index 180<br>
3955residue id #3/A:206 number 206 index 181<br>
3956residue id #3/A:207 number 207 index 182<br>
3957residue id #3/A:208 number 208 index 183<br>
3958<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-227</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-227">select #4/A:1-227</a></div></div>857 atoms, 885 bonds, 2 pseudobonds, 108 residues, 2 models selected<br>
3959<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel tan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel tan">color sel tan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:425-436</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:425-436">select #4/A:425-436</a></div></div>Nothing selected<br>
3960<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:410-421</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:410-421">select #4/A:410-421</a></div></div>76 atoms, 77 bonds, 12 residues, 1 model selected<br>
3961<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel peru</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel peru">color sel peru</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:456-535</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:456-535">select #4/A:456-535</a></div></div>611 atoms, 624 bonds, 80 residues, 1 model selected<br>
3962<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel violet</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel violet">color sel violet</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:572-685</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:572-685">select #4/A:572-685</a></div></div>908 atoms, 934 bonds, 114 residues, 1 model selected<br>
3963<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light steel blue">color sel light steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel powder blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel powder blue">color sel powder blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel sky blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel sky blue">color sel sky blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel medium orchid</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel medium orchid">color sel medium orchid</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light pink</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light pink">color sel light pink</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light coral</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light coral">color sel light coral</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light pink</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light pink">color sel light pink</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:749-814</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:749-814">select #4/A:749-814</a></div></div>528 atoms, 540 bonds, 66 residues, 1 model selected<br>
3964<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light coral</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light coral">color sel light coral</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.3 models">show #!2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.3 models">hide #!2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.3 models">show #!2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.4 models">show #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.5 models">show #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:1-16</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:1-16">select #2/A:1-16</a></div></div>130 atoms, 132 bonds, 16 residues, 1 model selected<br>
3965<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:1-16,54-58</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:1-16,54-58">select #2/A:1-16,54-58</a></div></div>170 atoms, 171 bonds, 21 residues, 1 model selected<br>
3966<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:1-16,54-146</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:1-16,54-146">select #2/A:1-16,54-146</a></div></div>809 atoms, 828 bonds, 3 pseudobonds, 97 residues, 2 models selected<br>
3967<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:SF4 :&lt;3 &amp;#2/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:SF4 :&lt;3 &amp;#2/A-E">select #2:SF4 :&lt;3 &amp;#2/A-E</a></div></div>109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected<br>
3968<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2 models">show #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #2.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #2.2">select add #2.2</a></div></div>1804 atoms, 1850 bonds, 14 pseudobonds, 226 residues, 6 models selected<br>
3969<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #2.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #2.2">select subtract #2.2</a></div></div>93 atoms, 95 bonds, 9 pseudobonds, 14 residues, 4 models selected<br>
3970<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/B:425-436</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/B:425-436">select #2/B:425-436</a></div></div>76 atoms, 77 bonds, 12 residues, 1 model selected<br>
3971<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:SF4 :&lt;3 &amp;#2/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:SF4 :&lt;3 &amp;#2/A-E">select #2:SF4 :&lt;3 &amp;#2/A-E</a></div></div>109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected<br>
3972<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:SF4 :&lt;3 &amp;#2/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:SF4 :&lt;3 &amp;#2/A-E">select #2:SF4 :&lt;3 &amp;#2/A-E</a></div></div>109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected<br>
3973<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:456-535</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:456-535">select #4/A:456-535</a></div></div>611 atoms, 624 bonds, 80 residues, 1 model selected<br>
3974<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.2 models">hide #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.4 models">hide #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!4 &amp; sel to #2.3/C pairing bs showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!4 &amp; sel to #2.3/C pairing bs showAlignment true">matchmaker #!4 &amp; sel to #2.3/C pairing bs showAlignment true</a></div></div>
3975 <table border=1 cellpadding=4 cellspacing=0>
3976 <tr>
3977 <th colspan="2">Parameters</th>
3978 </tr>
3979 <tr>
3980 <td>Chain pairing</td>
3981 <td>bs</td>
3982 </tr>
3983 <tr>
3984 <td>Alignment algorithm</td>
3985 <td>Needleman-Wunsch</td>
3986 </tr>
3987 <tr>
3988 <td>Similarity matrix</td>
3989 <td>BLOSUM-62</td>
3990 </tr>
3991
3992 <tr>
3993 <td>SS fraction</td>
3994 <td>0.3</td>
3995 </tr>
3996 <tr>
3997 <td>Gap open (HH/SS/other)</td>
3998 <td>18/18/6</td>
3999 </tr>
4000 <tr>
4001 <td>Gap extend</td>
4002 <td>1</td>
4003 </tr>
4004 <tr>
4005 <td>SS matrix</td>
4006 <td>
4007 <table>
4008 <tr>
4009 <th></th> <th>H</th> <th>S</th> <th>O</th>
4010 </tr>
4011 <tr>
4012 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
4013 </tr>
4014 <tr>
4015 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
4016 </tr>
4017 <tr>
4018 <th>O</th> <td></td> <td></td> <td align="right">4</td>
4019 </tr>
4020 </table>
4021 </td>
4022 </tr>
4023
4024 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
4025 </table>
4026 <br/>Matchmaker PSI chains C, chain C (#2.3) with best.pdb, chain A (#4), sequence alignment score = 401<br>
4027Alignment identifier is 1<br>
4028Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
4029Hiding conservation header for alignment 1<br>
4030Chains used in RMSD evaluation for alignment 1: PSI chains C #2.3/C, best.pdb #4/A<br>
4031Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
4032RMSD between 80 pruned atom pairs is 0.395 angstroms; (across all 80 pairs: 0.395)<br>
4033<br>
4034<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.2 models">show #!2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:CYS">select #4/A:CYS</a></div></div>84 atoms, 70 bonds, 14 residues, 1 model selected<br>
4035<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #2.1 atoms :SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #2.1 atoms :SF4">split #2.1 atoms :SF4</a></div></div>Split PSI chains A (#2.1) into 2 models<br>
4036<table border=1 cellpadding=4 cellspacing=0>
4037 <thead>
4038 <tr>
4039 <th colspan="2">Chain information for PSI chains A 2 #2.1.2</th>
4040 </tr>
4041 <tr>
4042 <th>Chain</th>
4043 <th>Description</th>
4044
4045 </tr>
4046 </thead>
4047 <tbody>
4048 <tr>
4049 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.1.2/A:1-227">A</a></td>
4050 <td><a title="Show sequence" href="cxcmd:sequence chain #2.1.2/A">No description available</a></td>
4051
4052 </tr>
4053 </tbody>
4054</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1.2 models">hide #!2.1.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #2.3 atoms :SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #2.3 atoms :SF4">split #2.3 atoms :SF4</a></div></div>Split PSI chains C (#2.3) into 2 models<br>
4055<table border=1 cellpadding=4 cellspacing=0>
4056 <thead>
4057 <tr>
4058 <th colspan="2">Chain information for PSI chains C 2 #2.3.2</th>
4059 </tr>
4060 <tr>
4061 <th>Chain</th>
4062 <th>Description</th>
4063
4064 </tr>
4065 </thead>
4066 <tbody>
4067 <tr>
4068 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2.3.2/C:471-550">C</a></td>
4069 <td><a title="Show sequence" href="cxcmd:sequence chain #2.3.2/C">No description available</a></td>
4070
4071 </tr>
4072 </tbody>
4073</table><br/>Associated PSI chains C 2 (2.3.2) chain C to best.pdb, chain A with 0 mismatches<br>
4074Chains used in RMSD evaluation for alignment 1: PSI chains C 2 #2.3.2/C, best.pdb #4/A<br>
4075<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3.2 models">hide #2.3.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3.1 models">hide #2.3.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.3.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.3.1 models">show #2.3.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3.1 models">hide #2.3.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.3.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.3.1 models">show #2.3.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 id 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 id 20">rename #3 id 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #2.1.1#2.3.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #2.1.1#2.3.1">combine #2.1.1#2.3.1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 &quot;Fe4S4 clusters&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 &quot;Fe4S4 clusters&quot;">rename #3 &quot;Fe4S4 clusters&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><a href="help:user/commands/select.html">select</a> #1 <span style="color:white; background-color:crimson;">&amp;!@@color=&#x27;lime&#x27;</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1 &amp;~@@color=&#x27;lime&#x27;</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1 &amp;~@@color=&#x27;lime&#x27;">select #1 &amp;~@@color=&#x27;lime&#x27;</a></div></div>669 atoms, 451 bonds, 8 pseudobonds, 151 residues, 2 models selected<br>
4076<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel orange</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel orange">color sel orange</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel dark orange</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel dark orange">color sel dark orange</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1 &amp;H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1 &amp;H">select #1 &amp;H</a></div></div>272 atoms, 48 residues, 1 model selected<br>
4077<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1">select #1</a></div></div>762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected<br>
4078<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #1">combine #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!18 to #4/B pairing bs showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!18 to #4/B pairing bs showAlignment true">matchmaker #!18 to #4/B pairing bs showAlignment true</a></div></div>
4079 <table border=1 cellpadding=4 cellspacing=0>
4080 <tr>
4081 <th colspan="2">Parameters</th>
4082 </tr>
4083 <tr>
4084 <td>Chain pairing</td>
4085 <td>bs</td>
4086 </tr>
4087 <tr>
4088 <td>Alignment algorithm</td>
4089 <td>Needleman-Wunsch</td>
4090 </tr>
4091 <tr>
4092 <td>Similarity matrix</td>
4093 <td>BLOSUM-62</td>
4094 </tr>
4095
4096 <tr>
4097 <td>SS fraction</td>
4098 <td>0.3</td>
4099 </tr>
4100 <tr>
4101 <td>Gap open (HH/SS/other)</td>
4102 <td>18/18/6</td>
4103 </tr>
4104 <tr>
4105 <td>Gap extend</td>
4106 <td>1</td>
4107 </tr>
4108 <tr>
4109 <td>SS matrix</td>
4110 <td>
4111 <table>
4112 <tr>
4113 <th></th> <th>H</th> <th>S</th> <th>O</th>
4114 </tr>
4115 <tr>
4116 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
4117 </tr>
4118 <tr>
4119 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
4120 </tr>
4121 <tr>
4122 <th>O</th> <td></td> <td></td> <td align="right">4</td>
4123 </tr>
4124 </table>
4125 </td>
4126 </tr>
4127
4128 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
4129 </table>
4130 <br/>Matchmaker best.pdb, chain B (#4) with copy of 2fdn, chain M (#18), sequence alignment score = 157.4<br>
4131Alignment identifier is 1<br>
4132Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
4133Hiding conservation header for alignment 1<br>
4134Chains used in RMSD evaluation for alignment 1: best.pdb #4/B, copy of 2fdn #18/M<br>
4135Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
4136RMSD between 38 pruned atom pairs is 0.829 angstroms; (across all 51 pairs: 2.274)<br>
4137<br>
4138<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:CYS">select #4:CYS</a></div></div>132 atoms, 110 bonds, 22 residues, 1 model selected<br>
4139<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:CYS">select #4/B:CYS</a></div></div>48 atoms, 40 bonds, 8 residues, 1 model selected<br>
4140<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #5-18/A:1-227 tan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color #5-18/A:1-227 tan">color #5-18/A:1-227 tan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #5-18/A:410-421 peru</div><div class="cxcmd_as_cmd"><a href="cxcmd:color #5-18/A:410-421 peru">color #5-18/A:410-421 peru</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #5-18/A:456-535 violet</div><div class="cxcmd_as_cmd"><a href="cxcmd:color #5-18/A:456-535 violet">color #5-18/A:456-535 violet</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #5-18/A:572-685 light pink</div><div class="cxcmd_as_cmd"><a href="cxcmd:color #5-18/A:572-685 light pink">color #5-18/A:572-685 light pink</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #5-18/A:749-814 light coral</div><div class="cxcmd_as_cmd"><a href="cxcmd:color #5-18/A:749-814 light coral">color #5-18/A:749-814 light coral</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!12 models">show #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #13 models">show #13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #14 models">show #14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #15 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #15 models">show #15 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #15 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #15 models">hide #15 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #14 models">hide #14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #14 models">show #14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #14 models">hide #14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #13 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #13 models">hide #13 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #13-17</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #13-17">close #13-17</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!18 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!18 models">hide #!18 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!12 models">show #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4">select add #4</a></div></div>3337 atoms, 3419 bonds, 6 pseudobonds, 434 residues, 2 models selected<br>
4141<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #4">select subtract #4</a></div></div>Nothing selected<br>
4142<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:CYS">select #1:CYS</a></div></div>80 atoms, 72 bonds, 8 residues, 1 model selected<br>
4143<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #4:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #4:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #4:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 84 reference atoms<br>
4144RMSD between 48 atom pairs is 8.311 angstroms<br>
4145<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #1:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #1:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #1:CYS matchAtomNames true move nothing</a></div></div>RMSD between 80 atom pairs is 0.000 angstroms<br>
4146<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #5:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #5:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #5:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 84 reference atoms<br>
4147RMSD between 48 atom pairs is 8.316 angstroms<br>
4148<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #6:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #6:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #6:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 84 reference atoms<br>
4149RMSD between 48 atom pairs is 8.305 angstroms<br>
4150<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #7:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #7:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #7:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 84 reference atoms<br>
4151RMSD between 48 atom pairs is 8.308 angstroms<br>
4152<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #8:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #8:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #8:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 84 reference atoms<br>
4153RMSD between 48 atom pairs is 8.316 angstroms<br>
4154<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #9:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #9:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #9:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 84 reference atoms<br>
4155RMSD between 48 atom pairs is 8.306 angstroms<br>
4156<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #10:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #10:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #10:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 84 reference atoms<br>
4157RMSD between 48 atom pairs is 8.309 angstroms<br>
4158<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #11:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #11:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #11:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 84 reference atoms<br>
4159RMSD between 48 atom pairs is 8.311 angstroms<br>
4160<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #12:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #12:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #12:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 84 reference atoms<br>
4161RMSD between 48 atom pairs is 8.309 angstroms<br>
4162<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5-12</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5-12">select #5-12</a></div></div>26753 atoms, 27419 bonds, 48 pseudobonds, 3472 residues, 16 models selected<br>
4163<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5-12/B:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5-12/B:CYS">select #5-12/B:CYS</a></div></div>384 atoms, 320 bonds, 64 residues, 8 models selected<br>
4164<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #4/B:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #4/B:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #4/B:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 0 reference atoms<br>
4165RMSD between 48 atom pairs is 1.745 angstroms<br>
4166<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #5/B:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #5/B:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #5/B:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 0 reference atoms<br>
4167RMSD between 48 atom pairs is 1.738 angstroms<br>
4168<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #6/B:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #6/B:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #6/B:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 0 reference atoms<br>
4169RMSD between 48 atom pairs is 1.898 angstroms<br>
4170<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #7/B:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #7/B:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #7/B:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 0 reference atoms<br>
4171RMSD between 48 atom pairs is 1.823 angstroms<br>
4172<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #8/B:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #8/B:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #8/B:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 0 reference atoms<br>
4173RMSD between 48 atom pairs is 1.953 angstroms<br>
4174<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #9/B:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #9/B:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #9/B:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 0 reference atoms<br>
4175RMSD between 48 atom pairs is 1.867 angstroms<br>
4176<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #10/B:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #10/B:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #10/B:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 0 reference atoms<br>
4177RMSD between 48 atom pairs is 1.898 angstroms<br>
4178<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #11/B:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #11/B:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #11/B:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 0 reference atoms<br>
4179RMSD between 48 atom pairs is 1.745 angstroms<br>
4180<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #18:CYS toAtoms #12/B:CYS matchAtomNames true move nothing</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #18:CYS toAtoms #12/B:CYS matchAtomNames true move nothing">align #18:CYS toAtoms #12/B:CYS matchAtomNames true move nothing</a></div></div>Pairing dropped 32 atoms and 0 reference atoms<br>
4181RMSD between 48 atom pairs is 1.874 angstroms<br>
4182<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Tue Jun 4 18:24:08 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
4183<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!18 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!18 models">show #!18 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #18/A:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #18/A:CYS">select #18/A:CYS</a></div></div>Nothing selected<br>
4184<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #18/A:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #18/A:CYS">select #18/A:CYS</a></div></div>Nothing selected<br>
4185<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #18:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #18:CYS">select #18:CYS</a></div></div>80 atoms, 72 bonds, 8 residues, 1 model selected<br>
4186<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:CYS">select #4/B:CYS</a></div></div>48 atoms, 40 bonds, 8 residues, 1 model selected<br>
4187<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3#!18 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3#!18 atoms">show #3#!18 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3#!18 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3#!18 atoms">hide #3#!18 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3">select #3</a></div></div>24 atoms, 36 bonds, 3 residues, 1 model selected<br>
4188<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #18:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #18:CYS">select #18:CYS</a></div></div>80 atoms, 72 bonds, 8 residues, 1 model selected<br>
4189<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select H">select H</a></div></div>544 atoms, 96 residues, 2 models selected<br>
4190<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!18 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!18 atoms">hide sel &amp; #!18 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #18:FS4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #18:FS4">select #18:FS4</a></div></div>Nothing selected<br>
4191<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #18:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #18:SF4">select #18:SF4</a></div></div>16 atoms, 24 bonds, 2 residues, 1 model selected<br>
4192<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #18</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #18">select add #18</a></div></div>762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected<br>
4193<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #18</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #18">select subtract #18</a></div></div>Nothing selected<br>
4194<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:CYS">select #4/B:CYS</a></div></div>48 atoms, 40 bonds, 8 residues, 1 model selected<br>
4195<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8design compare.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Tue Jun 4 19:01:21 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
4196<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!18 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!18 models">hide #!18 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!12 models">show #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/design.fasta&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/design.fasta&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/design.fasta&quot;</a></div></div>
4197<table border=1 cellpadding=4 cellspacing=0>
4198 <thead>
4199 <tr>
4200 <th colspan="2">Summary of feedback from opening /Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/PSI_fdn_8designs_result/PSI_fdn_8designs/design.fasta</th>
4201 </tr>
4202 </thead>
4203 <tbody>
4204 <tr>
4205 <td><i>notes</i></td> <td style="background-color:#ffffff">Alignment identifier is design.fasta<br>Associated PSI chains E (2.5) chain E to design:7 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches<br>Associated PSI chains C 2 (2.3.2) chain C to design:7 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches<br>Associated best.pdb chain A to design:7 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches<br>Associated best.pdb chain B to design:1 n:5|mpnn:1.001|plddt:0.854|ptm:0.806|pae:6.003|rmsd:0.817 with 0 mismatches<br>Associated best_design7.pdb chain A to design:7 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches<br>Associated best_design7.pdb chain B to design:7 n:0|mpnn:1.127|plddt:0.849|ptm:0.800|pae:6.051|rmsd:0.819 with 0 mismatches<br>Associated best_design6.pdb chain A to design:7 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches<br>Associated best_design6.pdb chain B to design:6 n:0|mpnn:1.068|plddt:0.846|ptm:0.805|pae:6.080|rmsd:0.975 with 0 mismatches<br>Associated best_design5.pdb chain A to design:7 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches<br>11 messages similar to the above omitted<br>Associated Stromal ridge target chain A to design:7 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches<br>Associated Stromal ridge target chain A to design:7 n:7|mpnn:1.070|plddt:0.839|ptm:0.796|pae:6.073|rmsd:1.232 with 0 mismatches<br>Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment design.fasta</td> </tr>
4206 </tbody>
4207</table><br/>Opened 64 sequences from design.fasta<br>
4208<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #11/B to #4/B pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #11/B to #4/B pairing ss showAlignment true">matchmaker #11/B to #4/B pairing ss showAlignment true</a></div></div>
4209 <table border=1 cellpadding=4 cellspacing=0>
4210 <tr>
4211 <th colspan="2">Parameters</th>
4212 </tr>
4213 <tr>
4214 <td>Chain pairing</td>
4215 <td>ss</td>
4216 </tr>
4217 <tr>
4218 <td>Alignment algorithm</td>
4219 <td>Needleman-Wunsch</td>
4220 </tr>
4221 <tr>
4222 <td>Similarity matrix</td>
4223 <td>BLOSUM-62</td>
4224 </tr>
4225
4226 <tr>
4227 <td>SS fraction</td>
4228 <td>0.3</td>
4229 </tr>
4230 <tr>
4231 <td>Gap open (HH/SS/other)</td>
4232 <td>18/18/6</td>
4233 </tr>
4234 <tr>
4235 <td>Gap extend</td>
4236 <td>1</td>
4237 </tr>
4238 <tr>
4239 <td>SS matrix</td>
4240 <td>
4241 <table>
4242 <tr>
4243 <th></th> <th>H</th> <th>S</th> <th>O</th>
4244 </tr>
4245 <tr>
4246 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
4247 </tr>
4248 <tr>
4249 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
4250 </tr>
4251 <tr>
4252 <th>O</th> <td></td> <td></td> <td align="right">4</td>
4253 </tr>
4254 </table>
4255 </td>
4256 </tr>
4257
4258 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
4259 </table>
4260 <br/>Matchmaker best.pdb, chain B (#4) with best_design1.pdb, chain B (#11), sequence alignment score = 287.3<br>
4261Alignment identifier is 2<br>
4262Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 2<br>
4263Hiding conservation header for alignment 2<br>
4264Chains used in RMSD evaluation for alignment 2: best.pdb #4/B, best_design1.pdb #11/B<br>
4265Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 2<br>
4266RMSD between 54 pruned atom pairs is 0.000 angstroms; (across all 54 pairs: 0.000)<br>
4267<br>
4268<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#header">sequence header</a> 2 consensus show</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence header 2 consensus show">sequence header 2 consensus show</a></div></div>Showing consensus header (&quot;seq_consensus&quot; residue attribute) for alignment 2<br>
4269<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #4 &quot;best (best design1).pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #4 &quot;best (best design1).pdb&quot;">rename #4 &quot;best (best design1).pdb&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.1 models">hide #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.1 models">show #!2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.5 models">show #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2.6 models">show #!2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.6 models">hide #!2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.4 models">show #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.4 models">hide #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:53-54 #11/B:53-54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:53-54 #11/B:53-54">select #4/B:53-54 #11/B:53-54</a></div></div>28 atoms, 26 bonds, 4 residues, 2 models selected<br>
4270<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:24-54 #11/B:24-54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:24-54 #11/B:24-54">select #4/B:24-54 #11/B:24-54</a></div></div>418 atoms, 418 bonds, 62 residues, 2 models selected<br>
4271<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #11/B:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #11/B:1">select add #11/B:1</a></div></div>5 atoms, 4 bonds, 1 residue, 1 model selected<br>
4272<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Thu Sep 19 17:01:48 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
4273<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!18 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!18 models">show #!18 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #2">close #2</a></div></div><p style="color:darkorange">Cell requested for row 10 is out of bounds for table with 14 rows! Resizing table model.<br>
4274</p><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><p style="color:darkorange">Cell requested for row 2 is out of bounds for table with 14 rows! Resizing table model.<br>
4275</p><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!20 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!20 models">show #!20 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!20 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!20 models">hide #!20 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #5-12</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #5-12">close #5-12</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #1/M to #4/B pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #1/M to #4/B pairing ss showAlignment true">matchmaker #1/M to #4/B pairing ss showAlignment true</a></div></div>
4276 <table border=1 cellpadding=4 cellspacing=0>
4277 <tr>
4278 <th colspan="2">Parameters</th>
4279 </tr>
4280 <tr>
4281 <td>Chain pairing</td>
4282 <td>ss</td>
4283 </tr>
4284 <tr>
4285 <td>Alignment algorithm</td>
4286 <td>Needleman-Wunsch</td>
4287 </tr>
4288 <tr>
4289 <td>Similarity matrix</td>
4290 <td>BLOSUM-62</td>
4291 </tr>
4292
4293 <tr>
4294 <td>SS fraction</td>
4295 <td>0.3</td>
4296 </tr>
4297 <tr>
4298 <td>Gap open (HH/SS/other)</td>
4299 <td>18/18/6</td>
4300 </tr>
4301 <tr>
4302 <td>Gap extend</td>
4303 <td>1</td>
4304 </tr>
4305 <tr>
4306 <td>SS matrix</td>
4307 <td>
4308 <table>
4309 <tr>
4310 <th></th> <th>H</th> <th>S</th> <th>O</th>
4311 </tr>
4312 <tr>
4313 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
4314 </tr>
4315 <tr>
4316 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
4317 </tr>
4318 <tr>
4319 <th>O</th> <td></td> <td></td> <td align="right">4</td>
4320 </tr>
4321 </table>
4322 </td>
4323 </tr>
4324
4325 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
4326 </table>
4327 <br/>Matchmaker best (best design1).pdb, chain B (#4) with 2fdn, chain M (#1), sequence alignment score = 157.4<br>
4328Alignment identifier is 1<br>
4329Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
4330Hiding conservation header for alignment 1<br>
4331Chains used in RMSD evaluation for alignment 1: 2fdn #1/M, best (best design1).pdb #4/B<br>
4332Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
4333RMSD between 40 pruned atom pairs is 0.905 angstroms; (across all 51 pairs: 2.218)<br>
4334<br>
4335<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#header">sequence header</a> 1 consensus show</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence header 1 consensus show">sequence header 1 consensus show</a></div></div>Showing consensus header (&quot;seq_consensus&quot; residue attribute) for alignment 1<br>
4336<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:9">select #4/B:9</a></div></div>4 atoms, 3 bonds, 1 residue, 1 model selected<br>
4337<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:9">select #4/B:9</a></div></div>4 atoms, 3 bonds, 1 residue, 1 model selected<br>
4338<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:9">select #4/B:9</a></div></div>4 atoms, 3 bonds, 1 residue, 1 model selected<br>
4339<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:9">select #4/B:9</a></div></div>4 atoms, 3 bonds, 1 residue, 1 model selected<br>
4340<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:9,23-30</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:9,23-30">select #4/B:9,23-30</a></div></div>64 atoms, 62 bonds, 9 residues, 1 model selected<br>
4341<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:9,23-32</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:9,23-32">select #4/B:9,23-32</a></div></div>77 atoms, 75 bonds, 11 residues, 1 model selected<br>
4342<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!18 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!18 models">hide #!18 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Contacts">ui tool show Contacts</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B">select #4/B</a></div></div>357 atoms, 359 bonds, 54 residues, 1 model selected<br>
4343<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #4/A resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #4/A resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true">contacts sel restrict #4/A resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
4344H-bond overlap reduction: 0.4
4345Ignore contacts between atoms separated by 4 bonds or less
4346Ignore contacts between atoms in residues less than 5 apart in sequence
4347Detect intra-residue contacts: False
4348Detect intra-molecule contacts: False
4349
435022 contacts
4351 atom1 atom2 overlap distance
4352best (best design1).pdb #4/B ALA 7 CB best (best design1).pdb #4/A ARG 473 NH2 0.873 2.647
4353best (best design1).pdb #4/B GLU 16 OE1 best (best design1).pdb #4/A THR 802 CB 0.734 2.566
4354best (best design1).pdb #4/B GLU 16 OE1 best (best design1).pdb #4/A THR 802 OG1 0.578 1.902
4355best (best design1).pdb #4/B GLY 10 O best (best design1).pdb #4/A ILE 466 CD1 0.308 2.992
4356best (best design1).pdb #4/B GLU 16 CD best (best design1).pdb #4/A THR 802 OG1 0.249 3.091
4357best (best design1).pdb #4/B GLU 30 CG best (best design1).pdb #4/A LYS 489 CE 0.245 3.515
4358best (best design1).pdb #4/B ALA 7 CB best (best design1).pdb #4/A ARG 473 CZ 0.119 3.371
4359best (best design1).pdb #4/B CYS 11 CA best (best design1).pdb #4/A ILE 466 CD1 0.070 3.690
4360best (best design1).pdb #4/B GLU 16 CD best (best design1).pdb #4/A THR 802 CB -0.041 3.801
4361best (best design1).pdb #4/B ALA 7 CB best (best design1).pdb #4/A ARG 473 NH1 -0.058 3.578
4362best (best design1).pdb #4/B VAL 25 CG2 best (best design1).pdb #4/A VAL 776 CG1 -0.063 3.823
4363best (best design1).pdb #4/B GLU 30 CG best (best design1).pdb #4/A LYS 489 NZ -0.072 3.592
4364best (best design1).pdb #4/B GLU 30 OE1 best (best design1).pdb #4/A LYS 489 CE -0.103 3.403
4365best (best design1).pdb #4/B GLY 10 O best (best design1).pdb #4/A ILE 466 CG1 -0.116 3.416
4366best (best design1).pdb #4/B CYS 11 CB best (best design1).pdb #4/A CYS 468 SG -0.142 3.792
4367best (best design1).pdb #4/B GLU 30 CD best (best design1).pdb #4/A LYS 489 CE -0.168 3.928
4368best (best design1).pdb #4/B GLU 30 CD best (best design1).pdb #4/A LYS 489 NZ -0.185 3.705
4369best (best design1).pdb #4/B GLU 46 OE1 best (best design1).pdb #4/A ARG 12 NH1 -0.272 2.932
4370best (best design1).pdb #4/B GLU 26 CG best (best design1).pdb #4/A ALA 777 CB -0.283 4.043
4371best (best design1).pdb #4/B GLU 16 OE1 best (best design1).pdb #4/A THR 802 CA -0.299 3.599
4372best (best design1).pdb #4/B ALA 7 CA best (best design1).pdb #4/A ARG 473 NH2 -0.367 3.887
4373best (best design1).pdb #4/B VAL 25 CG1 best (best design1).pdb #4/A VAL 789 CG1 -0.391 4.151
4374</pre><br/>22 contacts<br>
4375<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.2 models">hide #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.2 models">show #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.2">select add #4.2</a></div></div>357 atoms, 359 bonds, 22 pseudobonds, 54 residues, 2 models selected<br>
4376<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #4.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #4.2">select subtract #4.2</a></div></div>357 atoms, 359 bonds, 54 residues, 1 model selected<br>
4377<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.2 models">hide #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.2 models">show #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:7,10-11,16,25-26,30/A:473,802,466,489,776-777,468,12,789</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:7,10-11,16,25-26,30/A:473,802,466,489,776-777,468,12,789">select #4/B:7,10-11,16,25-26,30/A:473,802,466,489,776-777,468,12,789</a></div></div>120 atoms, 107 bonds, 21 pseudobonds, 16 residues, 2 models selected<br>
4378<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 120 atom styles<br>
4379<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 16 items<br>
4380<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> contacts sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen contacts sel">name frozen contacts sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B">select #4/B</a></div></div>357 atoms, 359 bonds, 54 residues, 1 model selected<br>
4381<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Clashes</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Clashes">ui tool show Clashes</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #4/A resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #4/A resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true">clashes sel restrict #4/A resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
4382H-bond overlap reduction: 0.4
4383Ignore clashes between atoms separated by 4 bonds or less
4384Ignore clashes between atoms in residues less than 5 apart in sequence
4385Detect intra-residue clashes: False
4386Detect intra-molecule clashes: False
4387
43882 clashes
4389 atom1 atom2 overlap distance
4390best (best design1).pdb #4/B ALA 7 CB best (best design1).pdb #4/A ARG 473 NH2 0.873 2.647
4391best (best design1).pdb #4/B GLU 16 OE1 best (best design1).pdb #4/A THR 802 CB 0.734 2.566
4392</pre><br/>2 clashes<br>
4393<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:7,16</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:7,16">select #4/B:7,16</a></div></div>14 atoms, 12 bonds, 2 residues, 1 model selected<br>
4394<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B">select #4/B</a></div></div>357 atoms, 359 bonds, 54 residues, 1 model selected<br>
4395<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff restrict #4/A interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff restrict #4/A interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff restrict #4/A interModel false intraMol false intraRes false reveal true log true</a></div></div><pre>Finding intramodel H-bonds
4396Constraints relaxed by 0.4 angstroms and 20 degrees
4397Models used:
4398 4 best (best design1).pdb
4399
44004 H-bonds
4401H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
4402best (best design1).pdb #4/A ARG 12 NH1 best (best design1).pdb #4/B GLU 46 OE1 no hydrogen 2.932 N/A
4403best (best design1).pdb #4/A LYS 489 NZ best (best design1).pdb #4/B GLU 26 O no hydrogen 3.483 N/A
4404best (best design1).pdb #4/A LYS 489 NZ best (best design1).pdb #4/B GLU 30 OE1 no hydrogen 3.116 N/A
4405best (best design1).pdb #4/A THR 802 OG1 best (best design1).pdb #4/B GLU 16 OE1 no hydrogen 1.902 N/A
4406</pre><br/>4 hydrogen bonds found<br>
4407<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:46,26,30,16/A:12,489,802</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:46,26,30,16/A:12,489,802">select #4/B:46,26,30,16/A:12,489,802</a></div></div>63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected<br>
4408<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 63 atom styles<br>
4409<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.2 models">hide #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.3 models">hide #4.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:46,26,30,16/A:12,489,802</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:46,26,30,16/A:12,489,802">select #4/B:46,26,30,16/A:12,489,802</a></div></div>63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected<br>
4410<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:1-6,10-23,33-48,51-54 #1/M:1-6,10-23,32-47,52-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:1-6,10-23,33-48,51-54 #1/M:1-6,10-23,32-47,52-55">select #4/B:1-6,10-23,33-48,51-54 #1/M:1-6,10-23,32-47,52-55</a></div></div>755 atoms, 754 bonds, 80 residues, 2 models selected<br>
4411<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:46,26,30,16/A:12,489,802</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:46,26,30,16/A:12,489,802">select #4/B:46,26,30,16/A:12,489,802</a></div></div>63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected<br>
4412<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> contacts &amp;~#4/B:46,26,30,16/A:12,489,802</div><div class="cxcmd_as_cmd"><a href="cxcmd:select contacts &amp;~#4/B:46,26,30,16/A:12,489,802">select contacts &amp;~#4/B:46,26,30,16/A:12,489,802</a></div></div>66 atoms, 58 bonds, 11 pseudobonds, 10 residues, 3 models selected<br>
4413<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 66 atom styles<br>
4414<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:26 &amp;~backbone</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:26 &amp;~backbone">select #4/B:26 &amp;~backbone</a></div></div>5 atoms, 4 bonds, 1 residue, 1 model selected<br>
4415<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 5 atom styles<br>
4416<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.2 models">show #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 5 atom styles<br>
4417<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.4 models">hide #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.4 models">show #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.2 models">hide #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.2 models">show #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.2 models">hide #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:26 &amp;~backbone</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:26 &amp;~backbone">select #4/B:26 &amp;~backbone</a></div></div>5 atoms, 4 bonds, 1 residue, 1 model selected<br>
4418<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 5 atom styles<br>
4419<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #4/A">surface #4/A</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #4/B">surface #4/B</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/B surfaces #4.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/B surfaces #4.6">coulombic #4/B surfaces #4.6</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
4420Coulombic values for best (best design1).pdb_B SES surface #4.6: minimum, -17.76, mean -5.37, maximum 4.03<br>
4421<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/A surfaces #4.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/A surfaces #4.5">coulombic #4/A surfaces #4.5</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
4422Coulombic values for best (best design1).pdb_A SES surface #4.5: minimum, -15.01, mean 1.13, maximum 14.51<br>
4423<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 6yez</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 6yez">open 6yez</a></div></div><i>6yez</i> title:<br><b>Plant PSI-ferredoxin-plastocyanin supercomplex</b> <a href="cxcmd:log metadata #2">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
4424 <thead>
4425 <tr>
4426 <th colspan="3">Chain information for 6yez #2</th>
4427 </tr>
4428 <tr>
4429 <th>Chain</th>
4430 <th>Description</th>
4431 <th>UniProt</th>
4432 </tr>
4433 </thead>
4434 <tbody>
4435 <tr>
4436 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/1:40-232">1</a></td>
4437 <td><a title="Show sequence" href="cxcmd:sequence chain #2/1">Lhca1</a></td>
4438 <td style="text-align:center"></td>
4439 </tr>
4440 <tr>
4441 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/2:58-265">2</a></td>
4442 <td><a title="Show sequence" href="cxcmd:sequence chain #2/2">Chlorophyll a-b binding protein, chloroplastic</a></td>
4443 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q41038 from uniprot associate #2/2">Q41038_PEA</a> <a title="Select sequence" href="cxcmd:select #2/2:58-265">58-265</a></td>
4444 </tr>
4445 <tr>
4446 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/3:55-275">3</a></td>
4447 <td><a title="Show sequence" href="cxcmd:sequence chain #2/3">Chlorophyll a-b binding protein 3, chloroplastic</a></td>
4448 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q32904 from uniprot associate #2/3">CB23_PEA</a> <a title="Select sequence" href="cxcmd:select #2/3:55-275">55-275</a></td>
4449 </tr>
4450 <tr>
4451 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/4:52-249">4</a></td>
4452 <td><a title="Show sequence" href="cxcmd:sequence chain #2/4">Chlorophyll a-b binding protein P4, chloroplastic</a></td>
4453 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q9SQL2 from uniprot associate #2/4">CB24_PEA</a> <a title="Select sequence" href="cxcmd:select #2/4:52-249">52-249</a></td>
4454 </tr>
4455 <tr>
4456 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/A:16-758">A</a></td>
4457 <td><a title="Show sequence" href="cxcmd:sequence chain #2/A">Photosystem I P700 chlorophyll a apoprotein A1</a></td>
4458 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open A0A0F6NFW5 from uniprot associate #2/A">A0A0F6NFW5_PEA</a> <a title="Select sequence" href="cxcmd:select #2/A:16-758">16-758</a></td>
4459 </tr>
4460 <tr>
4461 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/B:2-734">B</a></td>
4462 <td><a title="Show sequence" href="cxcmd:sequence chain #2/B">Photosystem I P700 chlorophyll a apoprotein A2</a></td>
4463 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open A0A0F6NGI2 from uniprot associate #2/B">A0A0F6NGI2_PEA</a> <a title="Select sequence" href="cxcmd:select #2/B:2-734">2-734</a></td>
4464 </tr>
4465 <tr>
4466 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/C:2-81">C</a></td>
4467 <td><a title="Show sequence" href="cxcmd:sequence chain #2/C">Photosystem I iron-sulfur center</a></td>
4468 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P10793 from uniprot associate #2/C">PSAC_PEA</a> <a title="Select sequence" href="cxcmd:select #2/C:2-81">2-81</a></td>
4469 </tr>
4470 <tr>
4471 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/D:69-211">D</a></td>
4472 <td><a title="Show sequence" href="cxcmd:sequence chain #2/D">PsaD</a></td>
4473 <td style="text-align:center"></td>
4474 </tr>
4475 <tr>
4476 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/E:64-129">E</a></td>
4477 <td><a title="Show sequence" href="cxcmd:sequence chain #2/E">PsaE</a></td>
4478 <td style="text-align:center"></td>
4479 </tr>
4480 <tr>
4481 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/F:78-231">F</a></td>
4482 <td><a title="Show sequence" href="cxcmd:sequence chain #2/F">PsaF</a></td>
4483 <td style="text-align:center"></td>
4484 </tr>
4485 <tr>
4486 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/G:58-154">G</a></td>
4487 <td><a title="Show sequence" href="cxcmd:sequence chain #2/G">PsaG</a></td>
4488 <td style="text-align:center"></td>
4489 </tr>
4490 <tr>
4491 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/H:48-140">H</a></td>
4492 <td><a title="Show sequence" href="cxcmd:sequence chain #2/H">PsaH</a></td>
4493 <td style="text-align:center"></td>
4494 </tr>
4495 <tr>
4496 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/I:2-32">I</a></td>
4497 <td><a title="Show sequence" href="cxcmd:sequence chain #2/I">Photosystem I reaction center subunit VIII</a></td>
4498 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P17227 from uniprot associate #2/I">PSAI_PEA</a> <a title="Select sequence" href="cxcmd:select #2/I:2-32">2-32</a></td>
4499 </tr>
4500 <tr>
4501 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/J:1-42">J</a></td>
4502 <td><a title="Show sequence" href="cxcmd:sequence chain #2/J">PsaJ</a></td>
4503 <td style="text-align:center"></td>
4504 </tr>
4505 <tr>
4506 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/K:46-126">K</a></td>
4507 <td><a title="Show sequence" href="cxcmd:sequence chain #2/K">Photosystem I reaction center subunit X psaK</a></td>
4508 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open E1C9L3 from uniprot associate #2/K">E1C9L3_PEA</a> <a title="Select sequence" href="cxcmd:select #2/K:46-126">46-126</a></td>
4509 </tr>
4510 <tr>
4511 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/L:54-212">L</a></td>
4512 <td><a title="Show sequence" href="cxcmd:sequence chain #2/L">PsaL</a></td>
4513 <td style="text-align:center"></td>
4514 </tr>
4515 <tr>
4516 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/N:1-97">N</a></td>
4517 <td><a title="Show sequence" href="cxcmd:sequence chain #2/N">Ferredoxin-1, chloroplastic</a></td>
4518 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P09911 from uniprot associate #2/N">FER1_PEA</a> <a title="Select sequence" href="cxcmd:select #2/N:1-97">1-97</a></td>
4519 </tr>
4520 <tr>
4521 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/P:1-99">P</a></td>
4522 <td><a title="Show sequence" href="cxcmd:sequence chain #2/P">Plastocyanin, chloroplastic</a></td>
4523 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P16002 from uniprot associate #2/P">PLAS_PEA</a> <a title="Select sequence" href="cxcmd:select #2/P:1-99">1-99</a></td>
4524 </tr>
4525 </tbody>
4526</table><br/><table border=1 cellpadding=4 cellspacing=0>
4527 <thead>
4528 <tr>
4529 <th>Non-standard residues in 6yez #2</th>
4530 </tr>
4531 </thead>
4532 <tbody>
4533 <tr>
4534 <td><a title="select residue" href="cxcmd:sel :3PH">3PH</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/3PH">1,2-diacyl-glycerol-3-Sn-phosphate</a> (phosphatidic acid)</td>
4535 </tr>
4536 <tr>
4537 <td><a title="select residue" href="cxcmd:sel :BCR">BCR</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/BCR">β-carotene</a></td>
4538 </tr>
4539 <tr>
4540 <td><a title="select residue" href="cxcmd:sel :C7Z">C7Z</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/C7Z">(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol</a></td>
4541 </tr>
4542 <tr>
4543 <td><a title="select residue" href="cxcmd:sel :CA">CA</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CA">calcium ion</a></td>
4544 </tr>
4545 <tr>
4546 <td><a title="select residue" href="cxcmd:sel :CHL">CHL</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CHL">chlorophyll B</a></td>
4547 </tr>
4548 <tr>
4549 <td><a title="select residue" href="cxcmd:sel :CL0">CL0</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CL0">chlorophyll A isomer</a></td>
4550 </tr>
4551 <tr>
4552 <td><a title="select residue" href="cxcmd:sel :CLA">CLA</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CLA">chlorophyll A</a></td>
4553 </tr>
4554 <tr>
4555 <td><a title="select residue" href="cxcmd:sel :CU">CU</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CU">copper (II) ion</a></td>
4556 </tr>
4557 <tr>
4558 <td><a title="select residue" href="cxcmd:sel :DGD">DGD</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/DGD">digalactosyl diacyl glycerol (DGDG)</a></td>
4559 </tr>
4560 <tr>
4561 <td><a title="select residue" href="cxcmd:sel :FES">FES</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/FES">FE2/S2 (inorganic) cluster</a></td>
4562 </tr>
4563 <tr>
4564 <td><a title="select residue" href="cxcmd:sel :LHG">LHG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LHG">1,2-dipalmitoyl-phosphatidyl-glycerole</a></td>
4565 </tr>
4566 <tr>
4567 <td><a title="select residue" href="cxcmd:sel :LMG">LMG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LMG">1,2-distearoyl-monogalactosyl-diglyceride</a></td>
4568 </tr>
4569 <tr>
4570 <td><a title="select residue" href="cxcmd:sel :LMT">LMT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LMT">dodecyl-β-D-maltoside</a></td>
4571 </tr>
4572 <tr>
4573 <td><a title="select residue" href="cxcmd:sel :LUT">LUT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/LUT">(3R,3&#x27;R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3&#x27;-diol</a> ((3R,3&#x27;R)-β,β-carotene-3,3&#x27;-diol; lutein)</td>
4574 </tr>
4575 <tr>
4576 <td><a title="select residue" href="cxcmd:sel :PQN">PQN</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PQN">phylloquinone</a> (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)</td>
4577 </tr>
4578 <tr>
4579 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
4580 </tr>
4581 <tr>
4582 <td><a title="select residue" href="cxcmd:sel :XAT">XAT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/XAT">(3S,5R,6S,3&#x27;S,5&#x27;R,6&#x27;S)-5,6,5&#x27;,6&#x27;-diepoxy-5,6,5&#x27;,6&#x27;- tetrahydro-β,β-carotene-3,3&#x27;-diol</a> (violaxanthin)</td>
4583 </tr>
4584 </tbody>
4585</table><br/>Associated 6yez chain C to design:0 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches<br>
4586Associated 6yez chain E to design:0 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches<br>
4587<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2 &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2 &amp;protein">select #2 &amp;protein</a></div></div>26851 atoms, 27685 bonds, 3438 residues, 1 model selected<br>
4588<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #2/C to #4/A pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #2/C to #4/A pairing ss">matchmaker #2/C to #4/A pairing ss</a></div></div>
4589 <table border=1 cellpadding=4 cellspacing=0>
4590 <tr>
4591 <th colspan="2">Parameters</th>
4592 </tr>
4593 <tr>
4594 <td>Chain pairing</td>
4595 <td>ss</td>
4596 </tr>
4597 <tr>
4598 <td>Alignment algorithm</td>
4599 <td>Needleman-Wunsch</td>
4600 </tr>
4601 <tr>
4602 <td>Similarity matrix</td>
4603 <td>BLOSUM-62</td>
4604 </tr>
4605
4606 <tr>
4607 <td>SS fraction</td>
4608 <td>0.3</td>
4609 </tr>
4610 <tr>
4611 <td>Gap open (HH/SS/other)</td>
4612 <td>18/18/6</td>
4613 </tr>
4614 <tr>
4615 <td>Gap extend</td>
4616 <td>1</td>
4617 </tr>
4618 <tr>
4619 <td>SS matrix</td>
4620 <td>
4621 <table>
4622 <tr>
4623 <th></th> <th>H</th> <th>S</th> <th>O</th>
4624 </tr>
4625 <tr>
4626 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
4627 </tr>
4628 <tr>
4629 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
4630 </tr>
4631 <tr>
4632 <th>O</th> <td></td> <td></td> <td align="right">4</td>
4633 </tr>
4634 </table>
4635 </td>
4636 </tr>
4637
4638 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
4639 </table>
4640 <br/>Matchmaker best (best design1).pdb, chain A (#4) with 6yez, chain C (#2), sequence alignment score = 401<br>
4641RMSD between 80 pruned atom pairs is 0.395 angstroms; (across all 80 pairs: 0.395)<br>
4642<br>
4643<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #2/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #2/E">coulombic #2/E</a></div></div><p style="color:darkorange">The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:<br>6yez #2/E LYS 129 OXT<br/></p>Using Amber 20 recommended default charges and atom types for standard residues<br>
4644Coulombic values for 6yez_E SES surface #2.2: minimum, -13.31, mean 0.69, maximum 9.65<br>
4645<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #2/C:2-81</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #2/C:2-81">coulombic #2/C:2-81</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
4646Coulombic values for 6yez_C SES surface #2.3: minimum, -12.54, mean -0.30, maximum 9.66<br>
4647<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #2/D</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #2/D">coulombic #2/D</a></div></div><p style="color:darkorange">The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:<br>6yez #2/D LEU 211 OXT<br/></p>Using Amber 20 recommended default charges and atom types for standard residues<br>
4648Coulombic values for 6yez_D SES surface #2.4: minimum, -11.93, mean 1.16, maximum 13.86<br>
4649<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/toolshed.html#show">toolshed show</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:toolshed show">toolshed show</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/volume.html">volume</a> showOutlineBox true</div><div class="cxcmd_as_cmd"><a href="cxcmd:volume showOutlineBox true">volume showOutlineBox true</a></div></div><font color="crimson"><b>No volumes specified</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/N/P</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/N/P">select #2/N/P</a></div></div>1457 atoms, 1483 bonds, 7 pseudobonds, 198 residues, 2 models selected<br>
4650<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:3001</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:3001">select #2:3001</a></div></div>8 atoms, 12 bonds, 1 residue, 1 model selected<br>
4651<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/cofr.html">cofr</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:cofr sel">cofr sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A">select #4/A</a></div></div>2980 atoms, 3060 bonds, 6 pseudobonds, 380 residues, 2 models selected<br>
4652<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> contacts :&lt;1 &amp;#2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select contacts :&lt;1 &amp;#2">select contacts :&lt;1 &amp;#2</a></div></div>128 atoms, 118 bonds, 17 residues, 1 model selected<br>
4653<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.4 models">hide #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3 models">hide #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2 models">hide #2.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A">select #4/A</a></div></div>2980 atoms, 3060 bonds, 7 pseudobonds, 380 residues, 3 models selected<br>
4654<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:CA,CU,DGD,3PH,C7Z,LHG</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:CA,CU,DGD,3PH,C7Z,LHG">select #2:CA,CU,DGD,3PH,C7Z,LHG</a></div></div>739 atoms, 735 bonds, 20 residues, 1 model selected<br>
4655<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/1">select #2/1</a></div></div>2580 atoms, 2690 bonds, 61 pseudobonds, 214 residues, 2 models selected<br>
4656<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/1-4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/1-4">select #2/1-4</a></div></div>10673 atoms, 11130 bonds, 241 pseudobonds, 907 residues, 2 models selected<br>
4657<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C-E">select #2/C-E</a></div></div>2288 atoms, 2352 bonds, 7 pseudobonds, 291 residues, 2 models selected<br>
4658<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/set.html">set</a> bgColor white</div><div class="cxcmd_as_cmd"><a href="cxcmd:set bgColor white">set bgColor white</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/graphics.html#silhouettes">graphics silhouettes</a> true</div><div class="cxcmd_as_cmd"><a href="cxcmd:graphics silhouettes true">graphics silhouettes true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.4 models">hide #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.4 models">show #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #2 enclose #2/A-B/F-L</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #2 enclose #2/A-B/F-L">surface #2 enclose #2/A-B/F-L</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #2.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #2.5">close #2.5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> contacts :&lt;1 &amp;#2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select contacts :&lt;1 &amp;#2">select contacts :&lt;1 &amp;#2</a></div></div>128 atoms, 118 bonds, 17 residues, 1 model selected<br>
4659<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A :&lt;1 &amp;#2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A :&lt;1 &amp;#2">select #4/A :&lt;1 &amp;#2</a></div></div>3059 atoms, 3141 bonds, 4 pseudobonds, 382 residues, 2 models selected<br>
4660<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A :&lt;1 &amp;#2 &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A :&lt;1 &amp;#2 &amp;protein">select #4/A :&lt;1 &amp;#2 &amp;protein</a></div></div>2994 atoms, 3072 bonds, 381 residues, 1 model selected<br>
4661<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> minAB sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen minAB sel">name frozen minAB sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-B/F-L &amp;~minAB</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-B/F-L &amp;~minAB">select #2/A-B/F-L &amp;~minAB</a></div></div>23858 atoms, 24789 bonds, 418 pseudobonds, 2167 residues, 2 models selected<br>
4662<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #2 enclose #2/A-B/F-L &amp;~minAB</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #2 enclose #2/A-B/F-L &amp;~minAB">surface #2 enclose #2/A-B/F-L &amp;~minAB</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:SF4">select #1:SF4</a></div></div>16 atoms, 24 bonds, 2 residues, 1 model selected<br>
4663<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1:1-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1:1-55">select #1:1-55</a></div></div>652 atoms, 657 bonds, 55 residues, 1 model selected<br>
4664<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A &amp;contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A &amp;contacts">select #4/A &amp;contacts</a></div></div>71 atoms, 63 bonds, 9 residues, 1 model selected<br>
4665<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 71 atom styles<br>
4666<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :CL0,CLA</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :CL0,CLA">select :CL0,CLA</a></div></div>8422 atoms, 8990 bonds, 568 pseudobonds, 142 residues, 2 models selected<br>
4667<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!2 &amp; sel) lime</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!2 &amp; sel) lime">color (#!2 &amp; sel) lime</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><p style="color:darkorange">Cell requested for row 8 is out of bounds for table with 17 rows! Resizing table model.<br>
4668</p><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.5">select add #4.5</a></div></div>2980 atoms, 380 residues, 1 model selected<br>
4669<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 30">transparency (#!4 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 20">transparency (#!4 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name front">view name front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png&quot; width 845 height 690 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png&quot; width 845 height 690 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png&quot; width 845 height 690 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png&quot; width 1470 height 1200 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png&quot; width 1470 height 1200 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png&quot; width 1470 height 1200 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:select contacts">select contacts</a></div></div>120 atoms, 107 bonds, 26 pseudobonds, 16 residues, 4 models selected<br>
4670<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 120 atom styles<br>
4671<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.6">select add #4.6</a></div></div>357 atoms, 54 residues, 1 model selected<br>
4672<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 20">transparency (#!4 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png&quot; width 1470 height 1200 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png&quot; width 1470 height 1200 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png&quot; width 1470 height 1200 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:select contacts">select contacts</a></div></div>120 atoms, 107 bonds, 26 pseudobonds, 16 residues, 4 models selected<br>
4673<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 120 atom styles<br>
4674<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B &amp;contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B &amp;contacts">select #4/B &amp;contacts</a></div></div>49 atoms, 44 bonds, 7 residues, 1 model selected<br>
4675<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 49 atom styles<br>
4676<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name back">view name back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:489</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:489">select #4/A:489</a></div></div>9 atoms, 8 bonds, 1 residue, 1 model selected<br>
4677<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 9 atom styles<br>
4678<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx back .png&quot; width 1470 height 1200 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx back .png&quot; width 1470 height 1200 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx back .png&quot; width 1470 height 1200 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx back .png&quot; width 1470 height 1200 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx back .png&quot; width 1470 height 1200 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx back .png&quot; width 1470 height 1200 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:12</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:12">select #4/A:12</a></div></div>11 atoms, 10 bonds, 1 residue, 1 model selected<br>
4679<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 11 atom styles<br>
4680<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:16,30,46</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:16,30,46">select #4/B:16,30,46</a></div></div>27 atoms, 24 bonds, 3 residues, 1 model selected<br>
4681<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 27 atom styles<br>
4682<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:26 &amp;backbone</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:26 &amp;backbone">select #4/B:26 &amp;backbone</a></div></div>4 atoms, 3 bonds, 1 residue, 1 model selected<br>
4683<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 4 atom styles<br>
4684<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><a href="help:user/commands/select.html">select</a> #4/A &amp;contacts <span style="color:white; background-color:crimson;">&amp;~489,802</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A &amp;contacts &amp;~:489,802</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A &amp;contacts &amp;~:489,802">select #4/A &amp;contacts &amp;~:489,802</a></div></div>55 atoms, 49 bonds, 7 residues, 1 model selected<br>
4685<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 55 atom styles<br>
4686<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:12,489,802</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:12,489,802">select #4/A:12,489,802</a></div></div>27 atoms, 24 bonds, 3 residues, 1 model selected<br>
4687<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 27 atom styles<br>
4688<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:16,26,30,46/A:12,489,802</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:16,26,30,46/A:12,489,802">select #4/B:16,26,30,46/A:12,489,802</a></div></div>63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected<br>
4689<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> hBonds sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen hBonds sel">name frozen hBonds sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B &amp;contacts &amp;~hBonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B &amp;contacts &amp;~hBonds">select #4/B &amp;contacts &amp;~hBonds</a></div></div>22 atoms, 19 bonds, 4 residues, 1 model selected<br>
4690<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 22 atom styles<br>
4691<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:26 &amp;~backbone</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:26 &amp;~backbone">select #4/B:26 &amp;~backbone</a></div></div>5 atoms, 4 bonds, 1 residue, 1 model selected<br>
4692<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 5 atom styles<br>
4693<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png&quot; width 1568 height 1280 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png&quot; width 1568 height 1280 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx front .png&quot; width 1568 height 1280 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B &amp;contacts &amp;~hBonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B &amp;contacts &amp;~hBonds">select #4/B &amp;contacts &amp;~hBonds</a></div></div>22 atoms, 19 bonds, 4 residues, 1 model selected<br>
4694<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 22 atom styles<br>
4695<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B:26 &amp;~backbone</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B:26 &amp;~backbone">select #4/B:26 &amp;~backbone</a></div></div>5 atoms, 4 bonds, 1 residue, 1 model selected<br>
4696<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 5 atom styles<br>
4697<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png&quot; width 1568 height 1280 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png&quot; width 1568 height 1280 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png&quot; width 1568 height 1280 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A &amp;contacts &amp;~hBonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A &amp;contacts &amp;~hBonds">select #4/A &amp;contacts &amp;~hBonds</a></div></div>44 atoms, 39 bonds, 6 residues, 1 model selected<br>
4698<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 44 atom styles<br>
4699<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> minAB</div><div class="cxcmd_as_cmd"><a href="cxcmd:select minAB">select minAB</a></div></div>3213 atoms, 3072 bonds, 410 residues, 1 model selected<br>
4700<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png&quot; width 1568 height 1280 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png&quot; width 1568 height 1280 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx 2 surfaces front .png&quot; width 1568 height 1280 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI Fdx best MPNN .cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Mon Sep 30 14:03:27 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
4701<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/neurosnap-66fc65140db6770388b10541 2/relaxed_structure.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/neurosnap-66fc65140db6770388b10541 2/relaxed_structure.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/neurosnap-66fc65140db6770388b10541 2/relaxed_structure.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
4702 <thead>
4703 <tr>
4704 <th colspan="2">Chain information for relaxed_structure.pdb #5</th>
4705 </tr>
4706 <tr>
4707 <th>Chain</th>
4708 <th>Description</th>
4709
4710 </tr>
4711 </thead>
4712 <tbody>
4713 <tr>
4714 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/A:1-380">A</a></td>
4715 <td><a title="Show sequence" href="cxcmd:sequence chain #5/A">No description available</a></td>
4716
4717 </tr>
4718 <tr>
4719 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/B:1-61">B</a></td>
4720 <td><a title="Show sequence" href="cxcmd:sequence chain #5/B">No description available</a></td>
4721
4722 </tr>
4723 </tbody>
4724</table><br/>Associated relaxed_structure.pdb chain A to design:0 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches<br>
4725<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5 models">hide #5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5 models">show #5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #5/A to #2/C pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #5/A to #2/C pairing ss">matchmaker #5/A to #2/C pairing ss</a></div></div>
4726 <table border=1 cellpadding=4 cellspacing=0>
4727 <tr>
4728 <th colspan="2">Parameters</th>
4729 </tr>
4730 <tr>
4731 <td>Chain pairing</td>
4732 <td>ss</td>
4733 </tr>
4734 <tr>
4735 <td>Alignment algorithm</td>
4736 <td>Needleman-Wunsch</td>
4737 </tr>
4738 <tr>
4739 <td>Similarity matrix</td>
4740 <td>BLOSUM-62</td>
4741 </tr>
4742
4743 <tr>
4744 <td>SS fraction</td>
4745 <td>0.3</td>
4746 </tr>
4747 <tr>
4748 <td>Gap open (HH/SS/other)</td>
4749 <td>18/18/6</td>
4750 </tr>
4751 <tr>
4752 <td>Gap extend</td>
4753 <td>1</td>
4754 </tr>
4755 <tr>
4756 <td>SS matrix</td>
4757 <td>
4758 <table>
4759 <tr>
4760 <th></th> <th>H</th> <th>S</th> <th>O</th>
4761 </tr>
4762 <tr>
4763 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
4764 </tr>
4765 <tr>
4766 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
4767 </tr>
4768 <tr>
4769 <th>O</th> <td></td> <td></td> <td align="right">4</td>
4770 </tr>
4771 </table>
4772 </td>
4773 </tr>
4774
4775 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
4776 </table>
4777 <br/>Matchmaker 6yez, chain C (#2) with relaxed_structure.pdb, chain A (#5), sequence alignment score = 364.4<br>
4778RMSD between 73 pruned atom pairs is 0.691 angstroms; (across all 80 pairs: 2.602)<br>
4779<br>
4780<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #5">close #5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/neurosnap-66fc7cd10db6770388b1055a/relaxed_structure.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/neurosnap-66fc7cd10db6770388b1055a/relaxed_structure.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/neurosnap-66fc7cd10db6770388b1055a/relaxed_structure.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
4781 <thead>
4782 <tr>
4783 <th colspan="2">Chain information for relaxed_structure.pdb #5</th>
4784 </tr>
4785 <tr>
4786 <th>Chain</th>
4787 <th>Description</th>
4788
4789 </tr>
4790 </thead>
4791 <tbody>
4792 <tr>
4793 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/A:1-743">A</a></td>
4794 <td><a title="Show sequence" href="cxcmd:sequence chain #5/A">No description available</a></td>
4795
4796 </tr>
4797 <tr>
4798 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/B:1-733">B</a></td>
4799 <td><a title="Show sequence" href="cxcmd:sequence chain #5/B">No description available</a></td>
4800
4801 </tr>
4802 <tr>
4803 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/C:1-80">C</a></td>
4804 <td><a title="Show sequence" href="cxcmd:sequence chain #5/C">No description available</a></td>
4805
4806 </tr>
4807 <tr>
4808 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/D:1-143">D</a></td>
4809 <td><a title="Show sequence" href="cxcmd:sequence chain #5/D">No description available</a></td>
4810
4811 </tr>
4812 <tr>
4813 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/E:1-66">E</a></td>
4814 <td><a title="Show sequence" href="cxcmd:sequence chain #5/E">No description available</a></td>
4815
4816 </tr>
4817 <tr>
4818 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/F:1-61">F</a></td>
4819 <td><a title="Show sequence" href="cxcmd:sequence chain #5/F">No description available</a></td>
4820
4821 </tr>
4822 </tbody>
4823</table><br/>Associated relaxed_structure.pdb chain C to design:0 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches<br>
4824Associated relaxed_structure.pdb chain E to design:0 n:0|mpnn:1.163|plddt:0.842|ptm:0.806|pae:6.047|rmsd:1.639 with 0 mismatches<br>
4825<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5 &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5 &amp;protein">select #5 &amp;protein</a></div></div>28495 atoms, 28969 bonds, 1826 residues, 1 model selected<br>
4826<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/surface.html">surface</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:surface #5">surface #5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/A surfaces #5.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/A surfaces #5.1">coulombic #5/A surfaces #5.1</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
4827Coulombic values for relaxed_structure.pdb_A SES surface #5.1: minimum, -11.84, mean -0.24, maximum 17.92<br>
4828<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/B surfaces #5.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/B surfaces #5.2">coulombic #5/B surfaces #5.2</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
4829Coulombic values for relaxed_structure.pdb_B SES surface #5.2: minimum, -13.17, mean 0.31, maximum 13.60<br>
4830<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/C surfaces #5.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/C surfaces #5.3">coulombic #5/C surfaces #5.3</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
4831Coulombic values for relaxed_structure.pdb_C SES surface #5.3: minimum, -14.28, mean 0.87, maximum 12.27<br>
4832<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/D surfaces #5.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/D surfaces #5.4">coulombic #5/D surfaces #5.4</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
4833Coulombic values for relaxed_structure.pdb_D SES surface #5.4: minimum, -9.85, mean 2.10, maximum 15.14<br>
4834<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/E surfaces #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/E surfaces #5.5">coulombic #5/E surfaces #5.5</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
4835Coulombic values for relaxed_structure.pdb_E SES surface #5.5: minimum, -10.97, mean 1.53, maximum 12.30<br>
4836<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/F surfaces #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/F surfaces #5.6">coulombic #5/F surfaces #5.6</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
4837Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum, -13.89, mean -3.67, maximum 7.01<br>
4838<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.1">select add #5.1</a></div></div>11581 atoms, 743 residues, 1 model selected<br>
4839<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.2">select add #5.2</a></div></div>23096 atoms, 1476 residues, 2 models selected<br>
4840<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.3">select add #5.3</a></div></div>24310 atoms, 1556 residues, 3 models selected<br>
4841<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.4">select add #5.4</a></div></div>26587 atoms, 1699 residues, 4 models selected<br>
4842<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.5">select add #5.5</a></div></div>27646 atoms, 1765 residues, 5 models selected<br>
4843<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.4">select subtract #5.4</a></div></div>25369 atoms, 1622 residues, 6 models selected<br>
4844<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.5">select subtract #5.5</a></div></div>24310 atoms, 1556 residues, 5 models selected<br>
4845<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.6">select add #5.6</a></div></div>25159 atoms, 1617 residues, 4 models selected<br>
4846<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.4">select add #5.4</a></div></div>27436 atoms, 1760 residues, 5 models selected<br>
4847<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.5">select add #5.5</a></div></div>28495 atoms, 1826 residues, 6 models selected<br>
4848<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 20">transparency (#!5 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C/F &amp;:Cys &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C/F &amp;:Cys &amp;~H">select #5/C/F &amp;:Cys &amp;~H</a></div></div>102 atoms, 85 bonds, 17 residues, 1 model selected<br>
4849<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 102 atom styles<br>
4850<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F#1/M &amp;:CYS</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F#1/M &amp;:CYS">select #5/F#1/M &amp;:CYS</a></div></div>168 atoms, 152 bonds, 16 residues, 2 models selected<br>
4851<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #1/M &amp; sel to #5/F &amp; sel pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #1/M &amp; sel to #5/F &amp; sel pairing ss">matchmaker #1/M &amp; sel to #5/F &amp; sel pairing ss</a></div></div>
4852 <table border=1 cellpadding=4 cellspacing=0>
4853 <tr>
4854 <th colspan="2">Parameters</th>
4855 </tr>
4856 <tr>
4857 <td>Chain pairing</td>
4858 <td>ss</td>
4859 </tr>
4860 <tr>
4861 <td>Alignment algorithm</td>
4862 <td>Needleman-Wunsch</td>
4863 </tr>
4864 <tr>
4865 <td>Similarity matrix</td>
4866 <td>BLOSUM-62</td>
4867 </tr>
4868
4869 <tr>
4870 <td>SS fraction</td>
4871 <td>0.3</td>
4872 </tr>
4873 <tr>
4874 <td>Gap open (HH/SS/other)</td>
4875 <td>18/18/6</td>
4876 </tr>
4877 <tr>
4878 <td>Gap extend</td>
4879 <td>1</td>
4880 </tr>
4881 <tr>
4882 <td>SS matrix</td>
4883 <td>
4884 <table>
4885 <tr>
4886 <th></th> <th>H</th> <th>S</th> <th>O</th>
4887 </tr>
4888 <tr>
4889 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
4890 </tr>
4891 <tr>
4892 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
4893 </tr>
4894 <tr>
4895 <th>O</th> <td></td> <td></td> <td align="right">4</td>
4896 </tr>
4897 </table>
4898 </td>
4899 </tr>
4900
4901 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
4902 </table>
4903 <br/>Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#1), sequence alignment score = 48<br>
4904RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)<br>
4905<br>
4906<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A-E">select #5/A-E</a></div></div>27646 atoms, 28113 bonds, 1765 residues, 1 model selected<br>
4907<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Clashes</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Clashes">ui tool show Clashes</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #5/F resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #5/F resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true">clashes sel restrict #5/F resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
4908H-bond overlap reduction: 0.4
4909Ignore clashes between atoms separated by 4 bonds or less
4910Ignore clashes between atoms in residues less than 5 apart in sequence
4911Detect intra-residue clashes: False
4912Detect intra-molecule clashes: False
4913
49140 clashes
4915atom1 atom2 overlap distance
4916</pre><br/>No clashes<br>
4917<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Contacts">ui tool show Contacts</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #15/B resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #15/B resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true">contacts sel restrict #15/B resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
4918H-bond overlap reduction: 0.4
4919Ignore contacts between atoms separated by 4 bonds or less
4920Ignore contacts between atoms in residues less than 5 apart in sequence
4921Detect intra-residue contacts: False
4922Detect intra-molecule contacts: False
4923
49240 contacts
4925atom1 atom2 overlap distance
4926</pre><br/>No contacts<br>
4927<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict #5/F resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict #5/F resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true">contacts sel restrict #5/F resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
4928H-bond overlap reduction: 0.4
4929Ignore contacts between atoms separated by 4 bonds or less
4930Ignore contacts between atoms in residues less than 5 apart in sequence
4931Detect intra-residue contacts: False
4932Detect intra-molecule contacts: False
4933
4934160 contacts
4935 atom1 atom2 overlap distance
4936relaxed_structure.pdb #5/C ARG 18 HH11 relaxed_structure.pdb #5/F GLU 17 CD 0.421 2.279
4937relaxed_structure.pdb #5/D LYS 109 HZ2 relaxed_structure.pdb #5/F GLU 19 CD 0.387 2.313
4938relaxed_structure.pdb #5/E THR 54 HG1 relaxed_structure.pdb #5/F GLU 9 OE2 0.371 1.709
4939relaxed_structure.pdb #5/D LYS 109 HZ2 relaxed_structure.pdb #5/F GLU 19 OE1 0.357 1.723
4940relaxed_structure.pdb #5/A LYS 31 HZ2 relaxed_structure.pdb #5/F ASP 30 OD2 0.353 1.727
4941relaxed_structure.pdb #5/A ARG 27 HH21 relaxed_structure.pdb #5/F ASP 30 OD1 0.348 1.732
4942relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 CD 0.340 2.985
4943relaxed_structure.pdb #5/E ARG 43 HH21 relaxed_structure.pdb #5/F GLU 9 OE1 0.335 1.745
4944relaxed_structure.pdb #5/E THR 54 HG1 relaxed_structure.pdb #5/F GLU 9 CD 0.326 2.374
4945relaxed_structure.pdb #5/C ARG 18 HH22 relaxed_structure.pdb #5/F GLU 17 OE2 0.323 1.757
4946relaxed_structure.pdb #5/A ARG 27 HH11 relaxed_structure.pdb #5/F ASP 30 OD1 0.313 1.767
4947relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH22 0.308 1.772
4948relaxed_structure.pdb #5/E ARG 43 HH22 relaxed_structure.pdb #5/F ALA 7 O 0.213 1.867
4949relaxed_structure.pdb #5/C PRO 58 CB relaxed_structure.pdb #5/F ILE 11 CD1 0.169 3.231
4950relaxed_structure.pdb #5/A ARG 27 HH21 relaxed_structure.pdb #5/F ASP 30 CG 0.166 2.534
4951relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F THR 8 HA 0.161 2.464
4952relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 HE 0.158 1.942
4953relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 N 0.152 3.098
4954relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH12 0.146 1.934
4955relaxed_structure.pdb #5/D LYS 109 HZ1 relaxed_structure.pdb #5/F PRO 18 O 0.146 1.934
4956relaxed_structure.pdb #5/C ARG 18 HH11 relaxed_structure.pdb #5/F GLU 17 OE1 0.136 1.944
4957relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 HG2 0.085 2.540
4958relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 CD 0.062 3.263
4959relaxed_structure.pdb #5/A ARG 27 CZ relaxed_structure.pdb #5/F ASP 30 OD1 0.055 3.125
4960relaxed_structure.pdb #5/C ARG 18 HH11 relaxed_structure.pdb #5/F GLU 17 OE2 0.055 2.025
4961relaxed_structure.pdb #5/D LYS 109 HZ3 relaxed_structure.pdb #5/F GLU 19 OE2 0.047 2.033
4962relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 OD1 0.038 2.667
4963relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F SER 12 O 0.034 3.146
4964relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE1 0.032 2.673
4965relaxed_structure.pdb #5/C ALA 35 CB relaxed_structure.pdb #5/F VAL 51 HA 0.028 2.672
4966relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 OD2 0.025 2.680
4967relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 OD1 0.020 2.685
4968relaxed_structure.pdb #5/C LYS 34 C relaxed_structure.pdb #5/F GLY 50 O 0.019 3.161
4969relaxed_structure.pdb #5/C PRO 58 CG relaxed_structure.pdb #5/F ILE 11 CD1 0.015 3.385
4970relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F PRO 53 HB3 0.012 2.688
4971relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE2 0.011 2.694
4972relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 CD -0.001 3.201
4973relaxed_structure.pdb #5/A ARG 27 HH11 relaxed_structure.pdb #5/F ASP 30 CG -0.002 2.702
4974relaxed_structure.pdb #5/C THR 14 HG1 relaxed_structure.pdb #5/F ALA 15 HB3 -0.006 2.006
4975relaxed_structure.pdb #5/C CYS 13 O relaxed_structure.pdb #5/F ALA 15 HB3 -0.012 2.492
4976relaxed_structure.pdb #5/D LYS 109 HZ3 relaxed_structure.pdb #5/F GLU 19 CD -0.015 2.715
4977relaxed_structure.pdb #5/C PRO 58 HG3 relaxed_structure.pdb #5/F ILE 11 CD1 -0.017 2.717
4978relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 NH2 -0.023 2.728
4979relaxed_structure.pdb #5/C PRO 58 CB relaxed_structure.pdb #5/F ILE 11 HD11 -0.027 2.727
4980relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 OE2 -0.028 2.733
4981relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F GLU 9 OE1 -0.044 2.749
4982relaxed_structure.pdb #5/C ARG 18 CZ relaxed_structure.pdb #5/F GLY 14 O -0.062 3.242
4983relaxed_structure.pdb #5/C ARG 18 HH22 relaxed_structure.pdb #5/F GLU 17 CD -0.064 2.764
4984relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 CG -0.076 3.401
4985relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 CZ -0.080 3.260
4986relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 OE2 -0.082 2.662
4987relaxed_structure.pdb #5/A ASP 34 CG relaxed_structure.pdb #5/F ARG 32 HH12 -0.083 2.783
4988relaxed_structure.pdb #5/A LYS 31 HZ2 relaxed_structure.pdb #5/F ASP 30 CG -0.084 2.784
4989relaxed_structure.pdb #5/E SER 53 C relaxed_structure.pdb #5/F GLU 9 OE2 -0.087 3.267
4990relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 HG3 -0.088 2.788
4991relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F ALA 15 N -0.094 3.344
4992relaxed_structure.pdb #5/C ARG 18 HH21 relaxed_structure.pdb #5/F PRO 18 HG2 -0.099 2.099
4993relaxed_structure.pdb #5/C ARG 18 CZ relaxed_structure.pdb #5/F GLU 17 OE2 -0.103 3.283
4994relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F PRO 53 O -0.106 2.586
4995relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 HB2 -0.106 2.586
4996relaxed_structure.pdb #5/A ARG 27 HH21 relaxed_structure.pdb #5/F ASP 30 HA -0.109 2.109
4997relaxed_structure.pdb #5/E SER 53 H relaxed_structure.pdb #5/F GLU 9 OE2 -0.109 2.189
4998relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 HA -0.113 2.593
4999relaxed_structure.pdb #5/C THR 14 HG1 relaxed_structure.pdb #5/F ALA 15 CB -0.115 2.815
5000relaxed_structure.pdb #5/C PRO 58 CB relaxed_structure.pdb #5/F ILE 11 HD13 -0.120 2.820
5001relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 C -0.122 3.447
5002relaxed_structure.pdb #5/C ILE 11 HG13 relaxed_structure.pdb #5/F PRO 53 CB -0.123 2.823
5003relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F PRO 18 O -0.123 2.828
5004relaxed_structure.pdb #5/C CYS 13 C relaxed_structure.pdb #5/F ALA 15 HB3 -0.125 2.825
5005relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE1 -0.132 2.837
5006relaxed_structure.pdb #5/C ILE 11 CG1 relaxed_structure.pdb #5/F PRO 53 CB -0.134 3.534
5007relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 CG -0.138 3.463
5008relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 NH1 -0.139 2.844
5009relaxed_structure.pdb #5/C GLN 15 HG2 relaxed_structure.pdb #5/F SER 12 O -0.148 2.628
5010relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F MET 54 CE -0.150 3.350
5011relaxed_structure.pdb #5/C GLN 15 CG relaxed_structure.pdb #5/F SER 12 O -0.153 3.333
5012relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F ALA 7 O -0.157 2.862
5013relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 HA -0.159 2.784
5014relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F PRO 53 CB -0.177 3.577
5015relaxed_structure.pdb #5/C GLN 15 CG relaxed_structure.pdb #5/F CYS 13 HA -0.183 2.883
5016relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F THR 8 CA -0.185 3.510
5017relaxed_structure.pdb #5/C ALA 35 CA relaxed_structure.pdb #5/F VAL 51 HA -0.194 2.894
5018relaxed_structure.pdb #5/C GLN 15 HE21 relaxed_structure.pdb #5/F GLY 14 C -0.195 2.895
5019relaxed_structure.pdb #5/D LYS 109 HG2 relaxed_structure.pdb #5/F GLU 19 OE1 -0.202 2.682
5020relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE2 -0.203 2.908
5021relaxed_structure.pdb #5/E THR 54 O relaxed_structure.pdb #5/F MET 54 CE -0.206 3.386
5022relaxed_structure.pdb #5/C GLN 15 OE1 relaxed_structure.pdb #5/F SER 12 O -0.206 3.166
5023relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F GLY 14 N -0.207 3.532
5024relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 CA -0.208 3.533
5025relaxed_structure.pdb #5/C PRO 58 HB2 relaxed_structure.pdb #5/F ILE 11 CD1 -0.211 2.911
5026relaxed_structure.pdb #5/E ARG 43 HH22 relaxed_structure.pdb #5/F ALA 7 C -0.212 2.912
5027relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 NE -0.215 2.940
5028relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F MET 54 SD -0.218 3.700
5029relaxed_structure.pdb #5/E THR 54 O relaxed_structure.pdb #5/F MET 54 HE2 -0.218 2.698
5030relaxed_structure.pdb #5/C LYS 34 CB relaxed_structure.pdb #5/F GLY 50 O -0.221 3.401
5031relaxed_structure.pdb #5/A THR 28 HG1 relaxed_structure.pdb #5/F ARG 32 HH21 -0.224 2.224
5032relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F PRO 53 HB3 -0.227 2.227
5033relaxed_structure.pdb #5/E ARG 43 HH22 relaxed_structure.pdb #5/F THR 8 HA -0.229 2.229
5034relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 CB -0.230 3.410
5035relaxed_structure.pdb #5/E THR 54 CG2 relaxed_structure.pdb #5/F GLU 9 OE1 -0.230 3.410
5036relaxed_structure.pdb #5/E SER 53 CA relaxed_structure.pdb #5/F GLU 9 OE2 -0.230 3.410
5037relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 CG -0.231 3.631
5038relaxed_structure.pdb #5/C PRO 58 CG relaxed_structure.pdb #5/F ILE 11 HD13 -0.233 2.933
5039relaxed_structure.pdb #5/C THR 14 HG1 relaxed_structure.pdb #5/F ALA 15 CA -0.234 2.934
5040relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 CG -0.235 3.560
5041relaxed_structure.pdb #5/C PRO 58 HB3 relaxed_structure.pdb #5/F ILE 11 HD11 -0.242 2.242
5042relaxed_structure.pdb #5/C ALA 35 CA relaxed_structure.pdb #5/F GLY 50 O -0.243 3.423
5043relaxed_structure.pdb #5/C ALA 35 HB3 relaxed_structure.pdb #5/F VAL 51 HA -0.244 2.244
5044relaxed_structure.pdb #5/A LYS 31 HZ1 relaxed_structure.pdb #5/F ASP 30 O -0.246 2.326
5045relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 CA -0.247 3.427
5046relaxed_structure.pdb #5/C CYS 13 HB2 relaxed_structure.pdb #5/F PRO 53 HG3 -0.250 2.250
5047relaxed_structure.pdb #5/A THR 28 HB relaxed_structure.pdb #5/F GLY 31 HA2 -0.251 2.251
5048relaxed_structure.pdb #5/C CYS 13 HB3 relaxed_structure.pdb #5/F PRO 53 CB -0.254 2.954
5049relaxed_structure.pdb #5/A ARG 27 HH21 relaxed_structure.pdb #5/F ASP 30 CA -0.255 2.955
5050relaxed_structure.pdb #5/C CYS 13 HB3 relaxed_structure.pdb #5/F PRO 53 HB2 -0.260 2.260
5051relaxed_structure.pdb #5/C PRO 58 HG3 relaxed_structure.pdb #5/F ILE 11 HD13 -0.265 2.265
5052relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 O -0.269 2.974
5053relaxed_structure.pdb #5/C PRO 58 HB2 relaxed_structure.pdb #5/F ILE 11 HD13 -0.269 2.269
5054relaxed_structure.pdb #5/C ALA 35 HA relaxed_structure.pdb #5/F VAL 51 HA -0.270 2.270
5055relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F PRO 53 C -0.274 2.974
5056relaxed_structure.pdb #5/E ARG 43 HH21 relaxed_structure.pdb #5/F GLU 9 CD -0.276 2.976
5057relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F GLY 14 H -0.276 2.976
5058relaxed_structure.pdb #5/A ASP 34 CG relaxed_structure.pdb #5/F ARG 32 HH22 -0.283 2.983
5059relaxed_structure.pdb #5/E THR 54 N relaxed_structure.pdb #5/F GLU 9 OE2 -0.285 2.990
5060relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 H -0.288 2.913
5061relaxed_structure.pdb #5/D LYS 109 HZ1 relaxed_structure.pdb #5/F PRO 18 C -0.290 2.990
5062relaxed_structure.pdb #5/E ARG 43 CZ relaxed_structure.pdb #5/F GLU 9 OE1 -0.291 3.471
5063relaxed_structure.pdb #5/C THR 14 HG22 relaxed_structure.pdb #5/F ALA 15 CB -0.292 2.992
5064relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F MET 54 HE1 -0.299 2.799
5065relaxed_structure.pdb #5/E THR 54 CB relaxed_structure.pdb #5/F GLU 9 OE2 -0.302 3.482
5066relaxed_structure.pdb #5/C CYS 13 HA relaxed_structure.pdb #5/F PRO 53 HD3 -0.306 2.306
5067relaxed_structure.pdb #5/C ILE 11 CG1 relaxed_structure.pdb #5/F PRO 53 HB3 -0.311 3.011
5068relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLY 14 O -0.312 3.017
5069relaxed_structure.pdb #5/A THR 28 HB relaxed_structure.pdb #5/F GLY 31 C -0.313 3.013
5070relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 CD -0.314 3.639
5071relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 CA -0.317 3.642
5072relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 CB -0.318 3.718
5073relaxed_structure.pdb #5/C ILE 11 HG13 relaxed_structure.pdb #5/F PRO 53 HB2 -0.319 2.319
5074relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 HB2 -0.326 3.026
5075relaxed_structure.pdb #5/E VAL 52 HG21 relaxed_structure.pdb #5/F ILE 11 CG2 -0.326 3.026
5076relaxed_structure.pdb #5/C CYS 13 O relaxed_structure.pdb #5/F ALA 15 CB -0.332 3.512
5077relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F CYS 13 C -0.336 3.661
5078relaxed_structure.pdb #5/D LYS 109 HZ2 relaxed_structure.pdb #5/F GLU 19 OE2 -0.338 2.418
5079relaxed_structure.pdb #5/C ALA 35 CB relaxed_structure.pdb #5/F VAL 51 CA -0.340 3.740
5080relaxed_structure.pdb #5/E SER 53 N relaxed_structure.pdb #5/F GLU 9 OE2 -0.349 3.054
5081relaxed_structure.pdb #5/A THR 28 HB relaxed_structure.pdb #5/F GLY 31 CA -0.353 3.053
5082relaxed_structure.pdb #5/C ARG 18 HH22 relaxed_structure.pdb #5/F PRO 18 HG2 -0.353 2.353
5083relaxed_structure.pdb #5/C ILE 11 HB relaxed_structure.pdb #5/F PRO 53 O -0.354 2.834
5084relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F MET 54 SD -0.357 3.139
5085relaxed_structure.pdb #5/C PRO 58 HB3 relaxed_structure.pdb #5/F ILE 11 CD1 -0.364 3.064
5086relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F CYS 13 HA -0.364 3.064
5087relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 CG -0.369 3.694
5088relaxed_structure.pdb #5/C THR 14 HG22 relaxed_structure.pdb #5/F ALA 15 HB3 -0.370 2.370
5089relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 CZ -0.377 3.577
5090relaxed_structure.pdb #5/C ALA 35 N relaxed_structure.pdb #5/F GLY 50 O -0.377 3.082
5091relaxed_structure.pdb #5/C GLN 15 HE21 relaxed_structure.pdb #5/F GLY 14 CA -0.381 3.081
5092relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 CD -0.381 3.706
5093relaxed_structure.pdb #5/C ARG 18 HH22 relaxed_structure.pdb #5/F PRO 18 CG -0.386 3.086
5094relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F PRO 53 CB -0.388 3.088
5095relaxed_structure.pdb #5/E THR 54 HG22 relaxed_structure.pdb #5/F GLU 9 OE1 -0.396 2.876
5096</pre><br/>160 contacts<br>
5097<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A-F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A-F">select #5/A-F</a></div></div>28495 atoms, 28969 bonds, 160 pseudobonds, 1826 residues, 2 models selected<br>
5098<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/A surfaces #5.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/A surfaces #5.1">coulombic #5/A surfaces #5.1</a></div></div>Coulombic values for relaxed_structure.pdb_A SES surface #5.1: minimum, -11.84, mean -0.24, maximum 17.92<br>
5099<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/B surfaces #5.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/B surfaces #5.2">coulombic #5/B surfaces #5.2</a></div></div>Coulombic values for relaxed_structure.pdb_B SES surface #5.2: minimum, -13.17, mean 0.31, maximum 13.60<br>
5100<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/C surfaces #5.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/C surfaces #5.3">coulombic #5/C surfaces #5.3</a></div></div>Coulombic values for relaxed_structure.pdb_C SES surface #5.3: minimum, -14.28, mean 0.87, maximum 12.27<br>
5101<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/D surfaces #5.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/D surfaces #5.4">coulombic #5/D surfaces #5.4</a></div></div>Coulombic values for relaxed_structure.pdb_D SES surface #5.4: minimum, -9.85, mean 2.10, maximum 15.14<br>
5102<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/E surfaces #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/E surfaces #5.5">coulombic #5/E surfaces #5.5</a></div></div>Coulombic values for relaxed_structure.pdb_E SES surface #5.5: minimum, -10.97, mean 1.53, maximum 12.30<br>
5103<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select H">select H</a></div></div>14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected<br>
5104<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!1,5 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!1,5 atoms">hide sel &amp; #!1,5 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A-E">select #5/A-E</a></div></div>27646 atoms, 28113 bonds, 1765 residues, 1 model selected<br>
5105<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.1 models">hide #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.2 models">hide #5.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true</a></div></div><pre>Finding intramodel H-bonds
5106Constraints relaxed by 0.4 angstroms and 20 degrees
5107Models used:
5108 5 relaxed_structure.pdb
5109
511018 H-bonds
5111H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5112relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 OD1 relaxed_structure.pdb #5/A ARG 27 HH11 2.685 1.767
5113relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 OD1 relaxed_structure.pdb #5/A ARG 27 HH21 2.667 1.732
5114relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 O relaxed_structure.pdb #5/A LYS 31 HZ1 2.974 2.326
5115relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 OD2 relaxed_structure.pdb #5/A LYS 31 HZ2 2.680 1.727
5116relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE1 relaxed_structure.pdb #5/C ARG 18 HH11 2.837 1.944
5117relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE2 relaxed_structure.pdb #5/C ARG 18 HH11 2.908 2.025
5118relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 OE2 relaxed_structure.pdb #5/C ARG 18 HH22 2.733 1.757
5119relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F PRO 18 O relaxed_structure.pdb #5/D LYS 109 HZ1 2.828 1.934
5120relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE1 relaxed_structure.pdb #5/D LYS 109 HZ2 2.673 1.723
5121relaxed_structure.pdb #5/E ARG 43 NE relaxed_structure.pdb #5/F GLU 9 OE1 relaxed_structure.pdb #5/E ARG 43 HE 3.322 2.487
5122relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F ALA 7 O relaxed_structure.pdb #5/E ARG 43 HH22 2.862 1.867
5123relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F GLU 9 OE1 relaxed_structure.pdb #5/E ARG 43 HH21 2.749 1.745
5124relaxed_structure.pdb #5/E SER 53 N relaxed_structure.pdb #5/F GLU 9 OE2 relaxed_structure.pdb #5/E SER 53 H 3.054 2.189
5125relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 OE2 relaxed_structure.pdb #5/E THR 54 HG1 2.662 1.709
5126relaxed_structure.pdb #5/F ARG 32 NE relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 HE 2.940 1.942
5127relaxed_structure.pdb #5/F ARG 32 NH1 relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH12 2.844 1.934
5128relaxed_structure.pdb #5/F ARG 32 NH2 relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 HH21 3.342 2.567
5129relaxed_structure.pdb #5/F ARG 32 NH2 relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH22 2.728 1.772
5130</pre><br/>18 hydrogen bonds found<br>
5131<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:7,9,17-19,30,28,30,34</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:7,9,17-19,30,28,30,34">select #5/F:7,9,17-19,30,28,30,34</a></div></div>111 atoms, 106 bonds, 8 residues, 1 model selected<br>
5132<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 111 atom styles<br>
5133<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:28,34</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:28,34">select #5/F:28,34</a></div></div>30 atoms, 28 bonds, 2 residues, 1 model selected<br>
5134<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 30 atom styles<br>
5135<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:32</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:32">select #5/F:32</a></div></div>24 atoms, 23 bonds, 1 residue, 1 model selected<br>
5136<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 24 atom styles<br>
5137<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54</a></div></div>167 atoms, 160 bonds, 9 residues, 1 model selected<br>
5138<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 167 atom styles<br>
5139<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.8 models">hide #5.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 9 items<br>
5140<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:7,9,17-19,30,32</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:7,9,17-19,30,32">select #5/F:7,9,17-19,30,32</a></div></div>105 atoms, 101 bonds, 7 residues, 1 model selected<br>
5141<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 7 items<br>
5142<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :SF4">select :SF4</a></div></div>104 atoms, 156 bonds, 13 residues, 5 models selected<br>
5143<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel &amp; #3#!1 ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel &amp; #3#!1 ball">style sel &amp; #3#!1 ball</a></div></div>Changed 40 atom styles<br>
5144<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel &amp; #3#!1 ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel &amp; #3#!1 ball">style sel &amp; #3#!1 ball</a></div></div>Changed 40 atom styles<br>
5145<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> hbond1</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name hbond1">view name hbond1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> hbond1</div><div class="cxcmd_as_cmd"><a href="cxcmd:view hbond1">view hbond1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> hbond2</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name hbond2">view name hbond2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> hbond3</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name hbond3">view name hbond3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/M:61@FE1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/M:61@FE1">select #1/M:61@FE1</a></div></div>1 atom, 1 residue, 1 model selected<br>
5146<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/M:61@FE2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/M:61@FE2">select #1/M:61@FE2</a></div></div>1 atom, 1 residue, 1 model selected<br>
5147<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/M:61@FE2#3/C:3003@FE2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/M:61@FE2#3/C:3003@FE2">select #1/M:61@FE2#3/C:3003@FE2</a></div></div>2 atoms, 2 residues, 2 models selected<br>
5148<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Distances</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Distances">ui tool show Distances</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> color #797979</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style color #797979">distance style color #797979</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> decimalPlaces 2</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style decimalPlaces 2">distance style decimalPlaces 2</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> radius 0.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style radius 0.2">distance style radius 0.2</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #1/M:61@FE2 #3/C:3003@FE2</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #1/M:61@FE2 #3/C:3003@FE2">distance #1/M:61@FE2 #3/C:3003@FE2</a></div></div>Distance between 2fdn #1/M SF4 61 FE2 and Fe4S4 clusters #3/C SF4 3003 FE2: 11.23Å
5149<br>
5150<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#~distance">~distance</a> #1/M:61@FE2 #3/C:3003@FE2</div><div class="cxcmd_as_cmd"><a href="cxcmd:~distance #1/M:61@FE2 #3/C:3003@FE2">~distance #1/M:61@FE2 #3/C:3003@FE2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/M:61@FE2#3/C:3003@FE1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/M:61@FE2#3/C:3003@FE1">select #1/M:61@FE2#3/C:3003@FE1</a></div></div>2 atoms, 2 residues, 2 models selected<br>
5151<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #1/M:61@FE2 #3/C:3003@FE1</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #1/M:61@FE2 #3/C:3003@FE1">distance #1/M:61@FE2 #3/C:3003@FE1</a></div></div>Distance between 2fdn #1/M SF4 61 FE2 and Fe4S4 clusters #3/C SF4 3003 FE1: 8.79Å
5152<br>
5153<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div>[Repeated 1 time(s)]<p>&mdash;&mdash;&mdash; End of log from Thu Oct 3 09:47:21 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
5154<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><a href="help:user/commands/view.html">view</a> <span style="color:white; background-color:crimson;">hBond1</span></div><font color="crimson"><b>Expected an objects specifier or a view name or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> hbond1</div><div class="cxcmd_as_cmd"><a href="cxcmd:view hbond1">view hbond1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #6.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #6.1 models">hide #6.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> hbond2</div><div class="cxcmd_as_cmd"><a href="cxcmd:view hbond2">view hbond2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> hbond3</div><div class="cxcmd_as_cmd"><a href="cxcmd:view hbond3">view hbond3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.1 models">show #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.2 models">show #5.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.5">select add #5.5</a></div></div>1059 atoms, 66 residues, 1 model selected<br>
5155<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.4">select add #5.4</a></div></div>3336 atoms, 209 residues, 2 models selected<br>
5156<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.3">select add #5.3</a></div></div>4550 atoms, 289 residues, 3 models selected<br>
5157<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.2">select add #5.2</a></div></div>16065 atoms, 1022 residues, 4 models selected<br>
5158<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.1">select add #5.1</a></div></div>27646 atoms, 1765 residues, 5 models selected<br>
5159<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 20">transparency (#!5 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 30">transparency (#!5 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/graphics.html#silhouettes">graphics silhouettes</a> false</div><div class="cxcmd_as_cmd"><a href="cxcmd:graphics silhouettes false">graphics silhouettes false</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/graphics.html#silhouettes">graphics silhouettes</a> true</div><div class="cxcmd_as_cmd"><a href="cxcmd:graphics silhouettes true">graphics silhouettes true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F">select #2/F</a></div></div>1633 atoms, 1673 bonds, 9 pseudobonds, 164 residues, 2 models selected<br>
5160<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/J</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/J">select #2/J</a></div></div>528 atoms, 546 bonds, 5 pseudobonds, 46 residues, 2 models selected<br>
5161<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:BCR</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:BCR">select #2:BCR</a></div></div>1080 atoms, 1107 bonds, 27 residues, 1 model selected<br>
5162<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:BCR,LUT</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:BCR,LUT">select #2:BCR,LUT</a></div></div>1374 atoms, 1408 bonds, 34 residues, 1 model selected<br>
5163<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel orange</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel orange">color sel orange</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/F surfaces #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/F surfaces #5.6">coulombic #5/F surfaces #5.6</a></div></div>Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum, -13.89, mean -3.67, maximum 7.01<br>
5164<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.7">select subtract #5.7</a></div></div>Nothing selected<br>
5165<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.6">select add #5.6</a></div></div>849 atoms, 61 residues, 1 model selected<br>
5166<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 30">transparency (#!5 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.2 models">hide #5.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.1 models">hide #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.1 models">show #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.2 models">show #5.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name front">view name front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 180">turn x 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name back">view name back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/I/H/L</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/I/H/L">select #2/I/H/L</a></div></div>2569 atoms, 2652 bonds, 18 pseudobonds, 292 residues, 2 models selected<br>
5167<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name back">view name back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name back">view name back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Thu Oct 3 21:28:49 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
5168<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><a href="help:user/commands/view.html">view</a> <span style="color:white; background-color:crimson;">backZoom</span></div><font color="crimson"><b>Expected an objects specifier or a view name or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> hbond2</div><div class="cxcmd_as_cmd"><a href="cxcmd:view hbond2">view hbond2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!18 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!18 models">show #!18 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #6 id #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #6 id #8">rename #6 id #8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #8">select add #8</a></div></div>2569 atoms, 2652 bonds, 19 pseudobonds, 292 residues, 4 models selected<br>
5169<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8.1 models">show #8.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1 id #6</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1 id #6">rename #1 id #6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 id #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 id #1">rename #2 id #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 id #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 id #2">rename #3 id #2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #4 id #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #4 id #3">rename #4 id #3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #18 id #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #18 id #4">rename #18 id #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!6 to #5/B pairing bs</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!6 to #5/B pairing bs">matchmaker #!6 to #5/B pairing bs</a></div></div>
5170 <table border=1 cellpadding=4 cellspacing=0>
5171 <tr>
5172 <th colspan="2">Parameters</th>
5173 </tr>
5174 <tr>
5175 <td>Chain pairing</td>
5176 <td>bs</td>
5177 </tr>
5178 <tr>
5179 <td>Alignment algorithm</td>
5180 <td>Needleman-Wunsch</td>
5181 </tr>
5182 <tr>
5183 <td>Similarity matrix</td>
5184 <td>BLOSUM-62</td>
5185 </tr>
5186
5187 <tr>
5188 <td>SS fraction</td>
5189 <td>0.3</td>
5190 </tr>
5191 <tr>
5192 <td>Gap open (HH/SS/other)</td>
5193 <td>18/18/6</td>
5194 </tr>
5195 <tr>
5196 <td>Gap extend</td>
5197 <td>1</td>
5198 </tr>
5199 <tr>
5200 <td>SS matrix</td>
5201 <td>
5202 <table>
5203 <tr>
5204 <th></th> <th>H</th> <th>S</th> <th>O</th>
5205 </tr>
5206 <tr>
5207 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
5208 </tr>
5209 <tr>
5210 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
5211 </tr>
5212 <tr>
5213 <th>O</th> <td></td> <td></td> <td align="right">4</td>
5214 </tr>
5215 </table>
5216 </td>
5217 </tr>
5218
5219 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
5220 </table>
5221 <br/>Matchmaker relaxed_structure.pdb, chain B (#5) with 2fdn, chain M (#6), sequence alignment score = 4<br>
5222<font color="crimson"><b>Fewer than 3 residues aligned; cannot match relaxed_structure.pdb, chain B with 2fdn, chain M<br>
5223</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!6 to #5/F pairing bs</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!6 to #5/F pairing bs">matchmaker #!6 to #5/F pairing bs</a></div></div>
5224 <table border=1 cellpadding=4 cellspacing=0>
5225 <tr>
5226 <th colspan="2">Parameters</th>
5227 </tr>
5228 <tr>
5229 <td>Chain pairing</td>
5230 <td>bs</td>
5231 </tr>
5232 <tr>
5233 <td>Alignment algorithm</td>
5234 <td>Needleman-Wunsch</td>
5235 </tr>
5236 <tr>
5237 <td>Similarity matrix</td>
5238 <td>BLOSUM-62</td>
5239 </tr>
5240
5241 <tr>
5242 <td>SS fraction</td>
5243 <td>0.3</td>
5244 </tr>
5245 <tr>
5246 <td>Gap open (HH/SS/other)</td>
5247 <td>18/18/6</td>
5248 </tr>
5249 <tr>
5250 <td>Gap extend</td>
5251 <td>1</td>
5252 </tr>
5253 <tr>
5254 <td>SS matrix</td>
5255 <td>
5256 <table>
5257 <tr>
5258 <th></th> <th>H</th> <th>S</th> <th>O</th>
5259 </tr>
5260 <tr>
5261 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
5262 </tr>
5263 <tr>
5264 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
5265 </tr>
5266 <tr>
5267 <th>O</th> <td></td> <td></td> <td align="right">4</td>
5268 </tr>
5269 </table>
5270 </td>
5271 </tr>
5272
5273 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
5274 </table>
5275 <br/>Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 170.3<br>
5276RMSD between 41 pruned atom pairs is 0.850 angstroms; (across all 54 pairs: 2.909)<br>
5277<br>
5278<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5@@draw_mode=0</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5@@draw_mode=0">select #5@@draw_mode=0</a></div></div>28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected<br>
5279<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.1 models">hide #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.7 models">hide #5.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.7">select subtract #5.7</a></div></div>28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 8 models selected<br>
5280<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.6">select subtract #5.6</a></div></div>27425 atoms, 27831 bonds, 1756 residues, 7 models selected<br>
5281<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.5">select subtract #5.5</a></div></div>26415 atoms, 26811 bonds, 1693 residues, 6 models selected<br>
5282<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.4">select subtract #5.4</a></div></div>24160 atoms, 24526 bonds, 1551 residues, 5 models selected<br>
5283<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.3">select subtract #5.3</a></div></div>23024 atoms, 23432 bonds, 1472 residues, 4 models selected<br>
5284<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.2">select subtract #5.2</a></div></div>11509 atoms, 11705 bonds, 739 residues, 3 models selected<br>
5285<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.1">select subtract #5.1</a></div></div>1 model selected<br>
5286<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.2 models">hide #5.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A-F@@draw_mode=0</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A-F@@draw_mode=0">select #5/A-F@@draw_mode=0</a></div></div>28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected<br>
5287<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.7">select subtract #5.7</a></div></div>Nothing selected<br>
5288<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:1-55@@draw_mode=0</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:1-55@@draw_mode=0">select #5/F:1-55@@draw_mode=0</a></div></div>600 atoms, 555 bonds, 48 residues, 1 model selected<br>
5289<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5 &amp;protein &amp;@@draw_mode=0</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5 &amp;protein &amp;@@draw_mode=0">select #5 &amp;protein &amp;@@draw_mode=0</a></div></div>28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected<br>
5290<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:1-100 &amp;@@draw_mode=0</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:1-100 &amp;@@draw_mode=0">select #5/C:1-100 &amp;@@draw_mode=0</a></div></div>1136 atoms, 1094 bonds, 79 residues, 1 model selected<br>
5291<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:1-100@@draw_mode=0</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:1-100@@draw_mode=0">select #5/C:1-100@@draw_mode=0</a></div></div>1136 atoms, 1094 bonds, 79 residues, 1 model selected<br>
5292<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.3">select subtract #5.3</a></div></div>1 model selected<br>
5293<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:1-100@@draw_mode=0</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:1-100@@draw_mode=0">select #5/C:1-100@@draw_mode=0</a></div></div>1136 atoms, 1094 bonds, 79 residues, 1 model selected<br>
5294<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,14-15,34-35/E:52/F:8,52-54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,14-15,34-35/E:52/F:8,52-54">select #5/C:11,14-15,34-35/E:52/F:8,52-54</a></div></div>154 atoms, 149 bonds, 17 pseudobonds, 10 residues, 2 models selected<br>
5295<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,14-15,34-35/E:52/F:8,51-54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,14-15,34-35/E:52/F:8,51-54">select #5/C:11,14-15,34-35/E:52/F:8,51-54</a></div></div>170 atoms, 165 bonds, 22 pseudobonds, 11 residues, 2 models selected<br>
5296<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,14-15,34-35/E:52/F:8,51,53,54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,14-15,34-35/E:52/F:8,51,53,54">select #5/C:11,14-15,34-35/E:52/F:8,51,53,54</a></div></div>159 atoms, 153 bonds, 22 pseudobonds, 10 residues, 2 models selected<br>
5297<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54">select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54</a></div></div>169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 2 models selected<br>
5298<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.7">select subtract #5.7</a></div></div>169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 5 models selected<br>
5299<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.6">select subtract #5.6</a></div></div>98 atoms, 94 bonds, 6 residues, 4 models selected<br>
5300<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.5">select subtract #5.5</a></div></div>82 atoms, 79 bonds, 5 residues, 3 models selected<br>
5301<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.3">select subtract #5.3</a></div></div>1 model selected<br>
5302<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54">select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54</a></div></div>169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 2 models selected<br>
5303<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54">select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54</a></div></div>202 atoms, 194 bonds, 40 pseudobonds, 13 residues, 2 models selected<br>
5304<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select H">select H</a></div></div>14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected<br>
5305<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!5-6 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!5-6 atoms">hide sel &amp; #!5-6 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel &amp; #!5-6 stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel &amp; #!5-6 stick">style sel &amp; #!5-6 stick</a></div></div>Changed 14343 atom styles<br>
5306<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54">select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54</a></div></div>202 atoms, 194 bonds, 40 pseudobonds, 13 residues, 2 models selected<br>
5307<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 202 atom styles<br>
5308<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:Cys">select #5/F:Cys</a></div></div>88 atoms, 80 bonds, 8 residues, 1 model selected<br>
5309<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:Cys|#6:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:Cys|#6:Cys">select #5/F:Cys|#6:Cys</a></div></div>168 atoms, 152 bonds, 16 residues, 2 models selected<br>
5310<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!6 &amp; sel to #5/B &amp; sel pairing bs</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!6 &amp; sel to #5/B &amp; sel pairing bs">matchmaker #!6 &amp; sel to #5/B &amp; sel pairing bs</a></div></div><font color="crimson"><b>No &#x27;to&#x27; chains specified<br>
5311</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!6 &amp; sel to #5/F &amp; sel pairing bs</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!6 &amp; sel to #5/F &amp; sel pairing bs">matchmaker #!6 &amp; sel to #5/F &amp; sel pairing bs</a></div></div>
5312 <table border=1 cellpadding=4 cellspacing=0>
5313 <tr>
5314 <th colspan="2">Parameters</th>
5315 </tr>
5316 <tr>
5317 <td>Chain pairing</td>
5318 <td>bs</td>
5319 </tr>
5320 <tr>
5321 <td>Alignment algorithm</td>
5322 <td>Needleman-Wunsch</td>
5323 </tr>
5324 <tr>
5325 <td>Similarity matrix</td>
5326 <td>BLOSUM-62</td>
5327 </tr>
5328
5329 <tr>
5330 <td>SS fraction</td>
5331 <td>0.3</td>
5332 </tr>
5333 <tr>
5334 <td>Gap open (HH/SS/other)</td>
5335 <td>18/18/6</td>
5336 </tr>
5337 <tr>
5338 <td>Gap extend</td>
5339 <td>1</td>
5340 </tr>
5341 <tr>
5342 <td>SS matrix</td>
5343 <td>
5344 <table>
5345 <tr>
5346 <th></th> <th>H</th> <th>S</th> <th>O</th>
5347 </tr>
5348 <tr>
5349 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
5350 </tr>
5351 <tr>
5352 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
5353 </tr>
5354 <tr>
5355 <th>O</th> <td></td> <td></td> <td align="right">4</td>
5356 </tr>
5357 </table>
5358 </td>
5359 </tr>
5360
5361 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
5362 </table>
5363 <br/>Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 48<br>
5364RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)<br>
5365<br>
5366<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:Cys">select #6:Cys</a></div></div>80 atoms, 72 bonds, 8 residues, 1 model selected<br>
5367<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:11-14</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:11-14">select #5:11-14</a></div></div>355 atoms, 352 bonds, 24 residues, 1 model selected<br>
5368<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 355 atom styles<br>
5369<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select H">select H</a></div></div>14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected<br>
5370<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> (#!5 &amp; sel) target a</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide (#!5 &amp; sel) target a">hide (#!5 &amp; sel) target a</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Fri Oct 4 09:37:44 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
5371<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:13</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:13">select #5/F:13</a></div></div>11 atoms, 10 bonds, 1 residue, 1 model selected<br>
5372<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Rotamers</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Rotamers">ui tool show Rotamers</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/swapaa.html#interactive">swapaa interactive</a> sel CYH rotLib Dunbrack</div><div class="cxcmd_as_cmd"><a href="cxcmd:swapaa interactive sel CYH rotLib Dunbrack">swapaa interactive sel CYH rotLib Dunbrack</a></div></div>relaxed_structure.pdb #5/F CYS 13: phi -84.1, psi 65.7 trans<br>
5373Changed 9 bond radii<br>
5374<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/swapaa.html">swapaa</a> #!5/F:13 CYH criteria 2 rotLib Dunbrack</div><div class="cxcmd_as_cmd"><a href="cxcmd:swapaa #!5/F:13 CYH criteria 2 rotLib Dunbrack">swapaa #!5/F:13 CYH criteria 2 rotLib Dunbrack</a></div></div>Using Dunbrack library<br>
5375relaxed_structure.pdb #!5/F CYS 13: phi -84.1, psi 65.7 trans<br>
5376Applying CYS rotamer (chi angles: -178.7) to relaxed_structure.pdb #!5/F CYS 13<br>
5377<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:Cys">select #6:Cys</a></div></div>80 atoms, 72 bonds, 8 residues, 1 model selected<br>
5378<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:Cys|#6:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:Cys|#6:Cys">select #5/F:Cys|#6:Cys</a></div></div>165 atoms, 149 bonds, 16 residues, 2 models selected<br>
5379<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!6 &amp; sel to #5/F &amp; sel pairing bs</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!6 &amp; sel to #5/F &amp; sel pairing bs">matchmaker #!6 &amp; sel to #5/F &amp; sel pairing bs</a></div></div>
5380 <table border=1 cellpadding=4 cellspacing=0>
5381 <tr>
5382 <th colspan="2">Parameters</th>
5383 </tr>
5384 <tr>
5385 <td>Chain pairing</td>
5386 <td>bs</td>
5387 </tr>
5388 <tr>
5389 <td>Alignment algorithm</td>
5390 <td>Needleman-Wunsch</td>
5391 </tr>
5392 <tr>
5393 <td>Similarity matrix</td>
5394 <td>BLOSUM-62</td>
5395 </tr>
5396
5397 <tr>
5398 <td>SS fraction</td>
5399 <td>0.3</td>
5400 </tr>
5401 <tr>
5402 <td>Gap open (HH/SS/other)</td>
5403 <td>18/18/6</td>
5404 </tr>
5405 <tr>
5406 <td>Gap extend</td>
5407 <td>1</td>
5408 </tr>
5409 <tr>
5410 <td>SS matrix</td>
5411 <td>
5412 <table>
5413 <tr>
5414 <th></th> <th>H</th> <th>S</th> <th>O</th>
5415 </tr>
5416 <tr>
5417 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
5418 </tr>
5419 <tr>
5420 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
5421 </tr>
5422 <tr>
5423 <th>O</th> <td></td> <td></td> <td align="right">4</td>
5424 </tr>
5425 </table>
5426 </td>
5427 </tr>
5428
5429 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
5430 </table>
5431 <br/>Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 48<br>
5432RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)<br>
5433<br>
5434<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!6 &amp; sel to #5/F &amp; sel pairing bs</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!6 &amp; sel to #5/F &amp; sel pairing bs">matchmaker #!6 &amp; sel to #5/F &amp; sel pairing bs</a></div></div>
5435 <table border=1 cellpadding=4 cellspacing=0>
5436 <tr>
5437 <th colspan="2">Parameters</th>
5438 </tr>
5439 <tr>
5440 <td>Chain pairing</td>
5441 <td>bs</td>
5442 </tr>
5443 <tr>
5444 <td>Alignment algorithm</td>
5445 <td>Needleman-Wunsch</td>
5446 </tr>
5447 <tr>
5448 <td>Similarity matrix</td>
5449 <td>BLOSUM-62</td>
5450 </tr>
5451
5452 <tr>
5453 <td>SS fraction</td>
5454 <td>0.3</td>
5455 </tr>
5456 <tr>
5457 <td>Gap open (HH/SS/other)</td>
5458 <td>18/18/6</td>
5459 </tr>
5460 <tr>
5461 <td>Gap extend</td>
5462 <td>1</td>
5463 </tr>
5464 <tr>
5465 <td>SS matrix</td>
5466 <td>
5467 <table>
5468 <tr>
5469 <th></th> <th>H</th> <th>S</th> <th>O</th>
5470 </tr>
5471 <tr>
5472 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
5473 </tr>
5474 <tr>
5475 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
5476 </tr>
5477 <tr>
5478 <th>O</th> <td></td> <td></td> <td align="right">4</td>
5479 </tr>
5480 </table>
5481 </td>
5482 </tr>
5483
5484 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
5485 </table>
5486 <br/>Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 48<br>
5487RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)<br>
5488<br>
5489<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!6 &amp; sel to #5/F &amp; sel pairing bs</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!6 &amp; sel to #5/F &amp; sel pairing bs">matchmaker #!6 &amp; sel to #5/F &amp; sel pairing bs</a></div></div>
5490 <table border=1 cellpadding=4 cellspacing=0>
5491 <tr>
5492 <th colspan="2">Parameters</th>
5493 </tr>
5494 <tr>
5495 <td>Chain pairing</td>
5496 <td>bs</td>
5497 </tr>
5498 <tr>
5499 <td>Alignment algorithm</td>
5500 <td>Needleman-Wunsch</td>
5501 </tr>
5502 <tr>
5503 <td>Similarity matrix</td>
5504 <td>BLOSUM-62</td>
5505 </tr>
5506
5507 <tr>
5508 <td>SS fraction</td>
5509 <td>0.3</td>
5510 </tr>
5511 <tr>
5512 <td>Gap open (HH/SS/other)</td>
5513 <td>18/18/6</td>
5514 </tr>
5515 <tr>
5516 <td>Gap extend</td>
5517 <td>1</td>
5518 </tr>
5519 <tr>
5520 <td>SS matrix</td>
5521 <td>
5522 <table>
5523 <tr>
5524 <th></th> <th>H</th> <th>S</th> <th>O</th>
5525 </tr>
5526 <tr>
5527 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
5528 </tr>
5529 <tr>
5530 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
5531 </tr>
5532 <tr>
5533 <th>O</th> <td></td> <td></td> <td align="right">4</td>
5534 </tr>
5535 </table>
5536 </td>
5537 </tr>
5538
5539 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
5540 </table>
5541 <br/>Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 48<br>
5542RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs: 1.008)<br>
5543<br>
5544<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name front">view name front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 30">turn x 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.1 models">show #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.2 models">show #5.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #5/F surfaces #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #5/F surfaces #5.6">coulombic #5/F surfaces #5.6</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
5545Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum, -13.91, mean -3.63, maximum 7.03<br>
5546<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5-6 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5-6 &amp; sel) 30">transparency (#!5-6 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.6">select add #5.6</a></div></div>844 atoms, 61 residues, 1 model selected<br>
5547<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 30">transparency (#!5 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name back">view name back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#list">view list</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view list">view list</a></div></div>Named views: <a href="cxcmd:view back">back</a>, <a href="cxcmd:view front">front</a>, <a href="cxcmd:view hbond1">hbond1</a>, <a href="cxcmd:view hbond2">hbond2</a>, <a href="cxcmd:view hbond3">hbond3</a><br/><div class="cxcmd"><a href="help:user/commands/view.html#delete">view delete</a> hbond1 <span style="color:white; background-color:crimson;">hbond2 hbond3</span></div><font color="crimson"><b>Expected fewer arguments</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#list">view list</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view list">view list</a></div></div>Named views: <a href="cxcmd:view back">back</a>, <a href="cxcmd:view front">front</a>, <a href="cxcmd:view hbond1">hbond1</a>, <a href="cxcmd:view hbond2">hbond2</a>, <a href="cxcmd:view hbond3">hbond3</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#delete">view delete</a> hbond1</div><div class="cxcmd_as_cmd"><a href="cxcmd:view delete hbond1">view delete hbond1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#delete">view delete</a> hbond2</div><div class="cxcmd_as_cmd"><a href="cxcmd:view delete hbond2">view delete hbond2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#delete">view delete</a> hbond3</div><div class="cxcmd_as_cmd"><a href="cxcmd:view delete hbond3">view delete hbond3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#list">view list</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view list">view list</a></div></div>Named views: <a href="cxcmd:view back">back</a>, <a href="cxcmd:view front">front</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.8 models">show #5.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.8">select add #5.8</a></div></div>160 pseudobonds, 1 model selected<br>
5548<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.7">select subtract #5.7</a></div></div>160 pseudobonds, 1 model selected<br>
5549<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Fri Oct 4 10:09:32 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
5550<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A-E">select #5/A-E</a></div></div>27646 atoms, 28113 bonds, 1765 residues, 1 model selected<br>
5551<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A-E &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A-E &amp;~H">select #5/A-E &amp;~H</a></div></div>13989 atoms, 14456 bonds, 1765 residues, 1 model selected<br>
5552<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Contacts">ui tool show Contacts</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel setAttrs true restrict &quot;#5/F &amp;~H&quot; resSeparation 5 interModel false intraMol false select true color #76d6ff radius 0.2 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel setAttrs true restrict &quot;#5/F &amp;~H&quot; resSeparation 5 interModel false intraMol false select true color #76d6ff radius 0.2 reveal true log true">contacts sel setAttrs true restrict &quot;#5/F &amp;~H&quot; resSeparation 5 interModel false intraMol false select true color #76d6ff radius 0.2 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
5553H-bond overlap reduction: 0.4
5554Ignore contacts between atoms separated by 4 bonds or less
5555Ignore contacts between atoms in residues less than 5 apart in sequence
5556Detect intra-residue contacts: False
5557Detect intra-molecule contacts: False
5558
555966 contacts
5560 atom1 atom2 overlap distance
5561relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 CD 0.340 2.985
5562relaxed_structure.pdb #5/C PRO 58 CB relaxed_structure.pdb #5/F ILE 11 CD1 0.169 3.231
5563relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 N 0.152 3.098
5564relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 CD 0.062 3.263
5565relaxed_structure.pdb #5/A ARG 27 CZ relaxed_structure.pdb #5/F ASP 30 OD1 0.055 3.125
5566relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 OD1 0.038 2.667
5567relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F SER 12 O 0.034 3.146
5568relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE1 0.032 2.673
5569relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 OD2 0.025 2.680
5570relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 OD1 0.020 2.685
5571relaxed_structure.pdb #5/C LYS 34 C relaxed_structure.pdb #5/F GLY 50 O 0.019 3.161
5572relaxed_structure.pdb #5/C PRO 58 CG relaxed_structure.pdb #5/F ILE 11 CD1 0.015 3.385
5573relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE2 0.011 2.694
5574relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 CD -0.001 3.201
5575relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 NH2 -0.023 2.728
5576relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 OE2 -0.028 2.733
5577relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F GLU 9 OE1 -0.044 2.749
5578relaxed_structure.pdb #5/C ARG 18 CZ relaxed_structure.pdb #5/F GLY 14 O -0.062 3.242
5579relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 CG -0.076 3.401
5580relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 CZ -0.080 3.260
5581relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 OE2 -0.082 2.662
5582relaxed_structure.pdb #5/E SER 53 C relaxed_structure.pdb #5/F GLU 9 OE2 -0.087 3.267
5583relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F ALA 15 N -0.094 3.344
5584relaxed_structure.pdb #5/C ARG 18 CZ relaxed_structure.pdb #5/F GLU 17 OE2 -0.103 3.283
5585relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 C -0.122 3.447
5586relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F PRO 18 O -0.123 2.828
5587relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE1 -0.132 2.837
5588relaxed_structure.pdb #5/C ILE 11 CG1 relaxed_structure.pdb #5/F PRO 53 CB -0.134 3.534
5589relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 CG -0.138 3.463
5590relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 NH1 -0.139 2.844
5591relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F MET 54 CE -0.150 3.350
5592relaxed_structure.pdb #5/C GLN 15 CG relaxed_structure.pdb #5/F SER 12 O -0.153 3.333
5593relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F ALA 7 O -0.157 2.862
5594relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F PRO 53 CB -0.177 3.577
5595relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F THR 8 CA -0.185 3.510
5596relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE2 -0.203 2.908
5597relaxed_structure.pdb #5/E THR 54 O relaxed_structure.pdb #5/F MET 54 CE -0.206 3.386
5598relaxed_structure.pdb #5/C GLN 15 OE1 relaxed_structure.pdb #5/F SER 12 O -0.206 3.166
5599relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F GLY 14 N -0.207 3.532
5600relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 CA -0.208 3.533
5601relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 NE -0.215 2.940
5602relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F MET 54 SD -0.218 3.700
5603relaxed_structure.pdb #5/C LYS 34 CB relaxed_structure.pdb #5/F GLY 50 O -0.221 3.401
5604relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 CB -0.230 3.410
5605relaxed_structure.pdb #5/E THR 54 CG2 relaxed_structure.pdb #5/F GLU 9 OE1 -0.230 3.410
5606relaxed_structure.pdb #5/E SER 53 CA relaxed_structure.pdb #5/F GLU 9 OE2 -0.230 3.410
5607relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 CG -0.231 3.631
5608relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 CG -0.235 3.560
5609relaxed_structure.pdb #5/C ALA 35 CA relaxed_structure.pdb #5/F GLY 50 O -0.243 3.423
5610relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 CA -0.247 3.427
5611relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 O -0.269 2.974
5612relaxed_structure.pdb #5/E THR 54 N relaxed_structure.pdb #5/F GLU 9 OE2 -0.285 2.990
5613relaxed_structure.pdb #5/E ARG 43 CZ relaxed_structure.pdb #5/F GLU 9 OE1 -0.291 3.471
5614relaxed_structure.pdb #5/E THR 54 CB relaxed_structure.pdb #5/F GLU 9 OE2 -0.302 3.482
5615relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLY 14 O -0.312 3.017
5616relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 CD -0.314 3.639
5617relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 CA -0.317 3.642
5618relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 CB -0.318 3.718
5619relaxed_structure.pdb #5/C CYS 13 O relaxed_structure.pdb #5/F ALA 15 CB -0.332 3.512
5620relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F CYS 13 C -0.336 3.661
5621relaxed_structure.pdb #5/C ALA 35 CB relaxed_structure.pdb #5/F VAL 51 CA -0.340 3.740
5622relaxed_structure.pdb #5/E SER 53 N relaxed_structure.pdb #5/F GLU 9 OE2 -0.349 3.054
5623relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 CG -0.369 3.694
5624relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 CZ -0.377 3.577
5625relaxed_structure.pdb #5/C ALA 35 N relaxed_structure.pdb #5/F GLY 50 O -0.377 3.082
5626relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 CD -0.381 3.706
5627</pre><br/>66 contacts<br>
5628<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 75 atom styles<br>
5629<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> contacts sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen contacts sel">name frozen contacts sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:select contacts">select contacts</a></div></div>16975 atoms, 38 bonds, 66 pseudobonds, 1093 residues, 2 models selected<br>
5630<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user/selectcontacts.html</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user/selectcontacts.html">help help:user/selectcontacts.html</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/interfaces.html#select">interfaces select</a> #5/A &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:interfaces select #5/A &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0">interfaces select #5/A &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</a></div></div>4 contacting residues<br>
5631<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:select contacts">select contacts</a></div></div>16975 atoms, 38 bonds, 66 pseudobonds, 1093 residues, 2 models selected<br>
5632<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 16975 atom styles<br>
5633<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.8 models">hide #5.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5.8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5.8">select subtract #5.8</a></div></div>16975 atoms, 38 bonds, 1093 residues, 6 models selected<br>
5634<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #5.8</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #5.8">close #5.8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.9 models">hide #5.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.9 models">show #5.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #5.9</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #5.9">close #5.9</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #5.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #5.7">close #5.7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A-E">select #5/A-E</a></div></div>27646 atoms, 28113 bonds, 1765 residues, 1 model selected<br>
5635<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true</a></div></div><pre>Finding intramodel H-bonds
5636Constraints relaxed by 0.4 angstroms and 20 degrees
5637Models used:
5638 5 relaxed_structure.pdb
5639
564019 H-bonds
5641H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5642relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 OD1 relaxed_structure.pdb #5/A ARG 27 HH11 2.685 1.767
5643relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 OD1 relaxed_structure.pdb #5/A ARG 27 HH21 2.667 1.732
5644relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 O relaxed_structure.pdb #5/A LYS 31 HZ1 2.974 2.326
5645relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 OD2 relaxed_structure.pdb #5/A LYS 31 HZ2 2.680 1.727
5646relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE1 relaxed_structure.pdb #5/C ARG 18 HH11 2.837 1.944
5647relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE2 relaxed_structure.pdb #5/C ARG 18 HH11 2.908 2.025
5648relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 OE2 relaxed_structure.pdb #5/C ARG 18 HH22 2.733 1.757
5649relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F PRO 18 O relaxed_structure.pdb #5/D LYS 109 HZ1 2.828 1.934
5650relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE1 relaxed_structure.pdb #5/D LYS 109 HZ2 2.673 1.723
5651relaxed_structure.pdb #5/E ARG 43 NE relaxed_structure.pdb #5/F GLU 9 OE1 relaxed_structure.pdb #5/E ARG 43 HE 3.322 2.487
5652relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F ALA 7 O relaxed_structure.pdb #5/E ARG 43 HH22 2.862 1.867
5653relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F GLU 9 OE1 relaxed_structure.pdb #5/E ARG 43 HH21 2.749 1.745
5654relaxed_structure.pdb #5/E SER 53 N relaxed_structure.pdb #5/F GLU 9 OE2 relaxed_structure.pdb #5/E SER 53 H 3.054 2.189
5655relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 OE2 relaxed_structure.pdb #5/E THR 54 HG1 2.662 1.709
5656relaxed_structure.pdb #5/F CYS 13 SG relaxed_structure.pdb #5/C CYS 13 O no hydrogen 3.816 N/A
5657relaxed_structure.pdb #5/F ARG 32 NE relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 HE 2.940 1.942
5658relaxed_structure.pdb #5/F ARG 32 NH1 relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH12 2.844 1.934
5659relaxed_structure.pdb #5/F ARG 32 NH2 relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 HH21 3.342 2.567
5660relaxed_structure.pdb #5/F ARG 32 NH2 relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH22 2.728 1.772
5661</pre><br/>19 hydrogen bonds found<br>
5662<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</a></div></div>272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected<br>
5663<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select H">select H</a></div></div>14612 atoms, 1922 residues, 3 models selected<br>
5664<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!5-6 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!5-6 atoms">hide sel &amp; #!5-6 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A-E">select #5/A-E</a></div></div>27646 atoms, 28113 bonds, 1765 residues, 1 model selected<br>
5665<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff restrict #5/F interModel false intraMol false intraRes false reveal true log true</a></div></div><pre>Finding intramodel H-bonds
5666Constraints relaxed by 0.4 angstroms and 20 degrees
5667Models used:
5668 5 relaxed_structure.pdb
5669
567019 H-bonds
5671H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5672relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 OD1 relaxed_structure.pdb #5/A ARG 27 HH11 2.685 1.767
5673relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 OD1 relaxed_structure.pdb #5/A ARG 27 HH21 2.667 1.732
5674relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 O relaxed_structure.pdb #5/A LYS 31 HZ1 2.974 2.326
5675relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 OD2 relaxed_structure.pdb #5/A LYS 31 HZ2 2.680 1.727
5676relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE1 relaxed_structure.pdb #5/C ARG 18 HH11 2.837 1.944
5677relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE2 relaxed_structure.pdb #5/C ARG 18 HH11 2.908 2.025
5678relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 OE2 relaxed_structure.pdb #5/C ARG 18 HH22 2.733 1.757
5679relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F PRO 18 O relaxed_structure.pdb #5/D LYS 109 HZ1 2.828 1.934
5680relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE1 relaxed_structure.pdb #5/D LYS 109 HZ2 2.673 1.723
5681relaxed_structure.pdb #5/E ARG 43 NE relaxed_structure.pdb #5/F GLU 9 OE1 relaxed_structure.pdb #5/E ARG 43 HE 3.322 2.487
5682relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F ALA 7 O relaxed_structure.pdb #5/E ARG 43 HH22 2.862 1.867
5683relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F GLU 9 OE1 relaxed_structure.pdb #5/E ARG 43 HH21 2.749 1.745
5684relaxed_structure.pdb #5/E SER 53 N relaxed_structure.pdb #5/F GLU 9 OE2 relaxed_structure.pdb #5/E SER 53 H 3.054 2.189
5685relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 OE2 relaxed_structure.pdb #5/E THR 54 HG1 2.662 1.709
5686relaxed_structure.pdb #5/F CYS 13 SG relaxed_structure.pdb #5/C CYS 13 O no hydrogen 3.816 N/A
5687relaxed_structure.pdb #5/F ARG 32 NE relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 HE 2.940 1.942
5688relaxed_structure.pdb #5/F ARG 32 NH1 relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH12 2.844 1.934
5689relaxed_structure.pdb #5/F ARG 32 NH2 relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 HH21 3.342 2.567
5690relaxed_structure.pdb #5/F ARG 32 NH2 relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH22 2.728 1.772
5691</pre><br/>19 hydrogen bonds found<br>
5692<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</a></div></div>272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected<br>
5693<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 272 atom styles<br>
5694<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 272 atom styles<br>
5695<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> hBonds sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen hBonds sel">name frozen hBonds sel</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#delete">name delete</a> all</div><div class="cxcmd_as_cmd"><a href="cxcmd:name delete all">name delete all</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</a></div></div>272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected<br>
5696<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> Hbonds sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen Hbonds sel">name frozen Hbonds sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/interfaces.html#select">interfaces select</a> #5/A &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:interfaces select #5/A &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0">interfaces select #5/A &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</a></div></div>4 contacting residues<br>
5697<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.1 models">hide #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.2 models">hide #5.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/interfaces.html#select">interfaces select</a> #5/B &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:interfaces select #5/B &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0">interfaces select #5/B &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</a></div></div>0 contacting residues<br>
5698<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/interfaces.html#select">interfaces select</a> #5/C &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:interfaces select #5/C &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0">interfaces select #5/C &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</a></div></div>9 contacting residues<br>
5699<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#residues">info residues</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:info residues sel">info residues sel</a></div></div>residue id #5/C:11 name ILE index 10<br>
5700residue id #5/C:13 name CYS index 12<br>
5701residue id #5/C:14 name THR index 13<br>
5702residue id #5/C:15 name GLN index 14<br>
5703residue id #5/C:18 name ARG index 17<br>
5704residue id #5/C:34 name LYS index 33<br>
5705residue id #5/C:35 name ALA index 34<br>
5706residue id #5/C:37 name GLN index 36<br>
5707residue id #5/C:58 name PRO index 57<br>
5708<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/interfaces.html#select">interfaces select</a> #5/C#5/F &amp; ::polymer_type&gt;0 contacting #1/1 &amp; ::polymer_type&gt;0 areaCutoff 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:interfaces select #5/C#5/F &amp; ::polymer_type&gt;0 contacting #1/1 &amp; ::polymer_type&gt;0 areaCutoff 0">interfaces select #5/C#5/F &amp; ::polymer_type&gt;0 contacting #1/1 &amp; ::polymer_type&gt;0 areaCutoff 0</a></div></div>0 contacting residues<br>
5709<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/interfaces.html#select">interfaces select</a> #5/F &amp; ::polymer_type&gt;0 contacting #5/C &amp; ::polymer_type&gt;0 areaCutoff 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:interfaces select #5/F &amp; ::polymer_type&gt;0 contacting #5/C &amp; ::polymer_type&gt;0 areaCutoff 0">interfaces select #5/F &amp; ::polymer_type&gt;0 contacting #5/C &amp; ::polymer_type&gt;0 areaCutoff 0</a></div></div>10 contacting residues<br>
5710<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/interfaces.html#select">interfaces select</a> #5/F &amp; ::polymer_type&gt;0 contacting #5/A#5/B#5/C#5/D &amp; ::polymer_type&gt;0 areaCutoff 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:interfaces select #5/F &amp; ::polymer_type&gt;0 contacting #5/A#5/B#5/C#5/D &amp; ::polymer_type&gt;0 areaCutoff 0">interfaces select #5/F &amp; ::polymer_type&gt;0 contacting #5/A#5/B#5/C#5/D &amp; ::polymer_type&gt;0 areaCutoff 0</a></div></div>15 contacting residues<br>
5711<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#residues">info residues</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:info residues sel">info residues sel</a></div></div>residue id #5/F:11 name ILE index 10<br>
5712residue id #5/F:12 name SER index 11<br>
5713residue id #5/F:13 name CYS index 12<br>
5714residue id #5/F:14 name GLY index 13<br>
5715residue id #5/F:15 name ALA index 14<br>
5716residue id #5/F:17 name GLU index 16<br>
5717residue id #5/F:18 name PRO index 17<br>
5718residue id #5/F:19 name GLU index 18<br>
5719residue id #5/F:30 name ASP index 29<br>
5720residue id #5/F:31 name GLY index 30<br>
5721residue id #5/F:32 name ARG index 31<br>
5722residue id #5/F:50 name GLY index 49<br>
5723residue id #5/F:51 name VAL index 50<br>
5724residue id #5/F:53 name PRO index 52<br>
5725residue id #5/F:54 name MET index 53<br>
5726<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:11-15,19,29,31,49,50,52,53</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:11-15,19,29,31,49,50,52,53">select #5/F:11-15,19,29,31,49,50,52,53</a></div></div>131 atoms, 126 bonds, 12 residues, 1 model selected<br>
5727<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:11-15,29,31,49,50,52,53</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:11-15,29,31,49,50,52,53">select #5/F:11-15,29,31,49,50,52,53</a></div></div>116 atoms, 112 bonds, 11 residues, 1 model selected<br>
5728<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:11-15,29,31,49,50,52,53</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:11-15,29,31,49,50,52,53">select #5/F:11-15,29,31,49,50,52,53</a></div></div>116 atoms, 112 bonds, 11 residues, 1 model selected<br>
5729<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 11 items<br>
5730<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:11-15,29,31,49,50,52,53</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:11-15,29,31,49,50,52,53">select #5/F:11-15,29,31,49,50,52,53</a></div></div>116 atoms, 112 bonds, 11 residues, 1 model selected<br>
5731<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> buriedFchain sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen buriedFchain sel">name frozen buriedFchain sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 116 atom styles<br>
5732<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/interfaces.html#select">interfaces select</a> #5/A#5/B#5/C#5/D#5/E &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:interfaces select #5/A#5/B#5/C#5/D#5/E &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0">interfaces select #5/A#5/B#5/C#5/D#5/E &amp; ::polymer_type&gt;0 contacting #5/F &amp; ::polymer_type&gt;0 areaCutoff 0</a></div></div>20 contacting residues<br>
5733<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/info.html#residues">info residues</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:info residues sel">info residues sel</a></div></div>residue id #5/A:27 name ARG index 26<br>
5734residue id #5/A:28 name THR index 27<br>
5735residue id #5/A:31 name LYS index 30<br>
5736residue id #5/A:34 name ASP index 33<br>
5737residue id #5/C:11 name ILE index 10<br>
5738residue id #5/C:13 name CYS index 12<br>
5739residue id #5/C:14 name THR index 13<br>
5740residue id #5/C:15 name GLN index 14<br>
5741residue id #5/C:18 name ARG index 17<br>
5742residue id #5/C:34 name LYS index 33<br>
5743residue id #5/C:35 name ALA index 34<br>
5744residue id #5/C:37 name GLN index 36<br>
5745residue id #5/C:58 name PRO index 57<br>
5746residue id #5/D:109 name LYS index 108<br>
5747residue id #5/E:41 name VAL index 40<br>
5748residue id #5/E:43 name ARG index 42<br>
5749residue id #5/E:51 name ASN index 50<br>
5750residue id #5/E:52 name VAL index 51<br>
5751residue id #5/E:54 name THR index 53<br>
5752residue id #5/E:56 name ASN index 55<br>
5753<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56">select #5/C:11,13-15,34-37,58/E:41,51-52,56</a></div></div>206 atoms, 200 bonds, 13 residues, 1 model selected<br>
5754<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 206 atom styles<br>
5755<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select H">select H</a></div></div>14612 atoms, 1922 residues, 3 models selected<br>
5756<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!5-6 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!5-6 atoms">hide sel &amp; #!5-6 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56">select #5/C:11,13-15,34-37,58/E:41,51-52,56</a></div></div>206 atoms, 200 bonds, 13 residues, 1 model selected<br>
5757<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> buriedA_Echain sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen buriedA_Echain sel">name frozen buriedA_Echain sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><a href="help:user/commands/select.html">select</a> <span style="color:white; background-color:crimson;">buriedA_Echain|buriedFChain</span></div><font color="crimson"><b>Expected an objects specifier or a keyword</b></font><br/><div class="cxcmd"><a href="help:user/commands/select.html">select</a> buriedA_Echain <span style="color:white; background-color:crimson;">| buriedFChain</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> buriedA_Echain</div><div class="cxcmd_as_cmd"><a href="cxcmd:select buriedA_Echain">select buriedA_Echain</a></div></div>2273 atoms, 200 bonds, 146 residues, 1 model selected<br>
5758<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> buriedA_Echain | buriedFchain</div><div class="cxcmd_as_cmd"><a href="cxcmd:select buriedA_Echain | buriedFchain">select buriedA_Echain | buriedFchain</a></div></div>3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected<br>
5759<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> buriedA_Echain</div><div class="cxcmd_as_cmd"><a href="cxcmd:select buriedA_Echain">select buriedA_Echain</a></div></div>2273 atoms, 200 bonds, 146 residues, 1 model selected<br>
5760<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> buriedA_Echain | buriedFchain</div><div class="cxcmd_as_cmd"><a href="cxcmd:select buriedA_Echain | buriedFchain">select buriedA_Echain | buriedFchain</a></div></div>3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected<br>
5761<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> Hbonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:select Hbonds">select Hbonds</a></div></div>16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected<br>
5762<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> buriedA_Echain | buriedFchain</div><div class="cxcmd_as_cmd"><a href="cxcmd:select buriedA_Echain | buriedFchain">select buriedA_Echain | buriedFchain</a></div></div>3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected<br>
5763<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> A_EinterfaceF sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen A_EinterfaceF sel">name frozen A_EinterfaceF sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</a></div></div>272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected<br>
5764<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:Cys/F:Cys &amp;~H &amp;~/C:33</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:Cys/F:Cys &amp;~H &amp;~/C:33">select #5/C:Cys/F:Cys &amp;~H &amp;~/C:33</a></div></div>96 atoms, 157 bonds, 1 pseudobond, 16 residues, 2 models selected<br>
5765<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> buriedA_Echain | buriedFchain</div><div class="cxcmd_as_cmd"><a href="cxcmd:select buriedA_Echain | buriedFchain">select buriedA_Echain | buriedFchain</a></div></div>3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected<br>
5766<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> buriedA_Echain</div><div class="cxcmd_as_cmd"><a href="cxcmd:select buriedA_Echain">select buriedA_Echain</a></div></div>2273 atoms, 200 bonds, 146 residues, 1 model selected<br>
5767<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56">select #5/C:11,13-15,34-37,58/E:41,51-52,56</a></div></div>206 atoms, 200 bonds, 13 residues, 1 model selected<br>
5768<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53">select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53</a></div></div>322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected<br>
5769<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H">select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H</a></div></div>162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected<br>
5770<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#delete">name delete</a> all</div><div class="cxcmd_as_cmd"><a href="cxcmd:name delete all">name delete all</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H">select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H</a></div></div>162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected<br>
5771<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> interfaceNoHB sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen interfaceNoHB sel">name frozen interfaceNoHB sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</a></div></div>272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected<br>
5772<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> interfaceHB sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen interfaceHB sel">name frozen interfaceHB sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> interfaceHB</div><div class="cxcmd_as_cmd"><a href="cxcmd:select interfaceHB">select interfaceHB</a></div></div>16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected<br>
5773<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 16975 atom styles<br>
5774<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 16975 atom styles<br>
5775<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> interfaceHB</div><div class="cxcmd_as_cmd"><a href="cxcmd:select interfaceHB">select interfaceHB</a></div></div>16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected<br>
5776<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 16975 atom styles<br>
5777<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H">select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H</a></div></div>162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected<br>
5778<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 162 atom styles<br>
5779<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.1 models">show #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.2 models">show #5.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8.1 models">hide #8.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Key&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Key&quot;">ui tool show &quot;Color Key&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> right &quot;color key&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode right &quot;color key&quot;">ui mousemode right &quot;color key&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> blue-white-red :min : :+</div><div class="cxcmd_as_cmd"><a href="cxcmd:key blue-white-red :min : :+">key blue-white-red :min : :+</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> blue-white-red :min :0 :+</div><div class="cxcmd_as_cmd"><a href="cxcmd:key blue-white-red :min :0 :+">key blue-white-red :min :0 :+</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> blue-white-red :+ :0 :+</div><div class="cxcmd_as_cmd"><a href="cxcmd:key blue-white-red :+ :0 :+">key blue-white-red :+ :0 :+</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> blue-white-red :+ :0 :-</div><div class="cxcmd_as_cmd"><a href="cxcmd:key blue-white-red :+ :0 :-">key blue-white-red :+ :0 :-</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> bold true</div><div class="cxcmd_as_cmd"><a href="cxcmd:key bold true">key bold true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 23</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 23">key fontSize 23</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 22</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 22">key fontSize 22</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 21</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 21">key fontSize 21</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 20">key fontSize 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 19</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 19">key fontSize 19</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 18</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 18">key fontSize 18</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 17</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 17">key fontSize 17</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 16</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 16">key fontSize 16</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 15</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 15">key fontSize 15</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 14</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 14">key fontSize 14</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 13</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 13">key fontSize 13</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 14</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 14">key fontSize 14</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 15</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 15">key fontSize 15</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 16</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 16">key fontSize 16</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> ticks true</div><div class="cxcmd_as_cmd"><a href="cxcmd:key ticks true">key ticks true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickLength 8.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickLength 8.0">key tickLength 8.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickThickness 3.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickThickness 3.0">key tickThickness 3.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickLength 6.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickLength 6.0">key tickLength 6.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickLength 4.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickLength 4.0">key tickLength 4.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickLength 2.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickLength 2.0">key tickLength 2.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickLength 0.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickLength 0.0">key tickLength 0.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickLength 2.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickLength 2.0">key tickLength 2.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickLength 4.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickLength 4.0">key tickLength 4.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> size 0.25000,0.04000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key size 0.25000,0.04000">key size 0.25000,0.04000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> size 0.25000,0.03000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key size 0.25000,0.03000">key size 0.25000,0.03000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> size 0.25000,0.02000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key size 0.25000,0.02000">key size 0.25000,0.02000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> size 0.25000,0.01000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key size 0.25000,0.01000">key size 0.25000,0.01000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.71000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.71000,0.08000">key pos 0.71000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.70000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.70000,0.08000">key pos 0.70000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.69000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.69000,0.08000">key pos 0.69000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.68000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.68000,0.08000">key pos 0.68000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.67000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.67000,0.08000">key pos 0.67000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.66000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.66000,0.08000">key pos 0.66000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.65000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.65000,0.08000">key pos 0.65000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.64000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.64000,0.08000">key pos 0.64000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.63000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.63000,0.08000">key pos 0.63000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.62000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.62000,0.08000">key pos 0.62000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.61000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.61000,0.08000">key pos 0.61000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.60000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.60000,0.08000">key pos 0.60000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.59000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.59000,0.08000">key pos 0.59000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.58000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.58000,0.08000">key pos 0.58000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.57000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.57000,0.08000">key pos 0.57000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.56000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.56000,0.08000">key pos 0.56000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.55000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.55000,0.08000">key pos 0.55000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.54000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.54000,0.08000">key pos 0.54000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.53000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.53000,0.08000">key pos 0.53000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.52000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.52000,0.08000">key pos 0.52000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.51000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.51000,0.08000">key pos 0.51000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.50000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.50000,0.08000">key pos 0.50000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.49000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.49000,0.08000">key pos 0.49000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.48000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.48000,0.08000">key pos 0.48000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.47000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.47000,0.08000">key pos 0.47000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.46000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.46000,0.08000">key pos 0.46000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.45000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.45000,0.08000">key pos 0.45000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.44000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.44000,0.08000">key pos 0.44000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.43000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.43000,0.08000">key pos 0.43000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.42000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.42000,0.08000">key pos 0.42000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.41000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.41000,0.08000">key pos 0.41000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.40000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.40000,0.08000">key pos 0.40000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.39000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.39000,0.08000">key pos 0.39000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.38000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.38000,0.08000">key pos 0.38000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.37000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.37000,0.08000">key pos 0.37000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.36000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.36000,0.08000">key pos 0.36000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.35000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.35000,0.08000">key pos 0.35000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.34000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.34000,0.08000">key pos 0.34000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.33000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.33000,0.08000">key pos 0.33000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.32000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.32000,0.08000">key pos 0.32000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.31000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.31000,0.08000">key pos 0.31000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.30000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.30000,0.08000">key pos 0.30000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.29000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.29000,0.08000">key pos 0.29000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.28000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.28000,0.08000">key pos 0.28000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.27000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.27000,0.08000">key pos 0.27000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.26000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.26000,0.08000">key pos 0.26000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.25000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.25000,0.08000">key pos 0.25000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.24000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.24000,0.08000">key pos 0.24000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.23000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.23000,0.08000">key pos 0.23000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.22000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.22000,0.08000">key pos 0.22000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.21000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.21000,0.08000">key pos 0.21000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.20000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.20000,0.08000">key pos 0.20000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.19000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.19000,0.08000">key pos 0.19000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.18000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.18000,0.08000">key pos 0.18000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.17000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.17000,0.08000">key pos 0.17000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.16000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.16000,0.08000">key pos 0.16000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.15000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.15000,0.08000">key pos 0.15000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.14000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.14000,0.08000">key pos 0.14000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.13000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.13000,0.08000">key pos 0.13000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.12000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.12000,0.08000">key pos 0.12000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.11000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.11000,0.08000">key pos 0.11000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.10000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.10000,0.08000">key pos 0.10000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.09000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.09000,0.08000">key pos 0.09000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.08000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.08000,0.08000">key pos 0.08000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.07000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.07000,0.08000">key pos 0.07000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.06000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.06000,0.08000">key pos 0.06000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.05000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.05000,0.08000">key pos 0.05000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.04000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.04000,0.08000">key pos 0.04000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.03000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.03000,0.08000">key pos 0.03000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.08000">key pos 0.02000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.09000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.09000">key pos 0.02000,0.09000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.10000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.10000">key pos 0.02000,0.10000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.11000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.11000">key pos 0.02000,0.11000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.12000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.12000">key pos 0.02000,0.12000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.13000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.13000">key pos 0.02000,0.13000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.14000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.14000">key pos 0.02000,0.14000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.15000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.15000">key pos 0.02000,0.15000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.16000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.16000">key pos 0.02000,0.16000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.17000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.17000">key pos 0.02000,0.17000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.18000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.18000">key pos 0.02000,0.18000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.19000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.19000">key pos 0.02000,0.19000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.20000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.20000">key pos 0.02000,0.20000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.21000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.21000">key pos 0.02000,0.21000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.22000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.22000">key pos 0.02000,0.22000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.23000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.23000">key pos 0.02000,0.23000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.24000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.24000">key pos 0.02000,0.24000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.25000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.25000">key pos 0.02000,0.25000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.26000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.26000">key pos 0.02000,0.26000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.27000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.27000">key pos 0.02000,0.27000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.28000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.28000">key pos 0.02000,0.28000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.29000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.29000">key pos 0.02000,0.29000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.30000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.30000">key pos 0.02000,0.30000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.31000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.31000">key pos 0.02000,0.31000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.32000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.32000">key pos 0.02000,0.32000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.33000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.33000">key pos 0.02000,0.33000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.34000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.34000">key pos 0.02000,0.34000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.35000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.35000">key pos 0.02000,0.35000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.36000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.36000">key pos 0.02000,0.36000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.37000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.37000">key pos 0.02000,0.37000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.38000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.38000">key pos 0.02000,0.38000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.39000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.39000">key pos 0.02000,0.39000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.40000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.40000">key pos 0.02000,0.40000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.41000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.41000">key pos 0.02000,0.41000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.42000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.42000">key pos 0.02000,0.42000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.43000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.43000">key pos 0.02000,0.43000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.44000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.44000">key pos 0.02000,0.44000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.45000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.45000">key pos 0.02000,0.45000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.46000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.46000">key pos 0.02000,0.46000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.47000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.47000">key pos 0.02000,0.47000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.48000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.48000">key pos 0.02000,0.48000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.49000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.49000">key pos 0.02000,0.49000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.50000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.50000">key pos 0.02000,0.50000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.51000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.51000">key pos 0.02000,0.51000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.52000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.52000">key pos 0.02000,0.52000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.53000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.53000">key pos 0.02000,0.53000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.54000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.54000">key pos 0.02000,0.54000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.55000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.55000">key pos 0.02000,0.55000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.56000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.56000">key pos 0.02000,0.56000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.57000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.57000">key pos 0.02000,0.57000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.58000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.58000">key pos 0.02000,0.58000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.59000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.59000">key pos 0.02000,0.59000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.60000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.60000">key pos 0.02000,0.60000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.61000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.61000">key pos 0.02000,0.61000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.62000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.62000">key pos 0.02000,0.62000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.63000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.63000">key pos 0.02000,0.63000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.64000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.64000">key pos 0.02000,0.64000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.65000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.65000">key pos 0.02000,0.65000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.66000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.66000">key pos 0.02000,0.66000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.67000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.67000">key pos 0.02000,0.67000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.68000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.68000">key pos 0.02000,0.68000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.69000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.69000">key pos 0.02000,0.69000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.70000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.70000">key pos 0.02000,0.70000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.71000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.71000">key pos 0.02000,0.71000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.72000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.72000">key pos 0.02000,0.72000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.73000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.73000">key pos 0.02000,0.73000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.74000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.74000">key pos 0.02000,0.74000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.75000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.75000">key pos 0.02000,0.75000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.76000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.76000">key pos 0.02000,0.76000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.77000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.77000">key pos 0.02000,0.77000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.78000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.78000">key pos 0.02000,0.78000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.79000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.79000">key pos 0.02000,0.79000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.80000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.80000">key pos 0.02000,0.80000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.81000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.81000">key pos 0.02000,0.81000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.82000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.82000">key pos 0.02000,0.82000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.83000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.83000">key pos 0.02000,0.83000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.84000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.84000">key pos 0.02000,0.84000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.85000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.85000">key pos 0.02000,0.85000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.86000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.86000">key pos 0.02000,0.86000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.87000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.87000">key pos 0.02000,0.87000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.88000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.88000">key pos 0.02000,0.88000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.89000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.89000">key pos 0.02000,0.89000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.90000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.90000">key pos 0.02000,0.90000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.91000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.91000">key pos 0.02000,0.91000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.92000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.92000">key pos 0.02000,0.92000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.93000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.93000">key pos 0.02000,0.93000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.94000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.94000">key pos 0.02000,0.94000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.95000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.95000">key pos 0.02000,0.95000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.96000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.96000">key pos 0.02000,0.96000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.97000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.97000">key pos 0.02000,0.97000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.02000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.02000,0.98000">key pos 0.02000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.03000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.03000,0.98000">key pos 0.03000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.04000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.04000,0.98000">key pos 0.04000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.05000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.05000,0.98000">key pos 0.05000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.06000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.06000,0.98000">key pos 0.06000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.07000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.07000,0.98000">key pos 0.07000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.08000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.08000,0.98000">key pos 0.08000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.09000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.09000,0.98000">key pos 0.09000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.10000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.10000,0.98000">key pos 0.10000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.11000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.11000,0.98000">key pos 0.11000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.12000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.12000,0.98000">key pos 0.12000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.13000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.13000,0.98000">key pos 0.13000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.14000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.14000,0.98000">key pos 0.14000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.15000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.15000,0.98000">key pos 0.15000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.16000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.16000,0.98000">key pos 0.16000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.17000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.17000,0.98000">key pos 0.17000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.18000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.18000,0.98000">key pos 0.18000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.19000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.19000,0.98000">key pos 0.19000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.20000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.20000,0.98000">key pos 0.20000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.21000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.21000,0.98000">key pos 0.21000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.22000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.22000,0.98000">key pos 0.22000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.23000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.23000,0.98000">key pos 0.23000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.24000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.24000,0.98000">key pos 0.24000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.25000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.25000,0.98000">key pos 0.25000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.26000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.26000,0.98000">key pos 0.26000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.27000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.27000,0.98000">key pos 0.27000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.28000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.28000,0.98000">key pos 0.28000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.29000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.29000,0.98000">key pos 0.29000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.30000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.30000,0.98000">key pos 0.30000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.31000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.31000,0.98000">key pos 0.31000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.32000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.32000,0.98000">key pos 0.32000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.33000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.33000,0.98000">key pos 0.33000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.34000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.34000,0.98000">key pos 0.34000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.35000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.35000,0.98000">key pos 0.35000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.36000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.36000,0.98000">key pos 0.36000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.37000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.37000,0.98000">key pos 0.37000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.38000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.38000,0.98000">key pos 0.38000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.39000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.39000,0.98000">key pos 0.39000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.40000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.40000,0.98000">key pos 0.40000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.41000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.41000,0.98000">key pos 0.41000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.42000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.42000,0.98000">key pos 0.42000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.43000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.43000,0.98000">key pos 0.43000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.44000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.44000,0.98000">key pos 0.44000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.45000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.45000,0.98000">key pos 0.45000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.46000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.46000,0.98000">key pos 0.46000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.47000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.47000,0.98000">key pos 0.47000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.48000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.48000,0.98000">key pos 0.48000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.49000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.49000,0.98000">key pos 0.49000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.50000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.50000,0.98000">key pos 0.50000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.51000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.51000,0.98000">key pos 0.51000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.52000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.52000,0.98000">key pos 0.52000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.53000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.53000,0.98000">key pos 0.53000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.54000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.54000,0.98000">key pos 0.54000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.55000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.55000,0.98000">key pos 0.55000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.56000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.56000,0.98000">key pos 0.56000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.57000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.57000,0.98000">key pos 0.57000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.58000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.58000,0.98000">key pos 0.58000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.59000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.59000,0.98000">key pos 0.59000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.60000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.60000,0.98000">key pos 0.60000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.61000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.61000,0.98000">key pos 0.61000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.62000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.62000,0.98000">key pos 0.62000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.63000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.63000,0.98000">key pos 0.63000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.64000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.64000,0.98000">key pos 0.64000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.65000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.65000,0.98000">key pos 0.65000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.66000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.66000,0.98000">key pos 0.66000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.67000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.67000,0.98000">key pos 0.67000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.68000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.68000,0.98000">key pos 0.68000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.69000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.69000,0.98000">key pos 0.69000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.70000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.70000,0.98000">key pos 0.70000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.71000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.71000,0.98000">key pos 0.71000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.72000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.72000,0.98000">key pos 0.72000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.73000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.73000,0.98000">key pos 0.73000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.74000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.74000,0.98000">key pos 0.74000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.73000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.73000,0.98000">key pos 0.73000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> right translate</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode right translate">ui mousemode right translate</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #7 models">hide #7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #7 models">show #7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32</a></div></div>272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected<br>
5780<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H">select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &amp;~H</a></div></div>162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected<br>
5781<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 80</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 80">transparency (#!5 &amp; sel) 80</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 100</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 100">transparency (#!5 &amp; sel) 100</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53">select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53</a></div></div>322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected<br>
5782<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 100</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 100">transparency (#!5 &amp; sel) 100</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53">select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53</a></div></div>322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected<br>
5783<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 90">transparency (#!5 &amp; sel) 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 70</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 70">transparency (#!5 &amp; sel) 70</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 100</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 100">transparency (#!5 &amp; sel) 100</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.6">select add #5.6</a></div></div>844 atoms, 61 residues, 1 model selected<br>
5784<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.5">select add #5.5</a></div></div>1903 atoms, 127 residues, 2 models selected<br>
5785<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.4">select add #5.4</a></div></div>4180 atoms, 270 residues, 3 models selected<br>
5786<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.3">select add #5.3</a></div></div>5394 atoms, 350 residues, 4 models selected<br>
5787<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.2">select add #5.2</a></div></div>16909 atoms, 1083 residues, 5 models selected<br>
5788<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.1">select add #5.1</a></div></div>28490 atoms, 1826 residues, 6 models selected<br>
5789<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 30">transparency (#!5 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53">select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53</a></div></div>322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected<br>
5790<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 322 atom styles<br>
5791<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt All surfaces front .png&quot; width 1508 height 1200 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt All surfaces front .png&quot; width 1508 height 1200 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt All surfaces front .png&quot; width 1508 height 1200 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt no F surface front .png&quot; width 1508 height 1200 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt no F surface front .png&quot; width 1508 height 1200 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt no F surface front .png&quot; width 1508 height 1200 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><span style="color:white; background-color:crimson;">trurn y 90</span></div><font color="crimson"><b>Unknown command: trurn y 90</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 90">turn y 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 30">turn y 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 30">turn y 30</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 10">turn y 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 10">turn x 10</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -10">turn y -10</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 10">turn x 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 30">turn y 30</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 10">turn x 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 60">turn x 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 60">turn y 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -30">turn y -30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 10">turn x 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 40</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 40">turn y 40</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 10">turn y 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 10">turn x 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 50</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 50">turn y 50</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 20">turn x 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name side">view name side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.3 models">show #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54</a></div></div>167 atoms, 160 bonds, 9 residues, 1 model selected<br>
5792<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 80</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 80">transparency (#!5 &amp; sel) 80</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54</a></div></div>167 atoms, 160 bonds, 9 residues, 1 model selected<br>
5793<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 90">transparency (#!5 &amp; sel) 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 10">turn x 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x -10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x -10">turn x -10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 5</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 5">turn x 5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x -5</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x -5">turn x -5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 5</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 5">turn x 5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 5</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 5">turn y 5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 5</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 5">turn x 5</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -5</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -5">turn y -5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 15</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 15">turn x 15</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.6">select add #5.6</a></div></div>844 atoms, 61 residues, 1 model selected<br>
5794<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.5">select add #5.5</a></div></div>1903 atoms, 127 residues, 2 models selected<br>
5795<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.4">select add #5.4</a></div></div>4180 atoms, 270 residues, 3 models selected<br>
5796<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.3">select add #5.3</a></div></div>5394 atoms, 350 residues, 4 models selected<br>
5797<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.2">select add #5.2</a></div></div>16909 atoms, 1083 residues, 5 models selected<br>
5798<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5.1">select add #5.1</a></div></div>28490 atoms, 1826 residues, 6 models selected<br>
5799<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 20">transparency (#!5 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.7 models">hide #5.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.7 models">show #5.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name front">view name front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 50</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 50">turn y 50</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 60">turn y 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 60">turn y 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -60">turn y -60</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 90">turn y 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 90">turn x 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><a href="help:user/commands/turn.html">turn</a> <span style="color:white; background-color:crimson;">30</span></div><font color="crimson"><b>Expected an axis vector or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 30">turn y 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.5 models">show #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -30">turn y -30</a></div></div>[Repeated 3 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 30">turn x 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 10">turn x 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 5</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 5">turn x 5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 45">turn x 45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x -45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x -45">turn x -45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 30">turn y 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 30">turn y 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -30">turn y -30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x -45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x -45">turn x -45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 45">turn x 45</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -45">turn y -45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -45">turn y -45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 45">turn x 45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -50</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -50">turn y -50</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x -45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x -45">turn x -45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -50</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -50">turn y -50</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 45">turn x 45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x -15</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x -15">turn x -15</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -50</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -50">turn y -50</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 30">turn x 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -60">turn y -60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><span style="color:white; background-color:crimson;">trun 1,1,0 45</span></div><font color="crimson"><b>Unknown command: trun 1,1,0 45</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> 1,1,0 45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn 1,1,0 45">turn 1,1,0 45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> 1,1,0 -45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn 1,1,0 -45">turn 1,1,0 -45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> -1,1,0 45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn -1,1,0 45">turn -1,1,0 45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> -1,1,0 -45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn -1,1,0 -45">turn -1,1,0 -45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 60">turn y 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y -60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y -60">turn y -60</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> back</div><div class="cxcmd_as_cmd"><a href="cxcmd:view back">view back</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 45">turn x 45</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.4 models">show #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 45</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 45">turn x 45</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 15</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 15">turn x 15</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 60">turn x 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 60">turn x 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 30">turn x 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 90">turn x 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #5.6 models">show #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 60</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 60">turn x 60</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 90">turn x 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 30">turn x 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 180</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 180">turn y 180</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 120</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 120">turn x 120</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 190</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 190">turn y 190</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 130</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 130">turn x 130</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 10">turn y 10</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 200</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 200">turn y 200</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 145</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 145">turn x 145</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> x 145</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn x 145">turn x 145</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/turn.html">turn</a> y 200</div><div class="cxcmd_as_cmd"><a href="cxcmd:turn y 200">turn y 200</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name side">view name side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.6 models">hide #5.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #8">select add #8</a></div></div>1 pseudobond, 2 models selected<br>
5800<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #8">select subtract #8</a></div></div>Nothing selected<br>
5801<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #8">select add #8</a></div></div>1 pseudobond, 2 models selected<br>
5802<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #8">select subtract #8</a></div></div>Nothing selected<br>
5803<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #8">select add #8</a></div></div>1 pseudobond, 2 models selected<br>
5804<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #8">select subtract #8</a></div></div>Nothing selected<br>
5805<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #8">select add #8</a></div></div>1 pseudobond, 2 models selected<br>
5806<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #8">select subtract #8</a></div></div>Nothing selected<br>
5807<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #8">select add #8</a></div></div>1 pseudobond, 2 models selected<br>
5808<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #8">select subtract #8</a></div></div>Nothing selected<br>
5809<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8.1 models">show #8.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8.1 models">hide #8.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:27,28,31,34/C:18/D:109/E:43,53,54</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:27,28,31,34/C:18/D:109/E:43,53,54">select #5/A:27,28,31,34/C:18/D:109/E:43,53,54</a></div></div>167 atoms, 160 bonds, 9 residues, 1 model selected<br>
5810<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 90">transparency (#!5 &amp; sel) 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #7 models">hide #7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> HbondsZoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name HbondsZoom">view name HbondsZoom</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> HbondsZoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view HbondsZoom">view HbondsZoom</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15,34-37,58</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15,34-37,58">select #5/C:11,13-15,34-37,58</a></div></div>146 atoms, 143 bonds, 9 residues, 1 model selected<br>
5811<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11,13-15</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11,13-15">select #5/C:11,13-15</a></div></div>61 atoms, 59 bonds, 4 residues, 1 model selected<br>
5812<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:13-15</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:13-15">select #5/C:13-15</a></div></div>42 atoms, 41 bonds, 3 residues, 1 model selected<br>
5813<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 90">transparency (#!5 &amp; sel) 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> HbondsZoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view HbondsZoom">view HbondsZoom</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:13-15</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:13-15">select #5/C:13-15</a></div></div>42 atoms, 41 bonds, 3 residues, 1 model selected<br>
5814<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 20">transparency (#!5 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/C:11</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/C:11">select #5/C:11</a></div></div>19 atoms, 18 bonds, 1 residue, 1 model selected<br>
5815<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!5 &amp; sel) 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!5 &amp; sel) 90">transparency (#!5 &amp; sel) 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/graphics.html#silhouettes">graphics silhouettes</a> false</div><div class="cxcmd_as_cmd"><a href="cxcmd:graphics silhouettes false">graphics silhouettes false</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/graphics.html#silhouettes">graphics silhouettes</a> true</div><div class="cxcmd_as_cmd"><a href="cxcmd:graphics silhouettes true">graphics silhouettes true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> HbondsZoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name HbondsZoom">view name HbondsZoom</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> HbondsZoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view HbondsZoom">view HbondsZoom</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Fri Oct 4 15:14:28 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
5816<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png&quot; width 1506 height 1200 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png&quot; width 1506 height 1200 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png&quot; width 1506 height 1200 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:1-2,8-24,30-47</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:1-2,8-24,30-47">select #6:1-2,8-24,30-47</a></div></div>447 atoms, 448 bonds, 37 residues, 1 model selected<br>
5817<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/B:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/B:1">select #3/B:1</a></div></div>5 atoms, 4 bonds, 1 residue, 1 model selected<br>
5818<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/B:1-2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/B:1-2">select #3/B:1-2</a></div></div>17 atoms, 17 bonds, 2 residues, 1 model selected<br>
5819<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:1-2,8-24,30-47</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:1-2,8-24,30-47">select #6:1-2,8-24,30-47</a></div></div>447 atoms, 448 bonds, 37 residues, 1 model selected<br>
5820<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/B:1-2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/B:1-2">select #3/B:1-2</a></div></div>17 atoms, 17 bonds, 2 residues, 1 model selected<br>
5821<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:1-2,8-24,30-47</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:1-2,8-24,30-47">select #6:1-2,8-24,30-47</a></div></div>447 atoms, 448 bonds, 37 residues, 1 model selected<br>
5822<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:1-2,8-24,30-47#5/F:1-2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:1-2,8-24,30-47#5/F:1-2">select #6:1-2,8-24,30-47#5/F:1-2</a></div></div>480 atoms, 481 bonds, 39 residues, 2 models selected<br>
5823<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:1-2,8-24,30-47#5/F:1-2,8-24</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:1-2,8-24,30-47#5/F:1-2,8-24">select #6:1-2,8-24,30-47#5/F:1-2,8-24</a></div></div>695 atoms, 697 bonds, 56 residues, 2 models selected<br>
5824<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!6 to #5/F pairing bs showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!6 to #5/F pairing bs showAlignment true">matchmaker #!6 to #5/F pairing bs showAlignment true</a></div></div>
5825 <table border=1 cellpadding=4 cellspacing=0>
5826 <tr>
5827 <th colspan="2">Parameters</th>
5828 </tr>
5829 <tr>
5830 <td>Chain pairing</td>
5831 <td>bs</td>
5832 </tr>
5833 <tr>
5834 <td>Alignment algorithm</td>
5835 <td>Needleman-Wunsch</td>
5836 </tr>
5837 <tr>
5838 <td>Similarity matrix</td>
5839 <td>BLOSUM-62</td>
5840 </tr>
5841
5842 <tr>
5843 <td>SS fraction</td>
5844 <td>0.3</td>
5845 </tr>
5846 <tr>
5847 <td>Gap open (HH/SS/other)</td>
5848 <td>18/18/6</td>
5849 </tr>
5850 <tr>
5851 <td>Gap extend</td>
5852 <td>1</td>
5853 </tr>
5854 <tr>
5855 <td>SS matrix</td>
5856 <td>
5857 <table>
5858 <tr>
5859 <th></th> <th>H</th> <th>S</th> <th>O</th>
5860 </tr>
5861 <tr>
5862 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
5863 </tr>
5864 <tr>
5865 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
5866 </tr>
5867 <tr>
5868 <th>O</th> <td></td> <td></td> <td align="right">4</td>
5869 </tr>
5870 </table>
5871 </td>
5872 </tr>
5873
5874 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
5875 </table>
5876 <br/>Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6), sequence alignment score = 170.3<br>
5877Alignment identifier is 1<br>
5878Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
5879Hiding conservation header for alignment 1<br>
5880Chains used in RMSD evaluation for alignment 1: relaxed_structure.pdb #5/F, 2fdn #6/M<br>
5881Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
5882RMSD between 41 pruned atom pairs is 0.850 angstroms; (across all 54 pairs: 2.909)<br>
5883<br>
5884<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#header">sequence header</a> 1 consensus show</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence header 1 consensus show">sequence header 1 consensus show</a></div></div>Showing consensus header (&quot;seq_consensus&quot; residue attribute) for alignment 1<br>
5885<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:1-2,8-24,30-47#5/F:1-2,10-26</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:1-2,8-24,30-47#5/F:1-2,10-26">select #6:1-2,8-24,30-47#5/F:1-2,10-26</a></div></div>696 atoms, 698 bonds, 56 residues, 2 models selected<br>
5886<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:1-2,8-24,30-47#5/F:1-2,10-26,35-52</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:1-2,8-24,30-47#5/F:1-2,10-26,35-52">select #6:1-2,8-24,30-47#5/F:1-2,10-26,35-52</a></div></div>925 atoms, 927 bonds, 74 residues, 2 models selected<br>
5887<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5">select #5</a></div></div>28492 atoms, 28966 bonds, 19 pseudobonds, 1826 residues, 2 models selected<br>
5888<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6">select #6</a></div></div>762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected<br>
5889<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F:1-2,10-26,35-52</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F:1-2,10-26,35-52">select #5/F:1-2,10-26,35-52</a></div></div>478 atoms, 479 bonds, 37 residues, 1 model selected<br>
5890<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!5 &amp; sel) orange</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!5 &amp; sel) orange">color (#!5 &amp; sel) orange</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png&quot; width 1506 height 1200 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png&quot; width 1506 height 1200 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png&quot; width 1506 height 1200 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png&quot; width 1506 height 1200 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png&quot; width 1506 height 1200 supersample 3 transparentBackground true">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/PSI-Fdx Alt zoom hbonds.png&quot; width 1506 height 1200 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sun Oct 6 13:38:31 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
5891<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #20</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #20">close #20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #8">close #8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #7">close #7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.5 models">hide #5.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.3 models">hide #5.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.2 models">hide #5.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.1 models">hide #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.4 models">hide #5.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2 models">hide #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2 models">show #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2">select #2</a></div></div>24 atoms, 36 bonds, 3 residues, 1 model selected<br>
5892<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2 :&lt;3 &amp;#5/A-C:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2 :&lt;3 &amp;#5/A-C:Cys">select #2 :&lt;3 &amp;#5/A-C:Cys</a></div></div>132 atoms, 120 bonds, 12 residues, 1 model selected<br>
5893<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2 :&lt;3 &amp;#5/A-C:Cys &amp;H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2 :&lt;3 &amp;#5/A-C:Cys &amp;H">select #2 :&lt;3 &amp;#5/A-C:Cys &amp;H</a></div></div>60 atoms, 12 residues, 1 model selected<br>
5894<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2 :&lt;3 &amp;#5/A-C:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2 :&lt;3 &amp;#5/A-C:Cys">select #2 :&lt;3 &amp;#5/A-C:Cys</a></div></div>132 atoms, 120 bonds, 12 residues, 1 model selected<br>
5895<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 132 atom styles<br>
5896<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2 models">hide #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/B:549</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/B:549">select #1/B:549</a></div></div>8 atoms, 7 bonds, 1 residue, 1 model selected<br>
5897<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/A-B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/A-B">select #1/A-B</a></div></div>18021 atoms, 18789 bonds, 361 pseudobonds, 1592 residues, 2 models selected<br>
5898<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2 models">show #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2 models">hide #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2 models">show #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2 models">hide #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2 models">show #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2 models">hide #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2 models">show #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2 models">hide #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #1">close #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2 models">show #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #3-4</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #3-4">close #3-4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> right &quot;translate selected atoms&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode right &quot;translate selected atoms&quot;">ui mousemode right &quot;translate selected atoms&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> right &quot;translate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode right &quot;translate selected models&quot;">ui mousemode right &quot;translate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 &quot;PSI Fx Fa Fb clusters&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 &quot;PSI Fx Fa Fb clusters&quot;">rename #2 &quot;PSI Fx Fa Fb clusters&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #5 id #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #5 id #1">rename #5 id #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #6 id #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #6 id #3">rename #6 id #3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1 &quot;relaxed PsaABCDE BFd(F) complex&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1 &quot;relaxed PsaABCDE BFd(F) complex&quot;">rename #1 &quot;relaxed PsaABCDE BFd(F) complex&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.1 models">show #1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.2 models">show #1.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.3 models">show #1.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.4 models">show #1.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.5 models">show #1.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.6 models">show #1.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.5 models">hide #1.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.4 models">hide #1.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.3 models">hide #1.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.2 models">hide #1.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.1 models">hide #1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.6 models">hide #1.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #5/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #5/F">rename #5/F</a></div></div><font color="crimson"><b>No name or id option specified for renaming</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/F">select #5/F</a></div></div>Nothing selected<br>
5899<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F">select #1/F</a></div></div>846 atoms, 853 bonds, 61 residues, 1 model selected<br>
5900<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel bychain</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel bychain">color sel bychain</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><a href="help:user/commands/color.html">color</a> #1 <span style="color:white; background-color:crimson;">chains pal sett3-9</span></div><font color="crimson"><b>Expected a color or one of &#x27;byatom&#x27;, &#x27;bychain&#x27;, &#x27;byelement&#x27;, &#x27;byhetero&#x27;, &#x27;byidentity&#x27;, &#x27;bymodel&#x27;, &#x27;bynucleotide&#x27;, &#x27;bypolymer&#x27;, &#x27;fromatoms&#x27;, &#x27;fromcartoons&#x27;, &#x27;fromribbons&#x27;, or &#x27;random&#x27; or a keyword</b></font><br/><div class="cxcmd"><a href="help:user/commands/color.html">color</a> bychain <span style="color:white; background-color:crimson;">#1 pal sett3-9</span></div><font color="crimson"><b>Expected a collection of one of &#x27;All&#x27;, &#x27;atoms&#x27;, &#x27;bonds&#x27;, &#x27;cartoons&#x27;, &#x27;labels&#x27;, &#x27;models&#x27;, &#x27;pseudobonds&#x27;, &#x27;ribbons&#x27;, &#x27;rings&#x27;, or &#x27;surfaces&#x27; or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#sequential">color sequential</a> #1 chains</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sequential #1 chains">color sequential #1 chains</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#sequential">color sequential</a> #1 chains palette set3-9</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sequential #1 chains palette set3-9">color sequential #1 chains palette set3-9</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#~select">~select</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:~select">~select</a></div></div>Nothing selected<br>
5901<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color byhetero">color byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#sequential">color sequential</a> #1 chains palette pastel1</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sequential #1 chains palette pastel1">color sequential #1 chains palette pastel1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color byhetero">color byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#sequential">color sequential</a> #1 chains palette accent</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sequential #1 chains palette accent">color sequential #1 chains palette accent</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color byhetero">color byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for minimization.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for minimization.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for minimization.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 &quot;BFd (2fdn)&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 &quot;BFd (2fdn)&quot;">rename #3 &quot;BFd (2fdn)&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for minimization.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for minimization.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for minimization.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #1.1-7</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #1.1-7">close #1.1-7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for relaxation.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for relaxation.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd for relaxation.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Tue Oct 8 17:54:27 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
5902<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
5903 <thead>
5904 <tr>
5905 <th colspan="2">Chain information for PSI_BFd.opt.pdb #4</th>
5906 </tr>
5907 <tr>
5908 <th>Chain</th>
5909 <th>Description</th>
5910
5911 </tr>
5912 </thead>
5913 <tbody>
5914 <tr>
5915 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4/?:1-1826">?</a></td>
5916 <td><a title="Show sequence" href="cxcmd:sequence chain #4/?">No description available</a></td>
5917
5918 </tr>
5919 </tbody>
5920</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828">split #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828</a></div></div>Split PSI_BFd.opt.pdb (#4) into 6 models<br>
5921<table border=1 cellpadding=4 cellspacing=0>
5922 <thead>
5923 <tr>
5924 <th colspan="2">Chain information for PSI_BFd.opt.pdb 1 #4.1</th>
5925 </tr>
5926 <tr>
5927 <th>Chain</th>
5928 <th>Description</th>
5929
5930 </tr>
5931 </thead>
5932 <tbody>
5933 <tr>
5934 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.1/?:1-743">?</a></td>
5935 <td><a title="Show sequence" href="cxcmd:sequence chain #4.1/?">No description available</a></td>
5936
5937 </tr>
5938 </tbody>
5939</table><br/><table border=1 cellpadding=4 cellspacing=0>
5940 <thead>
5941 <tr>
5942 <th colspan="2">Chain information for PSI_BFd.opt.pdb 2 #4.2</th>
5943 </tr>
5944 <tr>
5945 <th>Chain</th>
5946 <th>Description</th>
5947
5948 </tr>
5949 </thead>
5950 <tbody>
5951 <tr>
5952 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.2/?:744-1476">?</a></td>
5953 <td><a title="Show sequence" href="cxcmd:sequence chain #4.2/?">No description available</a></td>
5954
5955 </tr>
5956 </tbody>
5957</table><br/><table border=1 cellpadding=4 cellspacing=0>
5958 <thead>
5959 <tr>
5960 <th colspan="2">Chain information for PSI_BFd.opt.pdb 3 #4.3</th>
5961 </tr>
5962 <tr>
5963 <th>Chain</th>
5964 <th>Description</th>
5965
5966 </tr>
5967 </thead>
5968 <tbody>
5969 <tr>
5970 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.3/?:1477-1556">?</a></td>
5971 <td><a title="Show sequence" href="cxcmd:sequence chain #4.3/?">No description available</a></td>
5972
5973 </tr>
5974 </tbody>
5975</table><br/><table border=1 cellpadding=4 cellspacing=0>
5976 <thead>
5977 <tr>
5978 <th colspan="2">Chain information for PSI_BFd.opt.pdb 4 #4.4</th>
5979 </tr>
5980 <tr>
5981 <th>Chain</th>
5982 <th>Description</th>
5983
5984 </tr>
5985 </thead>
5986 <tbody>
5987 <tr>
5988 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.4/?:1557-1699">?</a></td>
5989 <td><a title="Show sequence" href="cxcmd:sequence chain #4.4/?">No description available</a></td>
5990
5991 </tr>
5992 </tbody>
5993</table><br/><table border=1 cellpadding=4 cellspacing=0>
5994 <thead>
5995 <tr>
5996 <th colspan="2">Chain information for PSI_BFd.opt.pdb 5 #4.5</th>
5997 </tr>
5998 <tr>
5999 <th>Chain</th>
6000 <th>Description</th>
6001
6002 </tr>
6003 </thead>
6004 <tbody>
6005 <tr>
6006 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.5/?:1700-1765">?</a></td>
6007 <td><a title="Show sequence" href="cxcmd:sequence chain #4.5/?">No description available</a></td>
6008
6009 </tr>
6010 </tbody>
6011</table><br/><table border=1 cellpadding=4 cellspacing=0>
6012 <thead>
6013 <tr>
6014 <th colspan="2">Chain information for PSI_BFd.opt.pdb 6 #4.6</th>
6015 </tr>
6016 <tr>
6017 <th>Chain</th>
6018 <th>Description</th>
6019
6020 </tr>
6021 </thead>
6022 <tbody>
6023 <tr>
6024 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.6/?:1767-1826">?</a></td>
6025 <td><a title="Show sequence" href="cxcmd:sequence chain #4.6/?">No description available</a></td>
6026
6027 </tr>
6028 </tbody>
6029</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4.1#4.2#4.3#4.4#4.5#4.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4.1#4.2#4.3#4.4#4.5#4.6">combine #4.1#4.2#4.3#4.4#4.5#4.6</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 2 #4.2 to &#x27;A&#x27;<br>
6030Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 3 #4.3 to &#x27;B&#x27;<br>
6031Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 4 #4.4 to &#x27;C&#x27;<br>
6032Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 5 #4.5 to &#x27;D&#x27;<br>
6033Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 6 #4.6 to &#x27;E&#x27;<br>
6034Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 1 #4.1 to &#x27;F&#x27;<br>
6035Traceback (most recent call last):<br>
6036&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6037&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6038&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6039&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6040&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6041&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6042&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6043&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6044&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6045&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6046ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6047<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4.1">combine #4.1</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 1 #4.1 to &#x27;A&#x27;<br>
6048Traceback (most recent call last):<br>
6049&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6050&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6051&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6052&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6053&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6054&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6055&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6056&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6057&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6058&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6059ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6060<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4.2#4.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4.2#4.3">combine #4.2#4.3</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 3 #4.3 to &#x27;A&#x27;<br>
6061Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 2 #4.2 to &#x27;B&#x27;<br>
6062Traceback (most recent call last):<br>
6063&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6064&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6065&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6066&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6067&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6068&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6069&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6070&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6071&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6072&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6073ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6074<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4.2#4.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4.2#4.4">combine #4.2#4.4</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 4 #4.4 to &#x27;A&#x27;<br>
6075Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 2 #4.2 to &#x27;B&#x27;<br>
6076Traceback (most recent call last):<br>
6077&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6078&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6079&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6080&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6081&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6082&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6083&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6084&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6085&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6086&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6087ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6088<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4.2#4.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4.2#4.5">combine #4.2#4.5</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 5 #4.5 to &#x27;A&#x27;<br>
6089Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 2 #4.2 to &#x27;B&#x27;<br>
6090Traceback (most recent call last):<br>
6091&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6092&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6093&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6094&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6095&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6096&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6097&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6098&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6099&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6100&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6101ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6102<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4.2">combine #4.2</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 2 #4.2 to &#x27;A&#x27;<br>
6103Traceback (most recent call last):<br>
6104&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6105&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6106&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6107&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6108&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6109&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6110&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6111&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6112&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6113&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6114ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6115<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4">combine #4</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 2 #4.2 to &#x27;A&#x27;<br>
6116Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 3 #4.3 to &#x27;B&#x27;<br>
6117Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 4 #4.4 to &#x27;C&#x27;<br>
6118Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 5 #4.5 to &#x27;D&#x27;<br>
6119Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 6 #4.6 to &#x27;E&#x27;<br>
6120Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 1 #4.1 to &#x27;F&#x27;<br>
6121Traceback (most recent call last):<br>
6122&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6123&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6124&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6125&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6126&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6127&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6128&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6129&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6130&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6131&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6132ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6133<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #4">close #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
6134 <thead>
6135 <tr>
6136 <th colspan="2">Chain information for PSI_BFd.opt.pdb #4</th>
6137 </tr>
6138 <tr>
6139 <th>Chain</th>
6140 <th>Description</th>
6141
6142 </tr>
6143 </thead>
6144 <tbody>
6145 <tr>
6146 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4/?:1-1826">?</a></td>
6147 <td><a title="Show sequence" href="cxcmd:sequence chain #4/?">No description available</a></td>
6148
6149 </tr>
6150 </tbody>
6151</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828">split #4 atoms :1-743,1829 atoms :744-1476 atoms :1477-1556,1830-1831 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826,1827-1828</a></div></div>Split PSI_BFd.opt.pdb (#4) into 6 models<br>
6152<table border=1 cellpadding=4 cellspacing=0>
6153 <thead>
6154 <tr>
6155 <th colspan="2">Chain information for PSI_BFd.opt.pdb 1 #4.1</th>
6156 </tr>
6157 <tr>
6158 <th>Chain</th>
6159 <th>Description</th>
6160
6161 </tr>
6162 </thead>
6163 <tbody>
6164 <tr>
6165 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.1/?:1-743">?</a></td>
6166 <td><a title="Show sequence" href="cxcmd:sequence chain #4.1/?">No description available</a></td>
6167
6168 </tr>
6169 </tbody>
6170</table><br/><table border=1 cellpadding=4 cellspacing=0>
6171 <thead>
6172 <tr>
6173 <th colspan="2">Chain information for PSI_BFd.opt.pdb 2 #4.2</th>
6174 </tr>
6175 <tr>
6176 <th>Chain</th>
6177 <th>Description</th>
6178
6179 </tr>
6180 </thead>
6181 <tbody>
6182 <tr>
6183 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.2/?:744-1476">?</a></td>
6184 <td><a title="Show sequence" href="cxcmd:sequence chain #4.2/?">No description available</a></td>
6185
6186 </tr>
6187 </tbody>
6188</table><br/><table border=1 cellpadding=4 cellspacing=0>
6189 <thead>
6190 <tr>
6191 <th colspan="2">Chain information for PSI_BFd.opt.pdb 3 #4.3</th>
6192 </tr>
6193 <tr>
6194 <th>Chain</th>
6195 <th>Description</th>
6196
6197 </tr>
6198 </thead>
6199 <tbody>
6200 <tr>
6201 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.3/?:1477-1556">?</a></td>
6202 <td><a title="Show sequence" href="cxcmd:sequence chain #4.3/?">No description available</a></td>
6203
6204 </tr>
6205 </tbody>
6206</table><br/><table border=1 cellpadding=4 cellspacing=0>
6207 <thead>
6208 <tr>
6209 <th colspan="2">Chain information for PSI_BFd.opt.pdb 4 #4.4</th>
6210 </tr>
6211 <tr>
6212 <th>Chain</th>
6213 <th>Description</th>
6214
6215 </tr>
6216 </thead>
6217 <tbody>
6218 <tr>
6219 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.4/?:1557-1699">?</a></td>
6220 <td><a title="Show sequence" href="cxcmd:sequence chain #4.4/?">No description available</a></td>
6221
6222 </tr>
6223 </tbody>
6224</table><br/><table border=1 cellpadding=4 cellspacing=0>
6225 <thead>
6226 <tr>
6227 <th colspan="2">Chain information for PSI_BFd.opt.pdb 5 #4.5</th>
6228 </tr>
6229 <tr>
6230 <th>Chain</th>
6231 <th>Description</th>
6232
6233 </tr>
6234 </thead>
6235 <tbody>
6236 <tr>
6237 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.5/?:1700-1765">?</a></td>
6238 <td><a title="Show sequence" href="cxcmd:sequence chain #4.5/?">No description available</a></td>
6239
6240 </tr>
6241 </tbody>
6242</table><br/><table border=1 cellpadding=4 cellspacing=0>
6243 <thead>
6244 <tr>
6245 <th colspan="2">Chain information for PSI_BFd.opt.pdb 6 #4.6</th>
6246 </tr>
6247 <tr>
6248 <th>Chain</th>
6249 <th>Description</th>
6250
6251 </tr>
6252 </thead>
6253 <tbody>
6254 <tr>
6255 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.6/?:1767-1826">?</a></td>
6256 <td><a title="Show sequence" href="cxcmd:sequence chain #4.6/?">No description available</a></td>
6257
6258 </tr>
6259 </tbody>
6260</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4.2">combine #4.2</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 2 #4.2 to &#x27;A&#x27;<br>
6261Traceback (most recent call last):<br>
6262&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6263&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6264&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6265&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6266&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6267&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6268&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6269&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6270&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6271&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6272ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6273<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4">combine #4</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 2 #4.2 to &#x27;A&#x27;<br>
6274Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 3 #4.3 to &#x27;B&#x27;<br>
6275Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 4 #4.4 to &#x27;C&#x27;<br>
6276Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 5 #4.5 to &#x27;D&#x27;<br>
6277Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 6 #4.6 to &#x27;E&#x27;<br>
6278Remapping chain ID &#x27; &#x27; in PSI_BFd.opt.pdb 1 #4.1 to &#x27;F&#x27;<br>
6279Traceback (most recent call last):<br>
6280&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6281&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6282&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6283&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6284&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6285&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6286&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6287&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6288&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6289&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6290ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6291<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.2 B</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.2 B">changechains #4.2 B</a></div></div>Chain IDs of 733 residues changed<br>
6292<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.3 C</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.3 C">changechains #4.3 C</a></div></div>Chain IDs of 82 residues changed<br>
6293<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.4 D</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.4 D">changechains #4.4 D</a></div></div>Chain IDs of 143 residues changed<br>
6294<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.5 E</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.5 E">changechains #4.5 E</a></div></div>Chain IDs of 67 residues changed<br>
6295<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.6 F</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.6 F">changechains #4.6 F</a></div></div>Chain IDs of 62 residues changed<br>
6296<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.1:1829 start 3001</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.1:1829 start 3001">renumber #4.1:1829 start 3001</a></div></div>1 residues renumbered<br>
6297<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.2 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.2 start 1">renumber #4.2 start 1</a></div></div>733 residues renumbered<br>
6298<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.3 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.3 start 1">renumber #4.3 start 1</a></div></div>82 residues renumbered<br>
6299<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.3:354-355 start 3002</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.3:354-355 start 3002">renumber #4.3:354-355 start 3002</a></div></div>2 residues renumbered<br>
6300<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.4 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.4 start 1">renumber #4.4 start 1</a></div></div>143 residues renumbered<br>
6301<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.5 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.5 start 1">renumber #4.5 start 1</a></div></div>67 residues renumbered<br>
6302<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.6 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.6 start 1">renumber #4.6 start 1</a></div></div>62 residues renumbered<br>
6303<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb&quot; models #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb&quot; models #4">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb&quot; models #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb&quot;</a></div></div>
6304<table border=1 cellpadding=4 cellspacing=0>
6305 <thead>
6306 <tr>
6307 <th colspan="2">Summary of feedback from opening /Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt.pdb</th>
6308 </tr>
6309 </thead>
6310 <tbody>
6311 <tr>
6312 <td><i>warnings</i></td> <td style="background-color:#ffb961">Start residue of secondary structure not found: HELIX 1 1 THR 36 ALA 44 1 9<br>Start residue of secondary structure not found: HELIX 2 2 PHE 49 HIE 52 1 4<br>Start residue of secondary structure not found: HELIX 3 3 LEU 56 GLY 85 1 30<br>Start residue of secondary structure not found: HELIX 4 4 TYR 91 ASN 96 1 6<br>Start residue of secondary structure not found: HELIX 5 5 GLN 114 LEU 117 1 4<br>180 messages similar to the above omitted</td> </tr>
6313 </tbody>
6314</table><br/><table border=1 cellpadding=4 cellspacing=0>
6315 <thead>
6316 <tr>
6317 <th colspan="2">Chain information for PSI_BFd_SF4_opt.pdb</th>
6318 </tr>
6319 <tr>
6320 <th>Chain</th>
6321 <th>Description</th>
6322
6323 </tr>
6324 </thead>
6325 <tbody>
6326 <tr>
6327 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5.1/?:1-743">5.1/?</a></td>
6328 <td><a title="Show sequence" href="cxcmd:sequence chain #5.1/?">No description available</a></td>
6329
6330 </tr>
6331 <tr>
6332 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5.2/B:1-733">5.2/B</a></td>
6333 <td><a title="Show sequence" href="cxcmd:sequence chain #5.2/B">No description available</a></td>
6334
6335 </tr>
6336 <tr>
6337 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5.3/C:1-80">5.3/C</a></td>
6338 <td><a title="Show sequence" href="cxcmd:sequence chain #5.3/C">No description available</a></td>
6339
6340 </tr>
6341 <tr>
6342 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5.4/D:1-143">5.4/D</a></td>
6343 <td><a title="Show sequence" href="cxcmd:sequence chain #5.4/D">No description available</a></td>
6344
6345 </tr>
6346 <tr>
6347 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5.5/E:1-66">5.5/E</a></td>
6348 <td><a title="Show sequence" href="cxcmd:sequence chain #5.5/E">No description available</a></td>
6349
6350 </tr>
6351 <tr>
6352 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5.6/F:1-60">5.6/F</a></td>
6353 <td><a title="Show sequence" href="cxcmd:sequence chain #5.6/F">No description available</a></td>
6354
6355 </tr>
6356 </tbody>
6357</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #5.1#5.2#5.3#5.4#5.5#5.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #5.1#5.2#5.3#5.4#5.5#5.6">combine #5.1#5.2#5.3#5.4#5.5#5.6</a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd_SF4_opt.pdb #5.1 to &#x27;A&#x27;<br>
6358Traceback (most recent call last):<br>
6359&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6360&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6361&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6362&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6363&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6364&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6365&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6366&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6367&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6368&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6369ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6370<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #5">close #5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_[NUMBER].pdb&quot; models #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_[NUMBER].pdb&quot; models #4">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_[NUMBER].pdb&quot; models #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_A.pdb&quot; models #4.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_A.pdb&quot; models #4.1">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_A.pdb&quot; models #4.1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_B.pdb&quot; models #4.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_B.pdb&quot; models #4.2">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_B.pdb&quot; models #4.2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_A.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_B.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_A.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_B.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_A.pdb&quot; &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd_SF4_opt_B.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
6371 <thead>
6372 <tr>
6373 <th colspan="2">Chain information for PSI_BFd_SF4_opt_A.pdb #5</th>
6374 </tr>
6375 <tr>
6376 <th>Chain</th>
6377 <th>Description</th>
6378
6379 </tr>
6380 </thead>
6381 <tbody>
6382 <tr>
6383 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/?:1-743">?</a></td>
6384 <td><a title="Show sequence" href="cxcmd:sequence chain #5/?">No description available</a></td>
6385
6386 </tr>
6387 </tbody>
6388</table><br/><table border=1 cellpadding=4 cellspacing=0>
6389 <thead>
6390 <tr>
6391 <th colspan="2">Chain information for PSI_BFd_SF4_opt_B.pdb #6</th>
6392 </tr>
6393 <tr>
6394 <th>Chain</th>
6395 <th>Description</th>
6396
6397 </tr>
6398 </thead>
6399 <tbody>
6400 <tr>
6401 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/B:1-733">B</a></td>
6402 <td><a title="Show sequence" href="cxcmd:sequence chain #6/B">No description available</a></td>
6403
6404 </tr>
6405 </tbody>
6406</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #5#6 </div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #5#6 ">combine #5#6 </a></div></div>Remapping chain ID &#x27; &#x27; in PSI_BFd_SF4_opt_A.pdb #5 to &#x27;A&#x27;<br>
6407Traceback (most recent call last):<br>
6408&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
6409&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
6410&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3213, in run<br>
6411&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
6412&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6413&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/cmd.py&quot;, line 144, in combine_cmd<br>
6414&nbsp;&nbsp;&nbsp;&nbsp;residues[residues.chain_ids == chain_id].chain_ids = new_id<br>
6415&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
6416&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 234, in set_prop<br>
6417&nbsp;&nbsp;&nbsp;&nbsp;cset(self._c_pointers, n, v)<br>
6418ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br>
6419<br/>ValueError: Cannot set polymeric chain ID directly from Residue; must use Chain<br><br> File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 234, in set_prop<br> cset(self._c_pointers, n, v)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #6#4-5</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #6#4-5">close #6#4-5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
6420 <thead>
6421 <tr>
6422 <th colspan="2">Chain information for PSI_BFd.opt.pdb #4</th>
6423 </tr>
6424 <tr>
6425 <th>Chain</th>
6426 <th>Description</th>
6427
6428 </tr>
6429 </thead>
6430 <tbody>
6431 <tr>
6432 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4/?:1-1826">?</a></td>
6433 <td><a title="Show sequence" href="cxcmd:sequence chain #4/?">No description available</a></td>
6434
6435 </tr>
6436 </tbody>
6437</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #4 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #4 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826">split #4 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699 atoms :1700-1766 atoms :1767-1826</a></div></div>Split PSI_BFd.opt.pdb (#4) into 7 models<br>
6438<table border=1 cellpadding=4 cellspacing=0>
6439 <thead>
6440 <tr>
6441 <th colspan="2">Chain information for PSI_BFd.opt.pdb 1 #4.1</th>
6442 </tr>
6443 <tr>
6444 <th>Chain</th>
6445 <th>Description</th>
6446
6447 </tr>
6448 </thead>
6449 <tbody>
6450 <tr>
6451 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.1/?:1-743">?</a></td>
6452 <td><a title="Show sequence" href="cxcmd:sequence chain #4.1/?">No description available</a></td>
6453
6454 </tr>
6455 </tbody>
6456</table><br/><table border=1 cellpadding=4 cellspacing=0>
6457 <thead>
6458 <tr>
6459 <th colspan="2">Chain information for PSI_BFd.opt.pdb 2 #4.2</th>
6460 </tr>
6461 <tr>
6462 <th>Chain</th>
6463 <th>Description</th>
6464
6465 </tr>
6466 </thead>
6467 <tbody>
6468 <tr>
6469 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.2/?:744-1476">?</a></td>
6470 <td><a title="Show sequence" href="cxcmd:sequence chain #4.2/?">No description available</a></td>
6471
6472 </tr>
6473 </tbody>
6474</table><br/><table border=1 cellpadding=4 cellspacing=0>
6475 <thead>
6476 <tr>
6477 <th colspan="2">Chain information for PSI_BFd.opt.pdb 3 #4.3</th>
6478 </tr>
6479 <tr>
6480 <th>Chain</th>
6481 <th>Description</th>
6482
6483 </tr>
6484 </thead>
6485 <tbody>
6486 <tr>
6487 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.3/?:1477-1556">?</a></td>
6488 <td><a title="Show sequence" href="cxcmd:sequence chain #4.3/?">No description available</a></td>
6489
6490 </tr>
6491 </tbody>
6492</table><br/><table border=1 cellpadding=4 cellspacing=0>
6493 <thead>
6494 <tr>
6495 <th colspan="2">Chain information for PSI_BFd.opt.pdb 4 #4.4</th>
6496 </tr>
6497 <tr>
6498 <th>Chain</th>
6499 <th>Description</th>
6500
6501 </tr>
6502 </thead>
6503 <tbody>
6504 <tr>
6505 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.4/?:1557-1699">?</a></td>
6506 <td><a title="Show sequence" href="cxcmd:sequence chain #4.4/?">No description available</a></td>
6507
6508 </tr>
6509 </tbody>
6510</table><br/><table border=1 cellpadding=4 cellspacing=0>
6511 <thead>
6512 <tr>
6513 <th colspan="2">Chain information for PSI_BFd.opt.pdb 5 #4.5</th>
6514 </tr>
6515 <tr>
6516 <th>Chain</th>
6517 <th>Description</th>
6518
6519 </tr>
6520 </thead>
6521 <tbody>
6522 <tr>
6523 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.5/?:1700-1765">?</a></td>
6524 <td><a title="Show sequence" href="cxcmd:sequence chain #4.5/?">No description available</a></td>
6525
6526 </tr>
6527 </tbody>
6528</table><br/><table border=1 cellpadding=4 cellspacing=0>
6529 <thead>
6530 <tr>
6531 <th colspan="2">Chain information for PSI_BFd.opt.pdb 6 #4.6</th>
6532 </tr>
6533 <tr>
6534 <th>Chain</th>
6535 <th>Description</th>
6536
6537 </tr>
6538 </thead>
6539 <tbody>
6540 <tr>
6541 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4.6/?:1767-1826">?</a></td>
6542 <td><a title="Show sequence" href="cxcmd:sequence chain #4.6/?">No description available</a></td>
6543
6544 </tr>
6545 </tbody>
6546</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4.7 models">hide #!4.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1 models">hide #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2 models">hide #2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.2 B</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.2 B">changechains #4.2 B</a></div></div>Chain IDs of 733 residues changed<br>
6547<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.3 C</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.3 C">changechains #4.3 C</a></div></div>Chain IDs of 80 residues changed<br>
6548<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.4 D</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.4 D">changechains #4.4 D</a></div></div>Chain IDs of 143 residues changed<br>
6549<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.5 E</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.5 E">changechains #4.5 E</a></div></div>Chain IDs of 67 residues changed<br>
6550<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.6 F</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.6 F">changechains #4.6 F</a></div></div>Chain IDs of 60 residues changed<br>
6551<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.2 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.2 start 1">renumber #4.2 start 1</a></div></div>733 residues renumbered<br>
6552<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.3 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.3 start 1">renumber #4.3 start 1</a></div></div>80 residues renumbered<br>
6553<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.4 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.4 start 1">renumber #4.4 start 1</a></div></div>143 residues renumbered<br>
6554<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.5 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.5 start 1">renumber #4.5 start 1</a></div></div>67 residues renumbered<br>
6555<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #4.6 start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #4.6 start 1">renumber #4.6 start 1</a></div></div>60 residues renumbered<br>
6556<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.1 A</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.1 A">changechains #4.1 A</a></div></div>Chain IDs of 743 residues changed<br>
6557<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #4.7 X</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #4.7 X">changechains #4.7 X</a></div></div>Chain IDs of 5 residues changed<br>
6558<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4.1#4.2#4.3#4.4#4.5#4.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4.1#4.2#4.3#4.4#4.5#4.6">combine #4.1#4.2#4.3#4.4#4.5#4.6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #4.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #4.7">combine #4.7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #5#6</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #5#6">combine #5#6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5 models">hide #5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#sequential">color sequential</a> #7 chains palette accent</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sequential #7 chains palette accent">color sequential #7 chains palette accent</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1 models">show #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1 models">hide #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #!7 byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color #!7 byhetero">color #!7 byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/X:1827@F2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/X:1827@F2">select #7/X:1827@F2</a></div></div>1 atom, 1 residue, 1 model selected<br>
6559<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #5#4,6</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #5#4,6">close #5#4,6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #7 PSI_BFD_SF4_opt.pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #7 PSI_BFD_SF4_opt.pdb">rename #7 PSI_BFD_SF4_opt.pdb</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #7 id #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #7 id #4">rename #7 id #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1 models">show #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #3">select add #3</a></div></div>763 atoms, 681 bonds, 8 pseudobonds, 152 residues, 3 models selected<br>
6560<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #3">select subtract #3</a></div></div>1 atom, 1 residue, 1 model selected<br>
6561<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3">select #3</a></div></div>762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected<br>
6562<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3:cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3:cys">select #3:cys</a></div></div>80 atoms, 72 bonds, 8 residues, 1 model selected<br>
6563<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1 models">hide #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #3:SF4 toAtoms #4:1827-1828</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #3:SF4 toAtoms #4:1827-1828">align #3:SF4 toAtoms #4:1827-1828</a></div></div>RMSD between 16 atom pairs is 0.346 angstroms<br>
6564<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1 models">show #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1 models">hide #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831 @&lt;9 &amp;#4/X:1827</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831 @&lt;9 &amp;#4/X:1827">select #4/X:1831 @&lt;9 &amp;#4/X:1827</a></div></div>Nothing selected<br>
6565<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831 @&lt;10 &amp;#4/X:1827</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831 @&lt;10 &amp;#4/X:1827">select #4/X:1831 @&lt;10 &amp;#4/X:1827</a></div></div>2 atoms, 1 pseudobond, 1 residue, 2 models selected<br>
6566<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831 @&lt;9.2 &amp;#4/X:1827</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831 @&lt;9.2 &amp;#4/X:1827">select #4/X:1831 @&lt;9.2 &amp;#4/X:1827</a></div></div>Nothing selected<br>
6567<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831 @&lt;9.5 &amp;#4/X:1827</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831 @&lt;9.5 &amp;#4/X:1827">select #4/X:1831 @&lt;9.5 &amp;#4/X:1827</a></div></div>Nothing selected<br>
6568<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831 @&lt;9.8 &amp;#4/X:1827</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831 @&lt;9.8 &amp;#4/X:1827">select #4/X:1831 @&lt;9.8 &amp;#4/X:1827</a></div></div>2 atoms, 1 pseudobond, 1 residue, 2 models selected<br>
6569<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831 @&lt;9.7 &amp;#4/X:1827</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831 @&lt;9.7 &amp;#4/X:1827">select #4/X:1831 @&lt;9.7 &amp;#4/X:1827</a></div></div>1 atom, 1 residue, 1 model selected<br>
6570<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1827 @&lt;9.7 &amp;#4/X:1831</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1827 @&lt;9.7 &amp;#4/X:1831">select #4/X:1827 @&lt;9.7 &amp;#4/X:1831</a></div></div>1 atom, 1 residue, 1 model selected<br>
6571<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831 @&lt;9.7 &amp;#4/X:1827</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831 @&lt;9.7 &amp;#4/X:1827">select #4/X:1831 @&lt;9.7 &amp;#4/X:1827</a></div></div>1 atom, 1 residue, 1 model selected<br>
6572<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831@F2:1827@F1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831@F2:1827@F1">select #4/X:1831@F2:1827@F1</a></div></div>2 atoms, 2 residues, 1 model selected<br>
6573<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831@F1:1827@F2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831@F1:1827@F2">select #4/X:1831@F1:1827@F2</a></div></div>2 atoms, 2 residues, 1 model selected<br>
6574<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Distances</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Distances">ui tool show Distances</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #4/X:1827@F2 #4/X:1831@F1</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #4/X:1827@F2 #4/X:1831@F1">distance #4/X:1827@F2 #4/X:1831@F1</a></div></div>Distance between PSI_BFD_SF4_opt.pdb #4/X SF4 1827 F2 and SF4 1831 F1: 9.521Å
6575<br>
6576<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A-F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A-F">select #4/A-F</a></div></div>28475 atoms, 28948 bonds, 1826 residues, 1 model selected<br>
6577<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A-F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A-F">select #4/A-F</a></div></div>28475 atoms, 28948 bonds, 1826 residues, 1 model selected<br>
6578<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel surfaces</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel surfaces">show sel surfaces</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/A">coulombic #4/A</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
6579Assigning partial charges to residue CYF (net charge +1) with am1-bcc method<br>
6580Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n<br>
6581(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.in.mol2); atoms read (22), bonds read (21).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 92; net charge: 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
6582Coulombic values for PSI_BFD_SF4_opt.pdb_A SES surface #4.2: minimum, -12.49, mean 0.00, maximum 20.13<br>
6583<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/B">coulombic #4/B</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
6584Assigning partial charges to residue CYF (net charge -1) with am1-bcc method<br>
6585Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n<br>
6586(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.in.mol2); atoms read (22), bonds read (21).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 94; net charge: -1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
6587Coulombic values for PSI_BFD_SF4_opt.pdb_B SES surface #4.3: minimum, -15.85, mean -0.16, maximum 13.13<br>
6588<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/C</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/C">coulombic #4/C</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
6589Assigning partial charges to residue CYF (net charge -1) with am1-bcc method<br>
6590Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n<br>
6591(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.in.mol2); atoms read (22), bonds read (21).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 94; net charge: -1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
6592Coulombic values for PSI_BFD_SF4_opt.pdb_C SES surface #4.4: minimum, -22.24, mean -4.06, maximum 8.43<br>
6593<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/D</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/D">coulombic #4/D</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
6594Coulombic values for PSI_BFD_SF4_opt.pdb_D SES surface #4.5: minimum, -11.15, mean 2.11, maximum 15.26<br>
6595<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/E">coulombic #4/E</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
6596Coulombic values for PSI_BFD_SF4_opt.pdb_E SES surface #4.6: minimum, -11.38, mean 1.55, maximum 11.87<br>
6597<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/F">coulombic #4/F</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
6598Assigning partial charges to residue CYF (net charge +0) with am1-bcc method<br>
6599Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n<br>
6600(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.in.mol2); atoms read (23), bonds read (22).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 94; net charge: 0</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
6601Coulombic values for PSI_BFD_SF4_opt.pdb_F SES surface #4.7: minimum, -16.02, mean -3.74, maximum 7.04<br>
6602<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Wed Oct 9 21:29:02 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
6603<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.7 models">hide #4.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.4 models">hide #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.4 models">show #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.4 models">hide #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.3 models">hide #4.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.2 models">hide #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>829 atoms, 836 bonds, 60 residues, 1 model selected<br>
6604<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false reveal true log true</a></div></div>Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt.pdb #4/A CYF 575 SG<br>
6605Wrong number of grandchild atoms for phi/psi acceptor PSI_BFD_SF4_opt.pdb #4/A CYF 575 SG<br>
6606<br>
6607[Repeated 1 time(s)]<p style="color:darkorange">Skipped 2 atom(s) with bad connectivities; see log for details<br>
6608</p><pre>Finding intramodel H-bonds
6609Constraints relaxed by 0.4 angstroms and 20 degrees
6610Models used:
6611 4 PSI_BFD_SF4_opt.pdb
6612
661321 H-bonds
6614H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6615PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1 PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 HH11 2.760 1.842
6616PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 HH21 2.719 1.800
6617PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ PSI_BFD_SF4_opt.pdb #4/F ASP 29 O PSI_BFD_SF4_opt.pdb #4/A LYS 31 HZ1 3.148 2.456
6618PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2 PSI_BFD_SF4_opt.pdb #4/A LYS 31 HZ2 2.746 1.778
6619PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1 PSI_BFD_SF4_opt.pdb #4/C ARG 18 HH11 2.812 1.825
6620PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 HH11 3.358 2.560
6621PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 HH22 2.780 1.765
6622PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ PSI_BFD_SF4_opt.pdb #4/F PRO 17 O PSI_BFD_SF4_opt.pdb #4/D LYS 109 HZ1 2.917 2.045
6623PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1 PSI_BFD_SF4_opt.pdb #4/D LYS 109 HZ2 2.737 1.813
6624PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 HE 2.875 1.950
6625PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1 PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 HH12 2.980 2.103
6626PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 HH22 2.848 1.943
6627PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 HH21 2.738 1.784
6628PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1 PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 HG1 2.666 1.685
6629PSI_BFD_SF4_opt.pdb #4/E ASN 56 ND2 PSI_BFD_SF4_opt.pdb #4/F PRO 52 O PSI_BFD_SF4_opt.pdb #4/E ASN 56 HD22 3.598 2.755
6630PSI_BFD_SF4_opt.pdb #4/E ALA 67 N PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD1 PSI_BFD_SF4_opt.pdb #4/E ALA 67 H1 3.484 2.798
6631PSI_BFD_SF4_opt.pdb #4/E ALA 67 N PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 H1 2.745 1.804
6632PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 PSI_BFD_SF4_opt.pdb #4/F ARG 31 HE 2.902 1.898
6633PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 PSI_BFD_SF4_opt.pdb #4/F ARG 31 HH12 2.894 1.970
6634PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2 PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 PSI_BFD_SF4_opt.pdb #4/F ARG 31 HH21 3.324 2.539
6635PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 PSI_BFD_SF4_opt.pdb #4/F ARG 31 HH22 2.784 1.818
6636</pre><br/>21 hydrogen bonds found<br>
6637<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 60 items<br>
6638<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:SF4">select #4:SF4</a></div></div>40 atoms, 91 pseudobonds, 5 residues, 3 models selected<br>
6639<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 40 atom styles<br>
6640<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>829 atoms, 836 bonds, 60 residues, 1 model selected<br>
6641<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Contacts">ui tool show Contacts</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F &amp;~H">select #4/F &amp;~H</a></div></div>430 atoms, 437 bonds, 60 residues, 1 model selected<br>
6642<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true">contacts sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false color #76d6ff radius 0.2 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
6643H-bond overlap reduction: 0.4
6644Ignore contacts between atoms separated by 4 bonds or less
6645Ignore contacts between atoms in residues less than 5 apart in sequence
6646Detect intra-residue contacts: False
6647Detect intra-molecule contacts: False
6648
664988 contacts
6650 atom1 atom2 overlap distance
6651PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 2.060 1.340
6652PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.981 2.479
6653PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA 0.878 2.462
6654PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.466 2.254
6655PSI_BFD_SF4_opt.pdb #4/F TYR 1 C PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.397 3.063
6656PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.361 2.819
6657PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.215 3.025
6658PSI_BFD_SF4_opt.pdb #4/F GLY 13 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 0.214 3.036
6659PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG 0.203 3.197
6660PSI_BFD_SF4_opt.pdb #4/F TYR 1 C PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.161 3.019
6661PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 C 0.154 3.026
6662PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 C 0.095 3.085
6663PSI_BFD_SF4_opt.pdb #4/F GLU 18 CD PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ 0.059 3.266
6664PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1 PSI_BFD_SF4_opt.pdb #4/C PRO 58 CB 0.048 3.352
6665PSI_BFD_SF4_opt.pdb #4/F THR 7 CA PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 0.005 3.320
6666PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 CZ -0.006 3.186
6667PSI_BFD_SF4_opt.pdb #4/F ALA 38 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA -0.013 3.193
6668PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.014 2.719
6669PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 O -0.032 3.212
6670PSI_BFD_SF4_opt.pdb #4/F TYR 1 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 C -0.032 3.272
6671PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1 PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ -0.032 2.737
6672PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.033 2.738
6673PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.040 2.745
6674PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2 PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ -0.041 2.746
6675PSI_BFD_SF4_opt.pdb #4/F THR 7 C PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.042 3.367
6676PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.049 3.449
6677PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 CG2 -0.052 3.232
6678PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 CB -0.054 3.234
6679PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1 -0.055 2.760
6680PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ -0.060 3.240
6681PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.075 2.780
6682PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.079 2.784
6683PSI_BFD_SF4_opt.pdb #4/F GLY 13 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.080 3.405
6684PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1 -0.086 2.666
6685PSI_BFD_SF4_opt.pdb #4/F ALA 38 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB -0.088 3.268
6686PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 -0.100 3.425
6687PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA -0.103 3.283
6688PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1 PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 -0.107 2.812
6689PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 CB -0.122 3.302
6690PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 C -0.130 3.530
6691PSI_BFD_SF4_opt.pdb #4/F GLY 13 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.134 3.459
6692PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.136 3.316
6693PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.143 2.848
6694PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB -0.146 3.486
6695PSI_BFD_SF4_opt.pdb #4/F GLY 13 O PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ -0.147 3.327
6696PSI_BFD_SF4_opt.pdb #4/F CYF 12 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.148 3.473
6697PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG -0.162 3.562
6698PSI_BFD_SF4_opt.pdb #4/F MET 53 SD PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1 -0.167 3.649
6699PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE -0.170 2.875
6700PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 -0.177 2.902
6701PSI_BFD_SF4_opt.pdb #4/F GLU 8 N PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.182 3.432
6702PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.182 3.507
6703PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ -0.183 3.363
6704PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.187 3.512
6705PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 CB -0.188 3.368
6706PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 CA -0.188 3.368
6707PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.189 2.894
6708PSI_BFD_SF4_opt.pdb #4/F ASP 43 CG PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.197 3.522
6709PSI_BFD_SF4_opt.pdb #4/F PRO 17 O PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ -0.212 2.917
6710PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 CG1 -0.215 3.615
6711PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.219 3.619
6712PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1 -0.225 3.625
6713PSI_BFD_SF4_opt.pdb #4/F PRO 17 CG PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.230 3.555
6714PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.238 3.503
6715PSI_BFD_SF4_opt.pdb #4/F GLY 13 O PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.254 2.959
6716PSI_BFD_SF4_opt.pdb #4/F ALA 14 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.256 3.506
6717PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 N -0.272 2.977
6718PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1 -0.275 2.980
6719PSI_BFD_SF4_opt.pdb #4/F TYR 1 CB PSI_BFD_SF4_opt.pdb #4/E ALA 67 C -0.275 3.735
6720PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1 PSI_BFD_SF4_opt.pdb #4/C PRO 58 CG -0.291 3.691
6721PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1 -0.299 3.499
6722PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1 -0.301 3.626
6723PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 CB -0.316 3.716
6724PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD PSI_BFD_SF4_opt.pdb #4/E SER 53 CB -0.323 3.723
6725PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.332 3.657
6726PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.337 3.662
6727PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 -0.342 3.542
6728PSI_BFD_SF4_opt.pdb #4/F ASP 29 CA PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.346 3.671
6729PSI_BFD_SF4_opt.pdb #4/F CYF 12 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.353 3.753
6730PSI_BFD_SF4_opt.pdb #4/F GLY 13 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.355 3.680
6731PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ -0.356 3.536
6732PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ -0.363 3.688
6733PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 O -0.366 3.546
6734PSI_BFD_SF4_opt.pdb #4/F VAL 50 CA PSI_BFD_SF4_opt.pdb #4/C ALA 35 CB -0.371 3.771
6735PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 O -0.372 3.332
6736PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB -0.376 3.776
6737PSI_BFD_SF4_opt.pdb #4/F PRO 52 CG PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB -0.389 3.789
6738PSI_BFD_SF4_opt.pdb #4/F PRO 17 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.394 3.719
6739</pre><br/>88 contacts<br>
6740<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false select true color #ff85ff radius 0.2 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false select true color #ff85ff radius 0.2 reveal true log true">contacts sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false select true color #ff85ff radius 0.2 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
6741H-bond overlap reduction: 0.4
6742Ignore contacts between atoms separated by 4 bonds or less
6743Ignore contacts between atoms in residues less than 5 apart in sequence
6744Detect intra-residue contacts: False
6745Detect intra-molecule contacts: False
6746
674788 contacts
6748 atom1 atom2 overlap distance
6749PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 2.060 1.340
6750PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.981 2.479
6751PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA 0.878 2.462
6752PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.466 2.254
6753PSI_BFD_SF4_opt.pdb #4/F TYR 1 C PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.397 3.063
6754PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.361 2.819
6755PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.215 3.025
6756PSI_BFD_SF4_opt.pdb #4/F GLY 13 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 0.214 3.036
6757PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG 0.203 3.197
6758PSI_BFD_SF4_opt.pdb #4/F TYR 1 C PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.161 3.019
6759PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 C 0.154 3.026
6760PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 C 0.095 3.085
6761PSI_BFD_SF4_opt.pdb #4/F GLU 18 CD PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ 0.059 3.266
6762PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1 PSI_BFD_SF4_opt.pdb #4/C PRO 58 CB 0.048 3.352
6763PSI_BFD_SF4_opt.pdb #4/F THR 7 CA PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 0.005 3.320
6764PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 CZ -0.006 3.186
6765PSI_BFD_SF4_opt.pdb #4/F ALA 38 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA -0.013 3.193
6766PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.014 2.719
6767PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 O -0.032 3.212
6768PSI_BFD_SF4_opt.pdb #4/F TYR 1 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 C -0.032 3.272
6769PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1 PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ -0.032 2.737
6770PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.033 2.738
6771PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.040 2.745
6772PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2 PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ -0.041 2.746
6773PSI_BFD_SF4_opt.pdb #4/F THR 7 C PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.042 3.367
6774PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.049 3.449
6775PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 CG2 -0.052 3.232
6776PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 CB -0.054 3.234
6777PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1 -0.055 2.760
6778PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ -0.060 3.240
6779PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.075 2.780
6780PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.079 2.784
6781PSI_BFD_SF4_opt.pdb #4/F GLY 13 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.080 3.405
6782PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1 -0.086 2.666
6783PSI_BFD_SF4_opt.pdb #4/F ALA 38 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB -0.088 3.268
6784PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 -0.100 3.425
6785PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA -0.103 3.283
6786PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1 PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 -0.107 2.812
6787PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 CB -0.122 3.302
6788PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 C -0.130 3.530
6789PSI_BFD_SF4_opt.pdb #4/F GLY 13 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.134 3.459
6790PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.136 3.316
6791PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.143 2.848
6792PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB -0.146 3.486
6793PSI_BFD_SF4_opt.pdb #4/F GLY 13 O PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ -0.147 3.327
6794PSI_BFD_SF4_opt.pdb #4/F CYF 12 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.148 3.473
6795PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG -0.162 3.562
6796PSI_BFD_SF4_opt.pdb #4/F MET 53 SD PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1 -0.167 3.649
6797PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE -0.170 2.875
6798PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 -0.177 2.902
6799PSI_BFD_SF4_opt.pdb #4/F GLU 8 N PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.182 3.432
6800PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.182 3.507
6801PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ -0.183 3.363
6802PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.187 3.512
6803PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 CB -0.188 3.368
6804PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 CA -0.188 3.368
6805PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.189 2.894
6806PSI_BFD_SF4_opt.pdb #4/F ASP 43 CG PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.197 3.522
6807PSI_BFD_SF4_opt.pdb #4/F PRO 17 O PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ -0.212 2.917
6808PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 CG1 -0.215 3.615
6809PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.219 3.619
6810PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1 -0.225 3.625
6811PSI_BFD_SF4_opt.pdb #4/F PRO 17 CG PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.230 3.555
6812PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.238 3.503
6813PSI_BFD_SF4_opt.pdb #4/F GLY 13 O PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.254 2.959
6814PSI_BFD_SF4_opt.pdb #4/F ALA 14 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.256 3.506
6815PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 N -0.272 2.977
6816PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1 -0.275 2.980
6817PSI_BFD_SF4_opt.pdb #4/F TYR 1 CB PSI_BFD_SF4_opt.pdb #4/E ALA 67 C -0.275 3.735
6818PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1 PSI_BFD_SF4_opt.pdb #4/C PRO 58 CG -0.291 3.691
6819PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1 -0.299 3.499
6820PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1 -0.301 3.626
6821PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 CB -0.316 3.716
6822PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD PSI_BFD_SF4_opt.pdb #4/E SER 53 CB -0.323 3.723
6823PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.332 3.657
6824PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.337 3.662
6825PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 -0.342 3.542
6826PSI_BFD_SF4_opt.pdb #4/F ASP 29 CA PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.346 3.671
6827PSI_BFD_SF4_opt.pdb #4/F CYF 12 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.353 3.753
6828PSI_BFD_SF4_opt.pdb #4/F GLY 13 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.355 3.680
6829PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ -0.356 3.536
6830PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ -0.363 3.688
6831PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 O -0.366 3.546
6832PSI_BFD_SF4_opt.pdb #4/F VAL 50 CA PSI_BFD_SF4_opt.pdb #4/C ALA 35 CB -0.371 3.771
6833PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 O -0.372 3.332
6834PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB -0.376 3.776
6835PSI_BFD_SF4_opt.pdb #4/F PRO 52 CG PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB -0.389 3.789
6836PSI_BFD_SF4_opt.pdb #4/F PRO 17 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.394 3.719
6837</pre><br/>88 contacts<br>
6838<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone true</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone true">setattr sel r ribbon_hide_backbone true</a></div></div>Assigning ribbon_hide_backbone attribute to 35 items<br>
6839<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 35 items<br>
6840<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.8 models">hide #4.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Clashes</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Clashes">ui tool show Clashes</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>829 atoms, 836 bonds, 60 residues, 1 model selected<br>
6841<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true">clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
6842H-bond overlap reduction: 0.4
6843Ignore clashes between atoms separated by 4 bonds or less
6844Ignore clashes between atoms in residues less than 5 apart in sequence
6845Detect intra-residue clashes: False
6846Detect intra-molecule clashes: False
6847
68484 clashes
6849 atom1 atom2 overlap distance
6850PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 2.060 1.340
6851PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.981 2.479
6852PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA 0.878 2.462
6853PSI_BFD_SF4_opt.pdb #4/F TYR 1 H PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.727 2.033
6854</pre><br/>4 clashes<br>
6855<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.9 models">hide #4.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/E">select #4/E</a></div></div>1071 atoms, 1082 bonds, 67 residues, 1 model selected<br>
6856<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1 models">show #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI_BFd.opt.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
6857 <thead>
6858 <tr>
6859 <th colspan="2">Chain information for PSI_BFd.opt.pdb #6</th>
6860 </tr>
6861 <tr>
6862 <th>Chain</th>
6863 <th>Description</th>
6864
6865 </tr>
6866 </thead>
6867 <tbody>
6868 <tr>
6869 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/?:1-1826">?</a></td>
6870 <td><a title="Show sequence" href="cxcmd:sequence chain #6/?">No description available</a></td>
6871
6872 </tr>
6873 </tbody>
6874</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #6 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699 atoms :1700-1765 atoms :1766-1826</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #6 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699 atoms :1700-1765 atoms :1766-1826">split #6 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699 atoms :1700-1765 atoms :1766-1826</a></div></div>Split PSI_BFd.opt.pdb (#6) into 7 models<br>
6875<table border=1 cellpadding=4 cellspacing=0>
6876 <thead>
6877 <tr>
6878 <th colspan="2">Chain information for PSI_BFd.opt.pdb 1 #6.1</th>
6879 </tr>
6880 <tr>
6881 <th>Chain</th>
6882 <th>Description</th>
6883
6884 </tr>
6885 </thead>
6886 <tbody>
6887 <tr>
6888 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6.1/?:1-743">?</a></td>
6889 <td><a title="Show sequence" href="cxcmd:sequence chain #6.1/?">No description available</a></td>
6890
6891 </tr>
6892 </tbody>
6893</table><br/><table border=1 cellpadding=4 cellspacing=0>
6894 <thead>
6895 <tr>
6896 <th colspan="2">Chain information for PSI_BFd.opt.pdb 2 #6.2</th>
6897 </tr>
6898 <tr>
6899 <th>Chain</th>
6900 <th>Description</th>
6901
6902 </tr>
6903 </thead>
6904 <tbody>
6905 <tr>
6906 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6.2/?:744-1476">?</a></td>
6907 <td><a title="Show sequence" href="cxcmd:sequence chain #6.2/?">No description available</a></td>
6908
6909 </tr>
6910 </tbody>
6911</table><br/><table border=1 cellpadding=4 cellspacing=0>
6912 <thead>
6913 <tr>
6914 <th colspan="2">Chain information for PSI_BFd.opt.pdb 3 #6.3</th>
6915 </tr>
6916 <tr>
6917 <th>Chain</th>
6918 <th>Description</th>
6919
6920 </tr>
6921 </thead>
6922 <tbody>
6923 <tr>
6924 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6.3/?:1477-1556">?</a></td>
6925 <td><a title="Show sequence" href="cxcmd:sequence chain #6.3/?">No description available</a></td>
6926
6927 </tr>
6928 </tbody>
6929</table><br/><table border=1 cellpadding=4 cellspacing=0>
6930 <thead>
6931 <tr>
6932 <th colspan="2">Chain information for PSI_BFd.opt.pdb 4 #6.4</th>
6933 </tr>
6934 <tr>
6935 <th>Chain</th>
6936 <th>Description</th>
6937
6938 </tr>
6939 </thead>
6940 <tbody>
6941 <tr>
6942 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6.4/?:1557-1699">?</a></td>
6943 <td><a title="Show sequence" href="cxcmd:sequence chain #6.4/?">No description available</a></td>
6944
6945 </tr>
6946 </tbody>
6947</table><br/><table border=1 cellpadding=4 cellspacing=0>
6948 <thead>
6949 <tr>
6950 <th colspan="2">Chain information for PSI_BFd.opt.pdb 5 #6.5</th>
6951 </tr>
6952 <tr>
6953 <th>Chain</th>
6954 <th>Description</th>
6955
6956 </tr>
6957 </thead>
6958 <tbody>
6959 <tr>
6960 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6.5/?:1700-1765">?</a></td>
6961 <td><a title="Show sequence" href="cxcmd:sequence chain #6.5/?">No description available</a></td>
6962
6963 </tr>
6964 </tbody>
6965</table><br/><table border=1 cellpadding=4 cellspacing=0>
6966 <thead>
6967 <tr>
6968 <th colspan="2">Chain information for PSI_BFd.opt.pdb 6 #6.6</th>
6969 </tr>
6970 <tr>
6971 <th>Chain</th>
6972 <th>Description</th>
6973
6974 </tr>
6975 </thead>
6976 <tbody>
6977 <tr>
6978 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6.6/?:1766-1826">?</a></td>
6979 <td><a title="Show sequence" href="cxcmd:sequence chain #6.6/?">No description available</a></td>
6980
6981 </tr>
6982 </tbody>
6983</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #6.1 A</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #6.1 A">changechains #6.1 A</a></div></div>Chain IDs of 743 residues changed<br>
6984<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #6.2 B</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #6.2 B">changechains #6.2 B</a></div></div>Chain IDs of 733 residues changed<br>
6985<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #6.3 C</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #6.3 C">changechains #6.3 C</a></div></div>Chain IDs of 80 residues changed<br>
6986<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #6.4 D</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #6.4 D">changechains #6.4 D</a></div></div>Chain IDs of 143 residues changed<br>
6987<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #6.5 E</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #6.5 E">changechains #6.5 E</a></div></div>Chain IDs of 66 residues changed<br>
6988<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #6.6 F</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #6.6 F">changechains #6.6 F</a></div></div>Chain IDs of 61 residues changed<br>
6989<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> #6.7 X</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains #6.7 X">changechains #6.7 X</a></div></div>Chain IDs of 5 residues changed<br>
6990<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #6.1#6.2#6.3#6.4#6.5#6.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #6.1#6.2#6.3#6.4#6.5#6.6">combine #6.1#6.2#6.3#6.4#6.5#6.6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #6.1#6.2#6.3#6.4#6.5#6.6#6.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #6.1#6.2#6.3#6.4#6.5#6.6#6.7">combine #6.1#6.2#6.3#6.4#6.5#6.6#6.7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #8/A-E seqStart 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #8/A-E seqStart 1">renumber #8/A-E seqStart 1</a></div></div>1022 residues renumbered<br>
6991<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.1 models">hide #4.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1 models">hide #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #7 models">hide #7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #8/A start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #8/A start 1">renumber #8/A start 1</a></div></div>0 residues renumbered<br>
6992<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #8/B start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #8/B start 1">renumber #8/B start 1</a></div></div>0 residues renumbered<br>
6993<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #8/C start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #8/C start 1">renumber #8/C start 1</a></div></div>0 residues renumbered<br>
6994<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #8/D start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #8/D start 1">renumber #8/D start 1</a></div></div>0 residues renumbered<br>
6995<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #8/E start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #8/E start 1">renumber #8/E start 1</a></div></div>0 residues renumbered<br>
6996<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/renumber.html">renumber</a> #8/F start 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:renumber #8/F start 1">renumber #8/F start 1</a></div></div>61 residues renumbered<br>
6997<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/F">select #8/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
6998<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true">clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
6999H-bond overlap reduction: 0.4
7000Ignore clashes between atoms separated by 4 bonds or less
7001Ignore clashes between atoms in residues less than 5 apart in sequence
7002Detect intra-residue clashes: False
7003Detect intra-molecule clashes: False
7004
70050 clashes
7006atom1 atom2 overlap distance
7007</pre><br/>No clashes<br>
7008<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #8/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #8/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true">clashes sel restrict #8/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
7009H-bond overlap reduction: 0.4
7010Ignore clashes between atoms separated by 4 bonds or less
7011Ignore clashes between atoms in residues less than 5 apart in sequence
7012Detect intra-residue clashes: False
7013Detect intra-molecule clashes: False
7014
70150 clashes
7016atom1 atom2 overlap distance
7017</pre><br/>No clashes<br>
7018<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #7#4-6</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #7#4-6">close #7#4-6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #8 id #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #8 id #4">rename #8 id #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #9">close #9</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
7019<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true">clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
7020H-bond overlap reduction: 0.4
7021Ignore clashes between atoms separated by 4 bonds or less
7022Ignore clashes between atoms in residues less than 5 apart in sequence
7023Detect intra-residue clashes: False
7024Detect intra-molecule clashes: False
7025
70260 clashes
7027atom1 atom2 overlap distance
7028</pre><br/>No clashes<br>
7029<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#sequential">color sequential</a> #4 chains palette accent</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sequential #4 chains palette accent">color sequential #4 chains palette accent</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
7030<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F &amp;~H">select #4/F &amp;~H</a></div></div>435 atoms, 442 bonds, 61 residues, 1 model selected<br>
7031<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 reveal true log true">contacts sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
7032H-bond overlap reduction: 0.4
7033Ignore contacts between atoms separated by 4 bonds or less
7034Ignore contacts between atoms in residues less than 5 apart in sequence
7035Detect intra-residue contacts: False
7036Detect intra-molecule contacts: False
7037
703871 contacts
7039 atom1 atom2 overlap distance
7040combination #4/F GLY 14 N combination #4/C GLN 15 NE2 0.214 3.036
7041combination #4/F CYF 13 CB combination #4/C GLN 15 CG 0.203 3.197
7042combination #4/F GLU 9 OE2 combination #4/E SER 53 C 0.154 3.026
7043combination #4/F GLY 50 O combination #4/C LYS 34 C 0.095 3.085
7044combination #4/F GLU 19 CD combination #4/D LYS 109 NZ 0.059 3.266
7045combination #4/F ILE 11 CD1 combination #4/C PRO 58 CB 0.048 3.352
7046combination #4/F THR 8 CA combination #4/E ARG 43 NH2 0.005 3.320
7047combination #4/F ASP 30 OD1 combination #4/A ARG 27 CZ -0.006 3.186
7048combination #4/F ASP 30 OD1 combination #4/A ARG 27 NH2 -0.014 2.719
7049combination #4/F MET 54 CE combination #4/E THR 54 O -0.032 3.212
7050combination #4/F GLU 19 OE1 combination #4/D LYS 109 NZ -0.032 2.737
7051combination #4/F GLU 9 OE1 combination #4/E ARG 43 NH2 -0.033 2.738
7052combination #4/F ASP 30 OD2 combination #4/A LYS 31 NZ -0.041 2.746
7053combination #4/F THR 8 C combination #4/E ARG 43 NH2 -0.042 3.367
7054combination #4/F CYF 13 CA combination #4/C GLN 15 CD -0.049 3.449
7055combination #4/F GLU 9 OE2 combination #4/E THR 54 CG2 -0.052 3.232
7056combination #4/F GLY 50 O combination #4/C LYS 34 CB -0.054 3.234
7057combination #4/F ASP 30 OD1 combination #4/A ARG 27 NH1 -0.055 2.760
7058combination #4/F GLU 9 OE1 combination #4/E ARG 43 CZ -0.060 3.240
7059combination #4/F GLU 17 OE2 combination #4/C ARG 18 NH2 -0.075 2.780
7060combination #4/F ARG 32 NH2 combination #4/A ASP 34 OD2 -0.079 2.784
7061combination #4/F GLY 14 N combination #4/C GLN 15 CD -0.080 3.405
7062combination #4/F GLU 9 OE2 combination #4/E THR 54 OG1 -0.086 2.666
7063combination #4/F GLU 17 CD combination #4/C ARG 18 NH1 -0.100 3.425
7064combination #4/F GLU 17 OE1 combination #4/C ARG 18 NH1 -0.107 2.812
7065combination #4/F GLU 9 OE2 combination #4/E THR 54 CB -0.122 3.302
7066combination #4/F MET 54 CE combination #4/E THR 54 C -0.130 3.530
7067combination #4/F GLY 14 C combination #4/C GLN 15 NE2 -0.134 3.459
7068combination #4/F ARG 32 CZ combination #4/A ASP 34 OD2 -0.136 3.316
7069combination #4/F ALA 7 O combination #4/E ARG 43 NH2 -0.143 2.848
7070combination #4/F GLY 14 O combination #4/C ARG 18 CZ -0.147 3.327
7071combination #4/F CYF 13 C combination #4/C GLN 15 NE2 -0.148 3.473
7072combination #4/F CYF 13 CA combination #4/C GLN 15 CG -0.162 3.562
7073combination #4/F MET 54 SD combination #4/C ILE 11 CD1 -0.167 3.649
7074combination #4/F GLU 9 OE1 combination #4/E ARG 43 NE -0.170 2.875
7075combination #4/F ARG 32 NE combination #4/A THR 28 OG1 -0.177 2.902
7076combination #4/F GLU 9 N combination #4/E ARG 43 NH2 -0.182 3.432
7077combination #4/F ASP 30 CG combination #4/A ARG 27 NH2 -0.182 3.507
7078combination #4/F ALA 7 O combination #4/E ARG 43 CZ -0.183 3.363
7079combination #4/F GLU 17 CD combination #4/C ARG 18 NH2 -0.187 3.512
7080combination #4/F GLU 9 OE2 combination #4/E SER 53 CB -0.188 3.368
7081combination #4/F GLU 9 OE2 combination #4/E SER 53 CA -0.188 3.368
7082combination #4/F ARG 32 NH1 combination #4/A ASP 34 OD2 -0.189 2.894
7083combination #4/F PRO 18 O combination #4/D LYS 109 NZ -0.212 2.917
7084combination #4/F PRO 53 CB combination #4/C ILE 11 CG1 -0.215 3.615
7085combination #4/F CYF 13 CB combination #4/C GLN 15 CD -0.219 3.619
7086combination #4/F PRO 53 CB combination #4/C ILE 11 CD1 -0.225 3.625
7087combination #4/F PRO 18 CG combination #4/C ARG 18 NH2 -0.230 3.555
7088combination #4/F GLY 14 O combination #4/C ARG 18 NH2 -0.254 2.959
7089combination #4/F ALA 15 N combination #4/C GLN 15 NE2 -0.256 3.506
7090combination #4/F GLU 9 OE2 combination #4/E THR 54 N -0.272 2.977
7091combination #4/F ALA 7 O combination #4/E ARG 43 NH1 -0.275 2.980
7092combination #4/F ILE 11 CD1 combination #4/C PRO 58 CG -0.291 3.691
7093combination #4/F MET 54 CE combination #4/E THR 54 OG1 -0.299 3.499
7094combination #4/F ASP 30 CG combination #4/A ARG 27 NH1 -0.301 3.626
7095combination #4/F MET 54 CE combination #4/E THR 54 CB -0.316 3.716
7096combination #4/F GLU 9 CD combination #4/E SER 53 CB -0.323 3.723
7097combination #4/F GLU 9 CD combination #4/E ARG 43 NH2 -0.332 3.657
7098combination #4/F CYF 13 CA combination #4/C GLN 15 NE2 -0.337 3.662
7099combination #4/F ARG 32 CZ combination #4/A THR 28 OG1 -0.342 3.542
7100combination #4/F ASP 30 CA combination #4/A ARG 27 NH2 -0.346 3.671
7101combination #4/F CYF 13 C combination #4/C GLN 15 CD -0.353 3.753
7102combination #4/F GLY 14 CA combination #4/C GLN 15 NE2 -0.355 3.680
7103combination #4/F GLU 17 OE2 combination #4/C ARG 18 CZ -0.356 3.536
7104combination #4/F ASP 30 CG combination #4/A LYS 31 NZ -0.363 3.688
7105combination #4/F PRO 53 CB combination #4/C ILE 11 O -0.366 3.546
7106combination #4/F VAL 51 CA combination #4/C ALA 35 CB -0.371 3.771
7107combination #4/F GLY 50 O combination #4/C LYS 34 O -0.372 3.332
7108combination #4/F PRO 53 CB combination #4/C CYF 13 CB -0.376 3.776
7109combination #4/F PRO 53 CG combination #4/C CYF 13 CB -0.389 3.789
7110combination #4/F PRO 18 CD combination #4/C ARG 18 NH2 -0.394 3.719
7111</pre><br/>71 contacts<br>
7112<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
7113<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false reveal true log true</a></div></div>Skipping possible acceptor with bad geometry: combination #4/A CYF 575 SG<br>
7114Wrong number of grandchild atoms for phi/psi acceptor combination #4/A CYF 575 SG<br>
7115<br>
7116[Repeated 1 time(s)]<p style="color:darkorange">Skipped 2 atom(s) with bad connectivities; see log for details<br>
7117</p><pre>Finding intramodel H-bonds
7118Constraints relaxed by 0.4 angstroms and 20 degrees
7119Models used:
7120 4 combination
7121
712219 H-bonds
7123H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
7124combination #4/A ARG 27 NH1 combination #4/F ASP 30 OD1 combination #4/A ARG 27 HH11 2.760 1.842
7125combination #4/A ARG 27 NH2 combination #4/F ASP 30 OD1 combination #4/A ARG 27 HH21 2.719 1.800
7126combination #4/A LYS 31 NZ combination #4/F ASP 30 O combination #4/A LYS 31 HZ1 3.148 2.456
7127combination #4/A LYS 31 NZ combination #4/F ASP 30 OD2 combination #4/A LYS 31 HZ2 2.746 1.778
7128combination #4/C ARG 18 NH1 combination #4/F GLU 17 OE1 combination #4/C ARG 18 HH11 2.812 1.825
7129combination #4/C ARG 18 NH1 combination #4/F GLU 17 OE2 combination #4/C ARG 18 HH11 3.358 2.560
7130combination #4/C ARG 18 NH2 combination #4/F GLU 17 OE2 combination #4/C ARG 18 HH22 2.780 1.765
7131combination #4/D LYS 109 NZ combination #4/F PRO 18 O combination #4/D LYS 109 HZ1 2.917 2.045
7132combination #4/D LYS 109 NZ combination #4/F GLU 19 OE1 combination #4/D LYS 109 HZ2 2.737 1.813
7133combination #4/E ARG 43 NE combination #4/F GLU 9 OE1 combination #4/E ARG 43 HE 2.875 1.950
7134combination #4/E ARG 43 NH1 combination #4/F ALA 7 O combination #4/E ARG 43 HH12 2.980 2.103
7135combination #4/E ARG 43 NH2 combination #4/F ALA 7 O combination #4/E ARG 43 HH22 2.848 1.943
7136combination #4/E ARG 43 NH2 combination #4/F GLU 9 OE1 combination #4/E ARG 43 HH21 2.738 1.784
7137combination #4/E THR 54 OG1 combination #4/F GLU 9 OE2 combination #4/E THR 54 HG1 2.666 1.685
7138combination #4/E ASN 56 ND2 combination #4/F PRO 53 O combination #4/E ASN 56 HD22 3.598 2.755
7139combination #4/F ARG 32 NE combination #4/A THR 28 OG1 combination #4/F ARG 32 HE 2.902 1.898
7140combination #4/F ARG 32 NH1 combination #4/A ASP 34 OD2 combination #4/F ARG 32 HH12 2.894 1.970
7141combination #4/F ARG 32 NH2 combination #4/A THR 28 OG1 combination #4/F ARG 32 HH21 3.324 2.539
7142combination #4/F ARG 32 NH2 combination #4/A ASP 34 OD2 combination #4/F ARG 32 HH22 2.784 1.818
7143</pre><br/>19 hydrogen bonds found<br>
7144<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4">select #4</a></div></div>28515 atoms, 28949 bonds, 180 pseudobonds, 1831 residues, 4 models selected<br>
7145<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.3 models">hide #4.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #4 PSI_BFd_SF4_opt.pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #4 PSI_BFd_SF4_opt.pdb">rename #4 PSI_BFd_SF4_opt.pdb</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4">select #4</a></div></div>28515 atoms, 28949 bonds, 180 pseudobonds, 1831 residues, 4 models selected<br>
7146<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 1831 items<br>
7147<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/A">coulombic #4/A</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
7148Assigning partial charges to residue CYF (net charge +1) with am1-bcc method<br>
7149Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n<br>
7150(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.in.mol2); atoms read (22), bonds read (21).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 92; net charge: 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
7151Coulombic values for PSI_BFd_SF4_opt.pdb_A SES surface #4.5: minimum, -12.49, mean 0.00, maximum 20.13<br>
7152<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/B">coulombic #4/B</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
7153Assigning partial charges to residue CYF (net charge -1) with am1-bcc method<br>
7154Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n<br>
7155(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.in.mol2); atoms read (22), bonds read (21).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 94; net charge: -1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
7156Coulombic values for PSI_BFd_SF4_opt.pdb_B SES surface #4.6: minimum, -15.84, mean -0.16, maximum 13.13<br>
7157<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/C</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/C">coulombic #4/C</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
7158Assigning partial charges to residue CYF (net charge -1) with am1-bcc method<br>
7159Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n<br>
7160(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.in.mol2); atoms read (25), bonds read (24).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 102; net charge: -1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
7161Coulombic values for PSI_BFd_SF4_opt.pdb_C SES surface #4.7: minimum, -21.93, mean -4.05, maximum 8.44<br>
7162<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/D</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/D">coulombic #4/D</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
7163Coulombic values for PSI_BFd_SF4_opt.pdb_D SES surface #4.8: minimum, -11.15, mean 2.11, maximum 15.26<br>
7164<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/E</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/E">coulombic #4/E</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
7165Coulombic values for PSI_BFd_SF4_opt.pdb_E SES surface #4.9: minimum, -11.38, mean 1.55, maximum 11.87<br>
7166<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic #4/F">coulombic #4/F</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
7167Assigning partial charges to residue CYF (net charge -1) with am1-bcc method<br>
7168Running ANTECHAMBER command: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n<br>
7169(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.in.mol2); atoms read (22), bonds read (21).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 94; net charge: -1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.8.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
7170Coulombic values for PSI_BFd_SF4_opt.pdb_F SES surface #4.10: minimum, -24.55, mean -9.44, maximum 5.59<br>
7171<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
7172<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel dark orange target acpf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel dark orange target acpf">color sel dark orange target acpf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero target acpf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero target acpf">color sel byhetero target acpf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1831@F1:1827@F2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1831@F1:1827@F2">select #4/X:1831@F1:1827@F2</a></div></div>2 atoms, 2 residues, 1 model selected<br>
7173<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Distances</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Distances">ui tool show Distances</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #4/X:1827@F2 #4/X:1831@F1</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #4/X:1827@F2 #4/X:1831@F1">distance #4/X:1827@F2 #4/X:1831@F1</a></div></div>Distance between PSI_BFd_SF4_opt.pdb #4/X SF4 1827 F2 and SF4 1831 F1: 9.521Å
7174<br>
7175<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> color #011993</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style color #011993">distance style color #011993</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> decimalPlaces 4</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style decimalPlaces 4">distance style decimalPlaces 4</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> decimalPlaces 5</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style decimalPlaces 5">distance style decimalPlaces 5</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> decimalPlaces 6</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style decimalPlaces 6">distance style decimalPlaces 6</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> decimalPlaces 5</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style decimalPlaces 5">distance style decimalPlaces 5</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> decimalPlaces 4</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style decimalPlaces 4">distance style decimalPlaces 4</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> decimalPlaces 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style decimalPlaces 3">distance style decimalPlaces 3</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> decimalPlaces 2</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style decimalPlaces 2">distance style decimalPlaces 2</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> decimalPlaces 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style decimalPlaces 1">distance style decimalPlaces 1</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> radius 0.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style radius 0.3">distance style radius 0.3</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#style">distance style</a> radius 0.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance style radius 0.2">distance style radius 0.2</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F:3-9,27-34,53-61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F:3-9,27-34,53-61">select #4/F:3-9,27-34,53-61</a></div></div>368 atoms, 369 bonds, 24 residues, 1 model selected<br>
7176<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1 models">show #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:1-2,8-24,30-47 :&lt;0.1 &amp;#4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:1-2,8-24,30-47 :&lt;0.1 &amp;#4/F">select #2:1-2,8-24,30-47 :&lt;0.1 &amp;#4/F</a></div></div>Nothing selected<br>
7177<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3:1-2,8-24,30-47 :&lt;0.1 &amp;#4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3:1-2,8-24,30-47 :&lt;0.1 &amp;#4/F">select #3:1-2,8-24,30-47 :&lt;0.1 &amp;#4/F</a></div></div>Nothing selected<br>
7178<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3:1-2,8-24,30-47 </div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3:1-2,8-24,30-47 ">select #3:1-2,8-24,30-47 </a></div></div>447 atoms, 448 bonds, 37 residues, 1 model selected<br>
7179<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3:1-2,8-24,30-47 </div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3:1-2,8-24,30-47 ">select #3:1-2,8-24,30-47 </a></div></div>447 atoms, 448 bonds, 37 residues, 1 model selected<br>
7180<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3 &amp;~:1-2,8-24,30-47 </div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3 &amp;~:1-2,8-24,30-47 ">select #3 &amp;~:1-2,8-24,30-47 </a></div></div>315 atoms, 228 bonds, 114 residues, 1 model selected<br>
7181<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan target acpf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan target acpf">color sel cyan target acpf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1 models">hide #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!3 to #4/F pairing bs</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!3 to #4/F pairing bs">matchmaker #!3 to #4/F pairing bs</a></div></div>
7182 <table border=1 cellpadding=4 cellspacing=0>
7183 <tr>
7184 <th colspan="2">Parameters</th>
7185 </tr>
7186 <tr>
7187 <td>Chain pairing</td>
7188 <td>bs</td>
7189 </tr>
7190 <tr>
7191 <td>Alignment algorithm</td>
7192 <td>Needleman-Wunsch</td>
7193 </tr>
7194 <tr>
7195 <td>Similarity matrix</td>
7196 <td>BLOSUM-62</td>
7197 </tr>
7198
7199 <tr>
7200 <td>SS fraction</td>
7201 <td>0.3</td>
7202 </tr>
7203 <tr>
7204 <td>Gap open (HH/SS/other)</td>
7205 <td>18/18/6</td>
7206 </tr>
7207 <tr>
7208 <td>Gap extend</td>
7209 <td>1</td>
7210 </tr>
7211 <tr>
7212 <td>SS matrix</td>
7213 <td>
7214 <table>
7215 <tr>
7216 <th></th> <th>H</th> <th>S</th> <th>O</th>
7217 </tr>
7218 <tr>
7219 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
7220 </tr>
7221 <tr>
7222 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
7223 </tr>
7224 <tr>
7225 <th>O</th> <td></td> <td></td> <td align="right">4</td>
7226 </tr>
7227 </table>
7228 </td>
7229 </tr>
7230
7231 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
7232 </table>
7233 <br/>Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with BFd (2fdn), chain M (#3), sequence alignment score = 115.9<br>
7234RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs: 3.340)<br>
7235<br>
7236<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!3 to #4/F pairing bs showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!3 to #4/F pairing bs showAlignment true">matchmaker #!3 to #4/F pairing bs showAlignment true</a></div></div>
7237 <table border=1 cellpadding=4 cellspacing=0>
7238 <tr>
7239 <th colspan="2">Parameters</th>
7240 </tr>
7241 <tr>
7242 <td>Chain pairing</td>
7243 <td>bs</td>
7244 </tr>
7245 <tr>
7246 <td>Alignment algorithm</td>
7247 <td>Needleman-Wunsch</td>
7248 </tr>
7249 <tr>
7250 <td>Similarity matrix</td>
7251 <td>BLOSUM-62</td>
7252 </tr>
7253
7254 <tr>
7255 <td>SS fraction</td>
7256 <td>0.3</td>
7257 </tr>
7258 <tr>
7259 <td>Gap open (HH/SS/other)</td>
7260 <td>18/18/6</td>
7261 </tr>
7262 <tr>
7263 <td>Gap extend</td>
7264 <td>1</td>
7265 </tr>
7266 <tr>
7267 <td>SS matrix</td>
7268 <td>
7269 <table>
7270 <tr>
7271 <th></th> <th>H</th> <th>S</th> <th>O</th>
7272 </tr>
7273 <tr>
7274 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
7275 </tr>
7276 <tr>
7277 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
7278 </tr>
7279 <tr>
7280 <th>O</th> <td></td> <td></td> <td align="right">4</td>
7281 </tr>
7282 </table>
7283 </td>
7284 </tr>
7285
7286 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
7287 </table>
7288 <br/>Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with BFd (2fdn), chain M (#3), sequence alignment score = 115.9<br>
7289Alignment identifier is 1<br>
7290Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
7291Hiding conservation header for alignment 1<br>
7292Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M, PSI_BFd_SF4_opt.pdb #4/F<br>
7293Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
7294RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs: 3.340)<br>
7295<br>
7296<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#header">sequence header</a> consensus show</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence header consensus show">sequence header consensus show</a></div></div>Showing consensus header (&quot;seq_consensus&quot; residue attribute) for alignment 1<br>
7297<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:3-9,27-34,53-61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:3-9,27-34,53-61">select #4:3-9,27-34,53-61</a></div></div>2226 atoms, 2237 bonds, 35 pseudobonds, 144 residues, 3 models selected<br>
7298<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F:3-9,27-34,53-61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F:3-9,27-34,53-61">select #4/F:3-9,27-34,53-61</a></div></div>368 atoms, 369 bonds, 24 residues, 1 model selected<br>
7299<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan target acpf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan target acpf">color sel cyan target acpf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero target acpf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero target acpf">color sel byhetero target acpf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.10 models">show #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:27,28,31,34</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:27,28,31,34">select #4/A:27,28,31,34</a></div></div>72 atoms, 69 bonds, 4 residues, 1 model selected<br>
7300<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 20">transparency (#!4 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 10">transparency (#!4 &amp; sel) 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 90">transparency (#!4 &amp; sel) 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/C:18/D:109/E:43,54,56,67</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/C:18/D:109/E:43,54,56,67">select #4/C:18/D:109/E:43,54,56,67</a></div></div>98 atoms, 93 bonds, 5 residues, 1 model selected<br>
7301<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 90">transparency (#!4 &amp; sel) 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67">select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</a></div></div>170 atoms, 162 bonds, 9 residues, 1 model selected<br>
7302<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 0</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 0">transparency (#!4 &amp; sel) 0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A-F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A-F">select #4/A-F</a></div></div>28475 atoms, 28949 bonds, 90 pseudobonds, 1826 residues, 3 models selected<br>
7303<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.10 models">show #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 30">transparency (#!4 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 20">transparency (#!4 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 10">transparency (#!4 &amp; sel) 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67">select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</a></div></div>170 atoms, 162 bonds, 9 residues, 1 model selected<br>
7304<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 90</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 90">transparency (#!4 &amp; sel) 90</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> #4.1-2,4-9#!4 80</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency #4.1-2,4-9#!4 80">transparency #4.1-2,4-9#!4 80</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> #4.1-2,4-9#!4 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency #4.1-2,4-9#!4 10">transparency #4.1-2,4-9#!4 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67">select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</a></div></div>170 atoms, 162 bonds, 9 residues, 1 model selected<br>
7305<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 80</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 80">transparency (#!4 &amp; sel) 80</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.7 models">hide #4.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X">select #4/X</a></div></div>40 atoms, 91 pseudobonds, 5 residues, 3 models selected<br>
7306<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 40 atom styles<br>
7307<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 40 atom styles<br>
7308<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1 models">show #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1 models">hide #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 40 atom styles<br>
7309<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.10 models">show #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.7 models">show #4.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A-E">select #4/A-E</a></div></div>27634 atoms, 28101 bonds, 1765 residues, 1 model selected<br>
7310<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 30">transparency (#!4 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.9 models">hide #4.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.8 models">hide #4.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.7 models">hide #4.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.7 models">show #4.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.8 models">show #4.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.9 models">show #4.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.10 models">show #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.10">select add #4.10</a></div></div>28475 atoms, 28101 bonds, 1826 residues, 6 models selected<br>
7311<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #4.10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #4.10">select subtract #4.10</a></div></div>27634 atoms, 28101 bonds, 1765 residues, 7 models selected<br>
7312<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.10">select add #4.10</a></div></div>28475 atoms, 28101 bonds, 1826 residues, 6 models selected<br>
7313<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #4.10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #4.10">select subtract #4.10</a></div></div>27634 atoms, 28101 bonds, 1765 residues, 7 models selected<br>
7314<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.10">select add #4.10</a></div></div>28475 atoms, 28101 bonds, 1826 residues, 6 models selected<br>
7315<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
7316<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 30</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 30">transparency (#!4 &amp; sel) 30</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.10 models">show #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.7 models">hide #4.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.9 models">hide #4.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.8 models">hide #4.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:SF4">select #4:SF4</a></div></div>40 atoms, 91 pseudobonds, 5 residues, 3 models selected<br>
7317<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 40 atom styles<br>
7318<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 40 atom styles<br>
7319<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F:42@SG</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F:42@SG">select #4/F:42@SG</a></div></div>1 atom, 1 residue, 1 model selected<br>
7320<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/X:1828@F1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/X:1828@F1">select #4/X:1828@F1</a></div></div>1 atom, 1 residue, 1 model selected<br>
7321<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Build Structure&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Build Structure&quot;">ui tool show &quot;Build Structure&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.1 models">hide #4.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.1 models">show #4.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.1 models">hide #4.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.1 models">show #4.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:1828@F1 </div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:1828@F1 ">select #4:1828@F1 </a></div></div>1 atom, 1 residue, 1 model selected<br>
7322<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #4:1828@F1 reasonable true</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #4:1828@F1 reasonable true">bond #4:1828@F1 reasonable true</a></div></div><font color="crimson"><b>Must specify two or more atoms</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:1828@F1,S2,S3,S4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:1828@F1,S2,S3,S4">select #4:1828@F1,S2,S3,S4</a></div></div>4 atoms, 3 pseudobonds, 1 residue, 2 models selected<br>
7323<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #4:1828@F1,S2,S3,S4</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #4:1828@F1,S2,S3,S4">bond #4:1828@F1,S2,S3,S4</a></div></div>Created 3 bonds<br>
7324<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #4:1828@F3,S1,S3,S2</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #4:1828@F3,S1,S3,S2">bond #4:1828@F3,S1,S3,S2</a></div></div>Created 2 bonds<br>
7325<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #4:1828@F3,S4</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #4:1828@F3,S4">bond #4:1828@F3,S4</a></div></div>Created 1 bond<br>
7326<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:1828@F2,S4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:1828@F2,S4">select #4:1828@F2,S4</a></div></div>2 atoms, 1 pseudobond, 1 residue, 2 models selected<br>
7327<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:1828@F2,S4,S1,S3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:1828@F2,S4,S1,S3">select #4:1828@F2,S4,S1,S3</a></div></div>4 atoms, 3 pseudobonds, 1 residue, 2 models selected<br>
7328<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #4:1828@F2,S4,S1,S3</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #4:1828@F2,S4,S1,S3">bond #4:1828@F2,S4,S1,S3</a></div></div>Created 3 bonds<br>
7329<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:1828@F4,S2,S1,S3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:1828@F4,S2,S1,S3">select #4:1828@F4,S2,S1,S3</a></div></div>4 atoms, 3 pseudobonds, 1 residue, 2 models selected<br>
7330<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #4:1828@F4,S2,S1,S3</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #4:1828@F4,S2,S1,S3">bond #4:1828@F4,S2,S1,S3</a></div></div>Created 3 bonds<br>
7331<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #4:1828</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #4:1828">bond #4:1828</a></div></div>Created 6 bonds<br>
7332<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html#~bond">~bond</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:~bond sel">~bond sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #4:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #4:SF4">bond #4:SF4</a></div></div>Created 78 bonds<br>
7333<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html#~bond">~bond</a> #4:SF4@F1,F2,F3,F4</div><div class="cxcmd_as_cmd"><a href="cxcmd:~bond #4:SF4@F1,F2,F3,F4">~bond #4:SF4@F1,F2,F3,F4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.1 models">hide #4.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:SF4">select #4:SF4</a></div></div>40 atoms, 60 bonds, 91 pseudobonds, 5 residues, 3 models selected<br>
7334<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 40 atom styles<br>
7335<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize">windowsize</a></div></div>window size 806 684<br>
7336<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 750</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 750">windowsize 750</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 800</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 800">windowsize 800</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 800 600</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 800 600">windowsize 800 600</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 800 800</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 800 800">windowsize 800 800</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 800 700</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 800 700">windowsize 800 700</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 800 670</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 800 670">windowsize 800 670</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 800 675</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 800 675">windowsize 800 675</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.10 models">show #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.9 models">show #4.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.8 models">show #4.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.7 models">show #4.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.6 models">show #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#list">view list</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view list">view list</a></div></div>Named views: <a href="cxcmd:view HbondsZoom">HbondsZoom</a>, <a href="cxcmd:view back">back</a>, <a href="cxcmd:view front">front</a>, <a href="cxcmd:view side">side</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> HbondsZoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view HbondsZoom">view HbondsZoom</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67">select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</a></div></div>170 atoms, 162 bonds, 9 residues, 1 model selected<br>
7337<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 80</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 80">transparency (#!4 &amp; sel) 80</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.9 models">hide #4.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.3 models">show #4.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Contacts">ui tool show Contacts</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
7338<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F &amp;~H">select #4/F &amp;~H</a></div></div>435 atoms, 442 bonds, 61 residues, 1 model selected<br>
7339<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 log true">contacts sel restrict &quot;#4/A-E &amp;~H&quot; resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 log true</a></div></div><pre>Allowed overlap: -0.4
7340H-bond overlap reduction: 0.4
7341Ignore contacts between atoms separated by 4 bonds or less
7342Ignore contacts between atoms in residues less than 5 apart in sequence
7343Detect intra-residue contacts: False
7344Detect intra-molecule contacts: False
7345
734671 contacts
7347 atom1 atom2 overlap distance
7348PSI_BFd_SF4_opt.pdb #4/F GLY 14 N PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 0.214 3.036
7349PSI_BFd_SF4_opt.pdb #4/F CYF 13 CB PSI_BFd_SF4_opt.pdb #4/C GLN 15 CG 0.203 3.197
7350PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E SER 53 C 0.154 3.026
7351PSI_BFd_SF4_opt.pdb #4/F GLY 50 O PSI_BFd_SF4_opt.pdb #4/C LYS 34 C 0.095 3.085
7352PSI_BFd_SF4_opt.pdb #4/F GLU 19 CD PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ 0.059 3.266
7353PSI_BFd_SF4_opt.pdb #4/F ILE 11 CD1 PSI_BFd_SF4_opt.pdb #4/C PRO 58 CB 0.048 3.352
7354PSI_BFd_SF4_opt.pdb #4/F THR 8 CA PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 0.005 3.320
7355PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1 PSI_BFd_SF4_opt.pdb #4/A ARG 27 CZ -0.006 3.186
7356PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1 PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2 -0.014 2.719
7357PSI_BFd_SF4_opt.pdb #4/F MET 54 CE PSI_BFd_SF4_opt.pdb #4/E THR 54 O -0.032 3.212
7358PSI_BFd_SF4_opt.pdb #4/F GLU 19 OE1 PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ -0.032 2.737
7359PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1 PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.033 2.738
7360PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD2 PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ -0.041 2.746
7361PSI_BFd_SF4_opt.pdb #4/F THR 8 C PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.042 3.367
7362PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD -0.049 3.449
7363PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E THR 54 CG2 -0.052 3.232
7364PSI_BFd_SF4_opt.pdb #4/F GLY 50 O PSI_BFd_SF4_opt.pdb #4/C LYS 34 CB -0.054 3.234
7365PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1 PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1 -0.055 2.760
7366PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1 PSI_BFd_SF4_opt.pdb #4/E ARG 43 CZ -0.060 3.240
7367PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2 PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.075 2.780
7368PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2 PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2 -0.079 2.784
7369PSI_BFd_SF4_opt.pdb #4/F GLY 14 N PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD -0.080 3.405
7370PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1 -0.086 2.666
7371PSI_BFd_SF4_opt.pdb #4/F GLU 17 CD PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1 -0.100 3.425
7372PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE1 PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1 -0.107 2.812
7373PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E THR 54 CB -0.122 3.302
7374PSI_BFd_SF4_opt.pdb #4/F MET 54 CE PSI_BFd_SF4_opt.pdb #4/E THR 54 C -0.130 3.530
7375PSI_BFd_SF4_opt.pdb #4/F GLY 14 C PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.134 3.459
7376PSI_BFd_SF4_opt.pdb #4/F ARG 32 CZ PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2 -0.136 3.316
7377PSI_BFd_SF4_opt.pdb #4/F ALA 7 O PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.143 2.848
7378PSI_BFd_SF4_opt.pdb #4/F GLY 14 O PSI_BFd_SF4_opt.pdb #4/C ARG 18 CZ -0.147 3.327
7379PSI_BFd_SF4_opt.pdb #4/F CYF 13 C PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.148 3.473
7380PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA PSI_BFd_SF4_opt.pdb #4/C GLN 15 CG -0.162 3.562
7381PSI_BFd_SF4_opt.pdb #4/F MET 54 SD PSI_BFd_SF4_opt.pdb #4/C ILE 11 CD1 -0.167 3.649
7382PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1 PSI_BFd_SF4_opt.pdb #4/E ARG 43 NE -0.170 2.875
7383PSI_BFd_SF4_opt.pdb #4/F ARG 32 NE PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1 -0.177 2.902
7384PSI_BFd_SF4_opt.pdb #4/F GLU 9 N PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.182 3.432
7385PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2 -0.182 3.507
7386PSI_BFd_SF4_opt.pdb #4/F ALA 7 O PSI_BFd_SF4_opt.pdb #4/E ARG 43 CZ -0.183 3.363
7387PSI_BFd_SF4_opt.pdb #4/F GLU 17 CD PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.187 3.512
7388PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E SER 53 CB -0.188 3.368
7389PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E SER 53 CA -0.188 3.368
7390PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH1 PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2 -0.189 2.894
7391PSI_BFd_SF4_opt.pdb #4/F PRO 18 O PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ -0.212 2.917
7392PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB PSI_BFd_SF4_opt.pdb #4/C ILE 11 CG1 -0.215 3.615
7393PSI_BFd_SF4_opt.pdb #4/F CYF 13 CB PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD -0.219 3.619
7394PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB PSI_BFd_SF4_opt.pdb #4/C ILE 11 CD1 -0.225 3.625
7395PSI_BFd_SF4_opt.pdb #4/F PRO 18 CG PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.230 3.555
7396PSI_BFd_SF4_opt.pdb #4/F GLY 14 O PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.254 2.959
7397PSI_BFd_SF4_opt.pdb #4/F ALA 15 N PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.256 3.506
7398PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E THR 54 N -0.272 2.977
7399PSI_BFd_SF4_opt.pdb #4/F ALA 7 O PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH1 -0.275 2.980
7400PSI_BFd_SF4_opt.pdb #4/F ILE 11 CD1 PSI_BFd_SF4_opt.pdb #4/C PRO 58 CG -0.291 3.691
7401PSI_BFd_SF4_opt.pdb #4/F MET 54 CE PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1 -0.299 3.499
7402PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1 -0.301 3.626
7403PSI_BFd_SF4_opt.pdb #4/F MET 54 CE PSI_BFd_SF4_opt.pdb #4/E THR 54 CB -0.316 3.716
7404PSI_BFd_SF4_opt.pdb #4/F GLU 9 CD PSI_BFd_SF4_opt.pdb #4/E SER 53 CB -0.323 3.723
7405PSI_BFd_SF4_opt.pdb #4/F GLU 9 CD PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.332 3.657
7406PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.337 3.662
7407PSI_BFd_SF4_opt.pdb #4/F ARG 32 CZ PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1 -0.342 3.542
7408PSI_BFd_SF4_opt.pdb #4/F ASP 30 CA PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2 -0.346 3.671
7409PSI_BFd_SF4_opt.pdb #4/F CYF 13 C PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD -0.353 3.753
7410PSI_BFd_SF4_opt.pdb #4/F GLY 14 CA PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.355 3.680
7411PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2 PSI_BFd_SF4_opt.pdb #4/C ARG 18 CZ -0.356 3.536
7412PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ -0.363 3.688
7413PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB PSI_BFd_SF4_opt.pdb #4/C ILE 11 O -0.366 3.546
7414PSI_BFd_SF4_opt.pdb #4/F VAL 51 CA PSI_BFd_SF4_opt.pdb #4/C ALA 35 CB -0.371 3.771
7415PSI_BFd_SF4_opt.pdb #4/F GLY 50 O PSI_BFd_SF4_opt.pdb #4/C LYS 34 O -0.372 3.332
7416PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB PSI_BFd_SF4_opt.pdb #4/C CYF 13 CB -0.376 3.776
7417PSI_BFd_SF4_opt.pdb #4/F PRO 53 CG PSI_BFd_SF4_opt.pdb #4/C CYF 13 CB -0.389 3.789
7418PSI_BFd_SF4_opt.pdb #4/F PRO 18 CD PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.394 3.719
7419</pre><br/>71 contacts<br>
7420<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F:14,9,50,19,11,8,30,54,19,9,17,32,7,18,53,51</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F:14,9,50,19,11,8,30,54,19,9,17,32,7,18,53,51">select #4/F:14,9,50,19,11,8,30,54,19,9,17,32,7,18,53,51</a></div></div>199 atoms, 193 bonds, 14 residues, 1 model selected<br>
7421<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
7422<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone true</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone true">setattr sel r ribbon_hide_backbone true</a></div></div>Assigning ribbon_hide_backbone attribute to 61 items<br>
7423<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F &amp;H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F &amp;H">select #4/F &amp;H</a></div></div>406 atoms, 61 residues, 1 model selected<br>
7424<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/F">select #4/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
7425<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false select true reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false select true reveal true log true">hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false intraRes false select true reveal true log true</a></div></div>Skipping possible acceptor with bad geometry: PSI_BFd_SF4_opt.pdb #4/A CYF 575 SG<br>
7426Wrong number of grandchild atoms for phi/psi acceptor PSI_BFd_SF4_opt.pdb #4/A CYF 575 SG<br>
7427<br>
7428[Repeated 1 time(s)]<p style="color:darkorange">Skipped 2 atom(s) with bad connectivities; see log for details<br>
7429</p><pre>Finding intramodel H-bonds
7430Constraints relaxed by 0.4 angstroms and 20 degrees
7431Models used:
7432 4 PSI_BFd_SF4_opt.pdb
7433
743419 H-bonds
7435H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
7436PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1 PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1 PSI_BFd_SF4_opt.pdb #4/A ARG 27 HH11 2.760 1.842
7437PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2 PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1 PSI_BFd_SF4_opt.pdb #4/A ARG 27 HH21 2.719 1.800
7438PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ PSI_BFd_SF4_opt.pdb #4/F ASP 30 O PSI_BFd_SF4_opt.pdb #4/A LYS 31 HZ1 3.148 2.456
7439PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD2 PSI_BFd_SF4_opt.pdb #4/A LYS 31 HZ2 2.746 1.778
7440PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1 PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE1 PSI_BFd_SF4_opt.pdb #4/C ARG 18 HH11 2.812 1.825
7441PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1 PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2 PSI_BFd_SF4_opt.pdb #4/C ARG 18 HH11 3.358 2.560
7442PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2 PSI_BFd_SF4_opt.pdb #4/C ARG 18 HH22 2.780 1.765
7443PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ PSI_BFd_SF4_opt.pdb #4/F PRO 18 O PSI_BFd_SF4_opt.pdb #4/D LYS 109 HZ1 2.917 2.045
7444PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ PSI_BFd_SF4_opt.pdb #4/F GLU 19 OE1 PSI_BFd_SF4_opt.pdb #4/D LYS 109 HZ2 2.737 1.813
7445PSI_BFd_SF4_opt.pdb #4/E ARG 43 NE PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1 PSI_BFd_SF4_opt.pdb #4/E ARG 43 HE 2.875 1.950
7446PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH1 PSI_BFd_SF4_opt.pdb #4/F ALA 7 O PSI_BFd_SF4_opt.pdb #4/E ARG 43 HH12 2.980 2.103
7447PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 PSI_BFd_SF4_opt.pdb #4/F ALA 7 O PSI_BFd_SF4_opt.pdb #4/E ARG 43 HH22 2.848 1.943
7448PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1 PSI_BFd_SF4_opt.pdb #4/E ARG 43 HH21 2.738 1.784
7449PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1 PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E THR 54 HG1 2.666 1.685
7450PSI_BFd_SF4_opt.pdb #4/E ASN 56 ND2 PSI_BFd_SF4_opt.pdb #4/F PRO 53 O PSI_BFd_SF4_opt.pdb #4/E ASN 56 HD22 3.598 2.755
7451PSI_BFd_SF4_opt.pdb #4/F ARG 32 NE PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1 PSI_BFd_SF4_opt.pdb #4/F ARG 32 HE 2.902 1.898
7452PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH1 PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2 PSI_BFd_SF4_opt.pdb #4/F ARG 32 HH12 2.894 1.970
7453PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2 PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1 PSI_BFd_SF4_opt.pdb #4/F ARG 32 HH21 3.324 2.539
7454PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2 PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2 PSI_BFd_SF4_opt.pdb #4/F ARG 32 HH22 2.784 1.818
7455</pre><br/>19 hydrogen bonds found<br>
7456<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone true</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone true">setattr sel r ribbon_hide_backbone true</a></div></div>Assigning ribbon_hide_backbone attribute to 17 items<br>
7457<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 17 items<br>
7458<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.3 models">hide #4.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.9 models">show #4.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.10 models">show #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png&quot; width 1600 height 1350 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png&quot; width 1600 height 1350 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png&quot; width 1600 height 1350 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.10 models">show #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.1 models">hide #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.10">select add #4.10</a></div></div>841 atoms, 61 residues, 1 model selected<br>
7459<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.9">select add #4.9</a></div></div>1900 atoms, 127 residues, 2 models selected<br>
7460<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.8">select add #4.8</a></div></div>4177 atoms, 270 residues, 3 models selected<br>
7461<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.7">select add #4.7</a></div></div>5383 atoms, 350 residues, 4 models selected<br>
7462<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.6">select add #4.6</a></div></div>16896 atoms, 1083 residues, 5 models selected<br>
7463<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4.5">select add #4.5</a></div></div>28475 atoms, 1826 residues, 6 models selected<br>
7464<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 20">transparency (#!4 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png&quot; width 1600 height 1350 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png&quot; width 1600 height 1350 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png&quot; width 1600 height 1350 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Key&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Key&quot;">ui tool show &quot;Color Key&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> right &quot;color key&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode right &quot;color key&quot;">ui mousemode right &quot;color key&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> blue-white-red :min : :-</div><div class="cxcmd_as_cmd"><a href="cxcmd:key blue-white-red :min : :-">key blue-white-red :min : :-</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> blue-white-red :min :0 :-</div><div class="cxcmd_as_cmd"><a href="cxcmd:key blue-white-red :min :0 :-">key blue-white-red :min :0 :-</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> blue-white-red :+ :0 :-</div><div class="cxcmd_as_cmd"><a href="cxcmd:key blue-white-red :+ :0 :-">key blue-white-red :+ :0 :-</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> size 0.25000,0.02000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key size 0.25000,0.02000">key size 0.25000,0.02000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> size 0.25000,0.01000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key size 0.25000,0.01000">key size 0.25000,0.01000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 23</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 23">key fontSize 23</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 22</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 22">key fontSize 22</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 21</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 21">key fontSize 21</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 20">key fontSize 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 19</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 19">key fontSize 19</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 18</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 18">key fontSize 18</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> ticks true</div><div class="cxcmd_as_cmd"><a href="cxcmd:key ticks true">key ticks true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickThickness 5.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickThickness 5.0">key tickThickness 5.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> tickThickness 4.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key tickThickness 4.0">key tickThickness 4.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -1.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -1.0">key labelOffset -1.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -2.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -2.0">key labelOffset -2.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -3.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -3.0">key labelOffset -3.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -4.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -4.0">key labelOffset -4.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -5.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -5.0">key labelOffset -5.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -6.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -6.0">key labelOffset -6.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -7.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -7.0">key labelOffset -7.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -8.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -8.0">key labelOffset -8.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -9.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -9.0">key labelOffset -9.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -10.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -10.0">key labelOffset -10.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -11.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -11.0">key labelOffset -11.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -12.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -12.0">key labelOffset -12.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -13.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -13.0">key labelOffset -13.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -14.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -14.0">key labelOffset -14.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -15.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -15.0">key labelOffset -15.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -16.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -16.0">key labelOffset -16.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -17.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -17.0">key labelOffset -17.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -16.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -16.0">key labelOffset -16.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> labelOffset -15.0</div><div class="cxcmd_as_cmd"><a href="cxcmd:key labelOffset -15.0">key labelOffset -15.0</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> fontSize 17</div><div class="cxcmd_as_cmd"><a href="cxcmd:key fontSize 17">key fontSize 17</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> bold true</div><div class="cxcmd_as_cmd"><a href="cxcmd:key bold true">key bold true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.1,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.1,0.08000">key pos 0.1,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.70000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.70000,0.08000">key pos 0.70000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.75000,0.08000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.75000,0.08000">key pos 0.75000,0.08000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.75000,0.8000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.75000,0.8000">key pos 0.75000,0.8000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.75000,0.9000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.75000,0.9000">key pos 0.75000,0.9000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.75000,0.95000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.75000,0.95000">key pos 0.75000,0.95000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 800 675</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 800 675">windowsize 800 675</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.75000,0.90000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.75000,0.90000">key pos 0.75000,0.90000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.75000,0.98000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.75000,0.98000">key pos 0.75000,0.98000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.75000,0.9000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.75000,0.9000">key pos 0.75000,0.9000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.75000,0.97000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.75000,0.97000">key pos 0.75000,0.97000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/key.html">key</a> pos 0.72000,0.97000</div><div class="cxcmd_as_cmd"><a href="cxcmd:key pos 0.72000,0.97000">key pos 0.72000,0.97000</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> right translate</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode right translate">ui mousemode right translate</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 800 675</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 800 675">windowsize 800 675</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67">select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</a></div></div>170 atoms, 162 bonds, 9 residues, 1 model selected<br>
7465<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67">select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</a></div></div>170 atoms, 162 bonds, 9 residues, 1 model selected<br>
7466<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> HbondsZoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view HbondsZoom">view HbondsZoom</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 80</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 80">transparency (#!4 &amp; sel) 80</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #6 models">hide #6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #6 models">show #6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png&quot; width 1600 height 1350 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png&quot; width 1600 height 1350 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png&quot; width 1600 height 1350 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67">select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</a></div></div>170 atoms, 162 bonds, 9 residues, 1 model selected<br>
7467<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 20</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 20">transparency (#!4 &amp; sel) 20</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.10 models">show #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png&quot; width 1600 height 1350 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png&quot; width 1600 height 1350 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png&quot; width 1600 height 1350 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> side</div><div class="cxcmd_as_cmd"><a href="cxcmd:view side">view side</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png&quot; width 1600 height 1350 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png&quot; width 1600 height 1350 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png&quot; width 1600 height 1350 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Thu Oct 10 08:30:31 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
7468<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/windowsize.html">windowsize</a> 900 675</div><div class="cxcmd_as_cmd"><a href="cxcmd:windowsize 900 675">windowsize 900 675</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png&quot; width 1800 height 1350 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png&quot; width 1800 height 1350 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png&quot; width 1800 height 1350 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#list">view list</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view list">view list</a></div></div>Named views: <a href="cxcmd:view HbondsZoom">HbondsZoom</a>, <a href="cxcmd:view back">back</a>, <a href="cxcmd:view front">front</a>, <a href="cxcmd:view side">side</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> front</div><div class="cxcmd_as_cmd"><a href="cxcmd:view front">view front</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png&quot; width 1800 height 1350 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png&quot; width 1800 height 1350 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt All surfaces front .png&quot; width 1800 height 1350 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67">select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67</a></div></div>170 atoms, 162 bonds, 9 residues, 1 model selected<br>
7469<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/transparency.html">transparency</a> (#!4 &amp; sel) 80</div><div class="cxcmd_as_cmd"><a href="cxcmd:transparency (#!4 &amp; sel) 80">transparency (#!4 &amp; sel) 80</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> HbondsZoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view HbondsZoom">view HbondsZoom</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.10 models">hide #4.10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png&quot; width 1800 height 1350 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png&quot; width 1800 height 1350 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom hbonds.png&quot; width 1800 height 1350 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/RFdiffusion with RoesttaDock H2ase BFdx dock/fdn_Alt/PSI BFd with 4Fe4S clusters AMBER relaxed.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Fri Oct 11 10:32:45 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
7470<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.9 models">hide #4.9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.7 models">hide #4.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.8 models">hide #4.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.6 models">hide #4.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.5 models">hide #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.4 models">hide #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.4 models">show #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/@fromDROR-NAS/Prabir/PS1/PS1_dehydrogenase_docking/docking/Dock_PS1_Fd_test_output.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/@fromDROR-NAS/Prabir/PS1/PS1_dehydrogenase_docking/docking/Dock_PS1_Fd_test_output.pdb&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/@fromDROR-NAS/Prabir/PS1/PS1_dehydrogenase_docking/docking/Dock_PS1_Fd_test_output.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
7471 <thead>
7472 <tr>
7473 <th colspan="2">Chain information for Dock_PS1_Fd_test_output.pdb #7</th>
7474 </tr>
7475 <tr>
7476 <th>Chain</th>
7477 <th>Description</th>
7478
7479 </tr>
7480 </thead>
7481 <tbody>
7482 <tr>
7483 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #7/Y:1-1181">Y</a></td>
7484 <td><a title="Show sequence" href="cxcmd:sequence chain #7/Y">No description available</a></td>
7485
7486 </tr>
7487 <tr>
7488 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #7/Z:1-1738">Z</a></td>
7489 <td><a title="Show sequence" href="cxcmd:sequence chain #7/Z">No description available</a></td>
7490
7491 </tr>
7492 </tbody>
7493</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #7/Z to #4/C pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #7/Z to #4/C pairing ss showAlignment true">matchmaker #7/Z to #4/C pairing ss showAlignment true</a></div></div>
7494 <table border=1 cellpadding=4 cellspacing=0>
7495 <tr>
7496 <th colspan="2">Parameters</th>
7497 </tr>
7498 <tr>
7499 <td>Chain pairing</td>
7500 <td>ss</td>
7501 </tr>
7502 <tr>
7503 <td>Alignment algorithm</td>
7504 <td>Needleman-Wunsch</td>
7505 </tr>
7506 <tr>
7507 <td>Similarity matrix</td>
7508 <td>BLOSUM-62</td>
7509 </tr>
7510
7511 <tr>
7512 <td>SS fraction</td>
7513 <td>0.3</td>
7514 </tr>
7515 <tr>
7516 <td>Gap open (HH/SS/other)</td>
7517 <td>18/18/6</td>
7518 </tr>
7519 <tr>
7520 <td>Gap extend</td>
7521 <td>1</td>
7522 </tr>
7523 <tr>
7524 <td>SS matrix</td>
7525 <td>
7526 <table>
7527 <tr>
7528 <th></th> <th>H</th> <th>S</th> <th>O</th>
7529 </tr>
7530 <tr>
7531 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
7532 </tr>
7533 <tr>
7534 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
7535 </tr>
7536 <tr>
7537 <th>O</th> <td></td> <td></td> <td align="right">4</td>
7538 </tr>
7539 </table>
7540 </td>
7541 </tr>
7542
7543 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
7544 </table>
7545 <br/>Matchmaker PSI_BFd_SF4_opt.pdb, chain C (#4) with Dock_PS1_Fd_test_output.pdb, chain Z (#7), sequence alignment score = 342.4<br>
7546Alignment identifier is 2<br>
7547Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 2<br>
7548Hiding conservation header for alignment 2<br>
7549Chains used in RMSD evaluation for alignment 2: PSI_BFd_SF4_opt.pdb #4/C, Dock_PS1_Fd_test_output.pdb #7/Z<br>
7550Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 2<br>
7551RMSD between 80 pruned atom pairs is 0.300 angstroms; (across all 80 pairs: 0.300)<br>
7552<br>
7553<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9:1183@S4:1741@F1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9:1183@S4:1741@F1">select #9:1183@S4:1741@F1</a></div></div>Nothing selected<br>
7554<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7:1183@S4:1741@F1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7:1183@S4:1741@F1">select #7:1183@S4:1741@F1</a></div></div>2 atoms, 2 residues, 1 model selected<br>
7555<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Distances</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Distances">ui tool show Distances</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html#~distance">~distance</a> #4/X:1827@F2 #4/X:1831@F1</div><div class="cxcmd_as_cmd"><a href="cxcmd:~distance #4/X:1827@F2 #4/X:1831@F1">~distance #4/X:1827@F2 #4/X:1831@F1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/distance.html">distance</a> #7/Z:1741@F1 #7/Y:1183@S4</div><div class="cxcmd_as_cmd"><a href="cxcmd:distance #7/Z:1741@F1 #7/Y:1183@S4">distance #7/Z:1741@F1 #7/Y:1183@S4</a></div></div>Distance between Dock_PS1_Fd_test_output.pdb #7/Z SF4 1741 F1 and /Y SF4 1183 S4: 11.458Å
7556<br>
7557<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/Z</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/Z">select #7/Z</a></div></div>13593 atoms, 13984 bonds, 54 pseudobonds, 1741 residues, 2 models selected<br>
7558<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Clashes</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Clashes">ui tool show Clashes</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #7/Y resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #7/Y resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true">clashes sel restrict #7/Y resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
7559H-bond overlap reduction: 0.4
7560Ignore clashes between atoms separated by 4 bonds or less
7561Ignore clashes between atoms in residues less than 5 apart in sequence
7562Detect intra-residue clashes: False
7563Detect intra-molecule clashes: False
7564
75659 clashes
7566 atom1 atom2 overlap distance
7567Dock_PS1_Fd_test_output.pdb #7/Z ARG 18 NH2 Dock_PS1_Fd_test_output.pdb #7/Y ASP 112 CB 1.695 1.825
7568Dock_PS1_Fd_test_output.pdb #7/Z LYS 189 CG Dock_PS1_Fd_test_output.pdb #7/Y LYS 132 NZ 1.265 2.255
7569Dock_PS1_Fd_test_output.pdb #7/Z ILE 11 CD1 Dock_PS1_Fd_test_output.pdb #7/Y ASP 88 OD1 0.807 2.493
7570Dock_PS1_Fd_test_output.pdb #7/Z ARG 18 NH1 Dock_PS1_Fd_test_output.pdb #7/Y ILE 111 CG2 0.798 2.722
7571Dock_PS1_Fd_test_output.pdb #7/Z ILE 11 CD1 Dock_PS1_Fd_test_output.pdb #7/Y ASP 88 CG 0.795 2.965
7572Dock_PS1_Fd_test_output.pdb #7/Z THR 277 CG2 Dock_PS1_Fd_test_output.pdb #7/Y GLU 90 OE1 0.792 2.508
7573Dock_PS1_Fd_test_output.pdb #7/Z ARG 18 NH2 Dock_PS1_Fd_test_output.pdb #7/Y ASP 112 CG 0.777 2.743
7574Dock_PS1_Fd_test_output.pdb #7/Z THR 277 CG2 Dock_PS1_Fd_test_output.pdb #7/Y GLU 90 CD 0.702 3.058
7575Dock_PS1_Fd_test_output.pdb #7/Z GLU 188 O Dock_PS1_Fd_test_output.pdb #7/Y ASP 112 OD1 0.639 2.201
7576</pre><br/>9 clashes<br>
7577<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
7578 <thead>
7579 <tr>
7580 <th colspan="2">Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8</th>
7581 </tr>
7582 <tr>
7583 <th>Chain</th>
7584 <th>Description</th>
7585
7586 </tr>
7587 </thead>
7588 <tbody>
7589 <tr>
7590 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #8/A:1-477">A</a></td>
7591 <td><a title="Show sequence" href="cxcmd:sequence chain #8/A">.</a></td>
7592
7593 </tr>
7594 </tbody>
7595</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #8/A to #7/Y pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #8/A to #7/Y pairing ss showAlignment true">matchmaker #8/A to #7/Y pairing ss showAlignment true</a></div></div>
7596 <table border=1 cellpadding=4 cellspacing=0>
7597 <tr>
7598 <th colspan="2">Parameters</th>
7599 </tr>
7600 <tr>
7601 <td>Chain pairing</td>
7602 <td>ss</td>
7603 </tr>
7604 <tr>
7605 <td>Alignment algorithm</td>
7606 <td>Needleman-Wunsch</td>
7607 </tr>
7608 <tr>
7609 <td>Similarity matrix</td>
7610 <td>BLOSUM-62</td>
7611 </tr>
7612
7613 <tr>
7614 <td>SS fraction</td>
7615 <td>0.3</td>
7616 </tr>
7617 <tr>
7618 <td>Gap open (HH/SS/other)</td>
7619 <td>18/18/6</td>
7620 </tr>
7621 <tr>
7622 <td>Gap extend</td>
7623 <td>1</td>
7624 </tr>
7625 <tr>
7626 <td>SS matrix</td>
7627 <td>
7628 <table>
7629 <tr>
7630 <th></th> <th>H</th> <th>S</th> <th>O</th>
7631 </tr>
7632 <tr>
7633 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
7634 </tr>
7635 <tr>
7636 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
7637 </tr>
7638 <tr>
7639 <th>O</th> <td></td> <td></td> <td align="right">4</td>
7640 </tr>
7641 </table>
7642 </td>
7643 </tr>
7644
7645 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
7646 </table>
7647 <br/>Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#8), sequence alignment score = 139.8<br>
7648Alignment identifier is 3<br>
7649Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 3<br>
7650Hiding conservation header for alignment 3<br>
7651Chains used in RMSD evaluation for alignment 3: Dock_PS1_Fd_test_output.pdb #7/Y, fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8/A<br>
7652Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 3<br>
7653RMSD between 7 pruned atom pairs is 1.406 angstroms; (across all 441 pairs: 35.668)<br>
7654<br>
7655<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #8">close #8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
7656 <thead>
7657 <tr>
7658 <th colspan="2">Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8</th>
7659 </tr>
7660 <tr>
7661 <th>Chain</th>
7662 <th>Description</th>
7663
7664 </tr>
7665 </thead>
7666 <tbody>
7667 <tr>
7668 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #8/A:1-477">A</a></td>
7669 <td><a title="Show sequence" href="cxcmd:sequence chain #8/A">.</a></td>
7670
7671 </tr>
7672 </tbody>
7673</table><br/>Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 0 mismatches<br>
7674Chains used in RMSD evaluation for alignment 3: Dock_PS1_Fd_test_output.pdb #7/Y, fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #8/A<br>
7675<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view">view</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Mon Oct 14 17:57:44 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
7676<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 1hfe</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 1hfe">open 1hfe</a></div></div><i>1hfe</i> title:<br><b>1.6 A resolution structure of the Fe-ONLY hydrogenase from desulfovibrio desulfuricans</b> <a href="cxcmd:log metadata #9">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
7677 <thead>
7678 <tr>
7679 <th colspan="3">Chain information for 1hfe #9</th>
7680 </tr>
7681 <tr>
7682 <th>Chain</th>
7683 <th>Description</th>
7684 <th>UniProt</th>
7685 </tr>
7686 </thead>
7687 <tbody>
7688 <tr>
7689 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9/L:2-398">L</a> <a title="Select chain" href="cxcmd:select #9/M:2-398">M</a></td>
7690 <td><a title="Show sequence" href="cxcmd:sequence chain #9/L#9/M">PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))</a></td>
7691 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07598 from uniprot associate #9/L,M">PHFL_DESVH</a> <a title="Select sequence" href="cxcmd:select #9/L,M:1-421">1-421</a></td>
7692 </tr>
7693 <tr>
7694 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9/S:36-123">S</a> <a title="Select chain" href="cxcmd:select #9/T:36-123">T</a></td>
7695 <td><a title="Show sequence" href="cxcmd:sequence chain #9/S#9/T">PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))</a></td>
7696 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07603 from uniprot associate #9/S,T">PHFS_DESVH</a> <a title="Select sequence" href="cxcmd:select #9/S,T:1-123">1-123</a></td>
7697 </tr>
7698 </tbody>
7699</table><br/><table border=1 cellpadding=4 cellspacing=0>
7700 <thead>
7701 <tr>
7702 <th>Non-standard residues in 1hfe #9</th>
7703 </tr>
7704 </thead>
7705 <tbody>
7706 <tr>
7707 <td><a title="select residue" href="cxcmd:sel :CMO">CMO</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CMO">carbon monoxide</a></td>
7708 </tr>
7709 <tr>
7710 <td><a title="select residue" href="cxcmd:sel :CYN">CYN</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CYN">cyanide ion</a></td>
7711 </tr>
7712 <tr>
7713 <td><a title="select residue" href="cxcmd:sel :CYS">CYS</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CYS">cysteine</a></td>
7714 </tr>
7715 <tr>
7716 <td><a title="select residue" href="cxcmd:sel :FE2">FE2</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/FE2">Fe (II) ion</a></td>
7717 </tr>
7718 <tr>
7719 <td><a title="select residue" href="cxcmd:sel :PDT">PDT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PDT">1,3-propanedithiol</a></td>
7720 </tr>
7721 <tr>
7722 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
7723 </tr>
7724 <tr>
7725 <td><a title="select residue" href="cxcmd:sel :ZN">ZN</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/ZN">zinc ion</a></td>
7726 </tr>
7727 </tbody>
7728</table><br/><table border=1 cellpadding=4 cellspacing=0 bgcolor="#f0f0f0">
7729<tr><th colspan=2>1hfe mmCIF Assemblies
7730<tr><td><a title="Generate assembly" href="cxcmd:sym #9 assembly 1 ; view">1</a><td>author_and_software_defined_assembly
7731<tr><td><a title="Generate assembly" href="cxcmd:sym #9 assembly 2 ; view">2</a><td>author_and_software_defined_assembly
7732<tr><td><a title="Generate assembly" href="cxcmd:sym #9 assembly 3 ; view">3</a><td>software_defined_assembly
7733</table><br/>351 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/>Associated 1hfe chain L to fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 25 mismatches<br>
7734Associated 1hfe chain M to fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 25 mismatches<br>
7735<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view">view</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 6sdv</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 6sdv">open 6sdv</a></div></div>
7736<table border=1 cellpadding=4 cellspacing=0>
7737 <thead>
7738 <tr>
7739 <th colspan="2">Summary of feedback from opening 6sdv fetched from pdb</th>
7740 </tr>
7741 </thead>
7742 <tbody>
7743 <tr>
7744 <td><i>note</i></td> <td style="background-color:#ffffff">Fetching compressed mmCIF 6sdv from http://files.rcsb.org/download/6sdv.cif</td> </tr>
7745 </tbody>
7746</table><br/><i>6sdv</i> title:<br><b>W-formate dehydrogenase from Desulfovibrio vulgaris - Formate reduced form</b> <a href="cxcmd:log metadata #10">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
7747 <thead>
7748 <tr>
7749 <th colspan="3">Chain information for 6sdv #10</th>
7750 </tr>
7751 <tr>
7752 <th>Chain</th>
7753 <th>Description</th>
7754 <th>UniProt</th>
7755 </tr>
7756 </thead>
7757 <tbody>
7758 <tr>
7759 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10/A:36-1009">A</a></td>
7760 <td><a title="Show sequence" href="cxcmd:sequence chain #10/A">Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit</a></td>
7761 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q72EJ1 from uniprot associate #10/A">Q72EJ1_DESVH</a> <a title="Select sequence" href="cxcmd:select #10/A:1-1005">1-1005</a></td>
7762 </tr>
7763 <tr>
7764 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10/B:2-215">B</a></td>
7765 <td><a title="Show sequence" href="cxcmd:sequence chain #10/B">Formate dehydrogenase, beta subunit, putative</a></td>
7766 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q72EJ0 from uniprot associate #10/B">Q72EJ0_DESVH</a> <a title="Select sequence" href="cxcmd:select #10/B:1-236">1-236</a></td>
7767 </tr>
7768 </tbody>
7769</table><br/><table border=1 cellpadding=4 cellspacing=0>
7770 <thead>
7771 <tr>
7772 <th>Non-standard residues in 6sdv #10</th>
7773 </tr>
7774 </thead>
7775 <tbody>
7776 <tr>
7777 <td><a title="select residue" href="cxcmd:sel :GOL">GOL</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/GOL">glycerol</a> (glycerin; propane-1,2,3-triol)</td>
7778 </tr>
7779 <tr>
7780 <td><a title="select residue" href="cxcmd:sel :H2S">H2S</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/H2S">hydrosulfuric acid</a> (hydrogen sulfide)</td>
7781 </tr>
7782 <tr>
7783 <td><a title="select residue" href="cxcmd:sel :MGD">MGD</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/MGD">2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-anthracen-4-one guanosine dinucleotide</a> (molybdopterin guanosine dinucleotide)</td>
7784 </tr>
7785 <tr>
7786 <td><a title="select residue" href="cxcmd:sel :NO3">NO3</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/NO3">nitrate ion</a></td>
7787 </tr>
7788 <tr>
7789 <td><a title="select residue" href="cxcmd:sel :PEG">PEG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PEG">di(hydroxyethyl)ether</a></td>
7790 </tr>
7791 <tr>
7792 <td><a title="select residue" href="cxcmd:sel :SEC">SEC</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SEC">selenocysteine</a></td>
7793 </tr>
7794 <tr>
7795 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
7796 </tr>
7797 <tr>
7798 <td><a title="select residue" href="cxcmd:sel :W">W</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/W">tungsten ion</a></td>
7799 </tr>
7800 </tbody>
7801</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Documents/Protein Designs/PSI H2ase/Prabir optimized structures/Dock_PS1_Fd_test_output.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Documents/Protein Designs/PSI H2ase/Prabir optimized structures/Dock_PS1_Fd_test_output.pdb&quot;">open &quot;/Users/drornoy/Documents/Protein Designs/PSI H2ase/Prabir optimized structures/Dock_PS1_Fd_test_output.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
7802 <thead>
7803 <tr>
7804 <th colspan="2">Chain information for Dock_PS1_Fd_test_output.pdb #11</th>
7805 </tr>
7806 <tr>
7807 <th>Chain</th>
7808 <th>Description</th>
7809
7810 </tr>
7811 </thead>
7812 <tbody>
7813 <tr>
7814 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #11/Y:1-1181">Y</a></td>
7815 <td><a title="Show sequence" href="cxcmd:sequence chain #11/Y">No description available</a></td>
7816
7817 </tr>
7818 <tr>
7819 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #11/Z:1-1738">Z</a></td>
7820 <td><a title="Show sequence" href="cxcmd:sequence chain #11/Z">No description available</a></td>
7821
7822 </tr>
7823 </tbody>
7824</table><br/>Associated Dock_PS1_Fd_test_output.pdb chain Z to Dock_PS1_Fd_test_output.pdb, chain Z with 0 mismatches<br>
7825Associated Dock_PS1_Fd_test_output.pdb chain Y to Dock_PS1_Fd_test_output.pdb, chain Y with 0 mismatches<br>
7826<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #11</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #11">close #11</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Mon Oct 14 18:11:28 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
7827<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #9/L to #4/F pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #9/L to #4/F pairing ss">matchmaker #9/L to #4/F pairing ss</a></div></div>
7828 <table border=1 cellpadding=4 cellspacing=0>
7829 <tr>
7830 <th colspan="2">Parameters</th>
7831 </tr>
7832 <tr>
7833 <td>Chain pairing</td>
7834 <td>ss</td>
7835 </tr>
7836 <tr>
7837 <td>Alignment algorithm</td>
7838 <td>Needleman-Wunsch</td>
7839 </tr>
7840 <tr>
7841 <td>Similarity matrix</td>
7842 <td>BLOSUM-62</td>
7843 </tr>
7844
7845 <tr>
7846 <td>SS fraction</td>
7847 <td>0.3</td>
7848 </tr>
7849 <tr>
7850 <td>Gap open (HH/SS/other)</td>
7851 <td>18/18/6</td>
7852 </tr>
7853 <tr>
7854 <td>Gap extend</td>
7855 <td>1</td>
7856 </tr>
7857 <tr>
7858 <td>SS matrix</td>
7859 <td>
7860 <table>
7861 <tr>
7862 <th></th> <th>H</th> <th>S</th> <th>O</th>
7863 </tr>
7864 <tr>
7865 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
7866 </tr>
7867 <tr>
7868 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
7869 </tr>
7870 <tr>
7871 <th>O</th> <td></td> <td></td> <td align="right">4</td>
7872 </tr>
7873 </table>
7874 </td>
7875 </tr>
7876
7877 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
7878 </table>
7879 <br/>Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with 1hfe, chain L (#9), sequence alignment score = 28.8<br>
7880RMSD between 22 pruned atom pairs is 0.734 angstroms; (across all 52 pairs: 15.360)<br>
7881<br>
7882<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/M/T</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/M/T">select #9/M/T</a></div></div>4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected<br>
7883<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1 models">show #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1 models">hide #1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><font color="crimson"><b>No reference and/or match structure/chain chosen<br>
7884</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #10/B to #7/Y pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #10/B to #7/Y pairing ss">matchmaker #10/B to #7/Y pairing ss</a></div></div>
7885 <table border=1 cellpadding=4 cellspacing=0>
7886 <tr>
7887 <th colspan="2">Parameters</th>
7888 </tr>
7889 <tr>
7890 <td>Chain pairing</td>
7891 <td>ss</td>
7892 </tr>
7893 <tr>
7894 <td>Alignment algorithm</td>
7895 <td>Needleman-Wunsch</td>
7896 </tr>
7897 <tr>
7898 <td>Similarity matrix</td>
7899 <td>BLOSUM-62</td>
7900 </tr>
7901
7902 <tr>
7903 <td>SS fraction</td>
7904 <td>0.3</td>
7905 </tr>
7906 <tr>
7907 <td>Gap open (HH/SS/other)</td>
7908 <td>18/18/6</td>
7909 </tr>
7910 <tr>
7911 <td>Gap extend</td>
7912 <td>1</td>
7913 </tr>
7914 <tr>
7915 <td>SS matrix</td>
7916 <td>
7917 <table>
7918 <tr>
7919 <th></th> <th>H</th> <th>S</th> <th>O</th>
7920 </tr>
7921 <tr>
7922 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
7923 </tr>
7924 <tr>
7925 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
7926 </tr>
7927 <tr>
7928 <th>O</th> <td></td> <td></td> <td align="right">4</td>
7929 </tr>
7930 </table>
7931 </td>
7932 </tr>
7933
7934 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
7935 </table>
7936 <br/>Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 6sdv, chain B (#10), sequence alignment score = 1014<br>
7937RMSD between 123 pruned atom pairs is 1.190 angstroms; (across all 214 pairs: 3.455)<br>
7938<br>
7939<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #9/L to #10/B pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #9/L to #10/B pairing ss">matchmaker #9/L to #10/B pairing ss</a></div></div>
7940 <table border=1 cellpadding=4 cellspacing=0>
7941 <tr>
7942 <th colspan="2">Parameters</th>
7943 </tr>
7944 <tr>
7945 <td>Chain pairing</td>
7946 <td>ss</td>
7947 </tr>
7948 <tr>
7949 <td>Alignment algorithm</td>
7950 <td>Needleman-Wunsch</td>
7951 </tr>
7952 <tr>
7953 <td>Similarity matrix</td>
7954 <td>BLOSUM-62</td>
7955 </tr>
7956
7957 <tr>
7958 <td>SS fraction</td>
7959 <td>0.3</td>
7960 </tr>
7961 <tr>
7962 <td>Gap open (HH/SS/other)</td>
7963 <td>18/18/6</td>
7964 </tr>
7965 <tr>
7966 <td>Gap extend</td>
7967 <td>1</td>
7968 </tr>
7969 <tr>
7970 <td>SS matrix</td>
7971 <td>
7972 <table>
7973 <tr>
7974 <th></th> <th>H</th> <th>S</th> <th>O</th>
7975 </tr>
7976 <tr>
7977 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
7978 </tr>
7979 <tr>
7980 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
7981 </tr>
7982 <tr>
7983 <th>O</th> <td></td> <td></td> <td align="right">4</td>
7984 </tr>
7985 </table>
7986 </td>
7987 </tr>
7988
7989 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
7990 </table>
7991 <br/>Matchmaker 6sdv, chain B (#10) with 1hfe, chain L (#9), sequence alignment score = 64.3<br>
7992RMSD between 6 pruned atom pairs is 1.458 angstroms; (across all 188 pairs: 28.430)<br>
7993<br>
7994<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/Y:1-73</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/Y:1-73">select #7/Y:1-73</a></div></div>585 atoms, 600 bonds, 73 residues, 1 model selected<br>
7995<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/Y:25-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/Y:25-84">select #9/Y:25-84</a></div></div>Nothing selected<br>
7996<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/S:25-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/S:25-84">select #9/S:25-84</a></div></div>393 atoms, 400 bonds, 49 residues, 1 model selected<br>
7997<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/L:25-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/L:25-84">select #9/L:25-84</a></div></div>450 atoms, 461 bonds, 60 residues, 1 model selected<br>
7998<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/Y:1-73#9/L:25-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/Y:1-73#9/L:25-84">select #7/Y:1-73#9/L:25-84</a></div></div>1035 atoms, 1061 bonds, 133 residues, 2 models selected<br>
7999<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #9/L &amp; sel to #7/Y &amp; sel pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #9/L &amp; sel to #7/Y &amp; sel pairing ss showAlignment true">matchmaker #9/L &amp; sel to #7/Y &amp; sel pairing ss showAlignment true</a></div></div>
8000 <table border=1 cellpadding=4 cellspacing=0>
8001 <tr>
8002 <th colspan="2">Parameters</th>
8003 </tr>
8004 <tr>
8005 <td>Chain pairing</td>
8006 <td>ss</td>
8007 </tr>
8008 <tr>
8009 <td>Alignment algorithm</td>
8010 <td>Needleman-Wunsch</td>
8011 </tr>
8012 <tr>
8013 <td>Similarity matrix</td>
8014 <td>BLOSUM-62</td>
8015 </tr>
8016
8017 <tr>
8018 <td>SS fraction</td>
8019 <td>0.3</td>
8020 </tr>
8021 <tr>
8022 <td>Gap open (HH/SS/other)</td>
8023 <td>18/18/6</td>
8024 </tr>
8025 <tr>
8026 <td>Gap extend</td>
8027 <td>1</td>
8028 </tr>
8029 <tr>
8030 <td>SS matrix</td>
8031 <td>
8032 <table>
8033 <tr>
8034 <th></th> <th>H</th> <th>S</th> <th>O</th>
8035 </tr>
8036 <tr>
8037 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
8038 </tr>
8039 <tr>
8040 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
8041 </tr>
8042 <tr>
8043 <th>O</th> <td></td> <td></td> <td align="right">4</td>
8044 </tr>
8045 </table>
8046 </td>
8047 </tr>
8048
8049 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
8050 </table>
8051 <br/>Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 1hfe, chain L (#9), sequence alignment score = 34.8<br>
8052Alignment identifier is 2<br>
8053Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 2<br>
8054Hiding conservation header for alignment 2<br>
8055Chains used in RMSD evaluation for alignment 2: Dock_PS1_Fd_test_output.pdb #7/Y, 1hfe #9/L<br>
8056Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 2<br>
8057RMSD between 8 pruned atom pairs is 1.316 angstroms; (across all 51 pairs: 12.843)<br>
8058<br>
8059<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #9/L &amp; sel to #10/B pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #9/L &amp; sel to #10/B pairing ss showAlignment true">matchmaker #9/L &amp; sel to #10/B pairing ss showAlignment true</a></div></div>
8060 <table border=1 cellpadding=4 cellspacing=0>
8061 <tr>
8062 <th colspan="2">Parameters</th>
8063 </tr>
8064 <tr>
8065 <td>Chain pairing</td>
8066 <td>ss</td>
8067 </tr>
8068 <tr>
8069 <td>Alignment algorithm</td>
8070 <td>Needleman-Wunsch</td>
8071 </tr>
8072 <tr>
8073 <td>Similarity matrix</td>
8074 <td>BLOSUM-62</td>
8075 </tr>
8076
8077 <tr>
8078 <td>SS fraction</td>
8079 <td>0.3</td>
8080 </tr>
8081 <tr>
8082 <td>Gap open (HH/SS/other)</td>
8083 <td>18/18/6</td>
8084 </tr>
8085 <tr>
8086 <td>Gap extend</td>
8087 <td>1</td>
8088 </tr>
8089 <tr>
8090 <td>SS matrix</td>
8091 <td>
8092 <table>
8093 <tr>
8094 <th></th> <th>H</th> <th>S</th> <th>O</th>
8095 </tr>
8096 <tr>
8097 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
8098 </tr>
8099 <tr>
8100 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
8101 </tr>
8102 <tr>
8103 <th>O</th> <td></td> <td></td> <td align="right">4</td>
8104 </tr>
8105 </table>
8106 </td>
8107 </tr>
8108
8109 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
8110 </table>
8111 <br/>Matchmaker 6sdv, chain B (#10) with 1hfe, chain L (#9), sequence alignment score = 34.1<br>
8112Alignment identifier is 3<br>
8113Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 3<br>
8114Hiding conservation header for alignment 3<br>
8115Chains used in RMSD evaluation for alignment 3: 1hfe #9/L, 6sdv #10/B<br>
8116Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 3<br>
8117RMSD between 4 pruned atom pairs is 1.059 angstroms; (across all 59 pairs: 15.580)<br>
8118<br>
8119<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/Y:75-137#9/L:25-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/Y:75-137#9/L:25-84">select #7/Y:75-137#9/L:25-84</a></div></div>910 atoms, 928 bonds, 123 residues, 2 models selected<br>
8120<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #9/L &amp; sel to #10/B &amp; sel pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #9/L &amp; sel to #10/B &amp; sel pairing ss showAlignment true">matchmaker #9/L &amp; sel to #10/B &amp; sel pairing ss showAlignment true</a></div></div><font color="crimson"><b>No &#x27;to&#x27; chains specified<br>
8121</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #9/L &amp; sel to #7/Y &amp; sel pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #9/L &amp; sel to #7/Y &amp; sel pairing ss showAlignment true">matchmaker #9/L &amp; sel to #7/Y &amp; sel pairing ss showAlignment true</a></div></div>
8122 <table border=1 cellpadding=4 cellspacing=0>
8123 <tr>
8124 <th colspan="2">Parameters</th>
8125 </tr>
8126 <tr>
8127 <td>Chain pairing</td>
8128 <td>ss</td>
8129 </tr>
8130 <tr>
8131 <td>Alignment algorithm</td>
8132 <td>Needleman-Wunsch</td>
8133 </tr>
8134 <tr>
8135 <td>Similarity matrix</td>
8136 <td>BLOSUM-62</td>
8137 </tr>
8138
8139 <tr>
8140 <td>SS fraction</td>
8141 <td>0.3</td>
8142 </tr>
8143 <tr>
8144 <td>Gap open (HH/SS/other)</td>
8145 <td>18/18/6</td>
8146 </tr>
8147 <tr>
8148 <td>Gap extend</td>
8149 <td>1</td>
8150 </tr>
8151 <tr>
8152 <td>SS matrix</td>
8153 <td>
8154 <table>
8155 <tr>
8156 <th></th> <th>H</th> <th>S</th> <th>O</th>
8157 </tr>
8158 <tr>
8159 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
8160 </tr>
8161 <tr>
8162 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
8163 </tr>
8164 <tr>
8165 <th>O</th> <td></td> <td></td> <td align="right">4</td>
8166 </tr>
8167 </table>
8168 </td>
8169 </tr>
8170
8171 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
8172 </table>
8173 <br/>Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 1hfe, chain L (#9), sequence alignment score = 52.2<br>
8174Alignment identifier is 4<br>
8175Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 4<br>
8176Hiding conservation header for alignment 4<br>
8177Chains used in RMSD evaluation for alignment 4: Dock_PS1_Fd_test_output.pdb #7/Y, 1hfe #9/L<br>
8178Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 4<br>
8179RMSD between 22 pruned atom pairs is 1.074 angstroms; (across all 46 pairs: 6.759)<br>
8180<br>
8181<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/Y</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/Y">select #7/Y</a></div></div>9266 atoms, 9474 bonds, 90 pseudobonds, 1186 residues, 2 models selected<br>
8182<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!7 &amp; sel) gray</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!7 &amp; sel) gray">color (#!7 &amp; sel) gray</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #9/L:422-423 toAtoms #7/Y:1183-1184</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #9/L:422-423 toAtoms #7/Y:1183-1184">align #9/L:422-423 toAtoms #7/Y:1183-1184</a></div></div>RMSD between 16 atom pairs is 1.724 angstroms<br>
8183<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/L:35,38,41,76, 45,66,69,72#7/Y:73,76,81,120,85,110,113,116</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/L:35,38,41,76, 45,66,69,72#7/Y:73,76,81,120,85,110,113,116">select #9/L:35,38,41,76, 45,66,69,72#7/Y:73,76,81,120,85,110,113,116</a></div></div>96 atoms, 80 bonds, 16 residues, 2 models selected<br>
8184<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/L:35-41 #7/Y:73-81</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/L:35-41 #7/Y:73-81">select #9/L:35-41 #7/Y:73-81</a></div></div>114 atoms, 115 bonds, 16 residues, 2 models selected<br>
8185<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> ~sel &amp; ##selected</div><div class="cxcmd_as_cmd"><a href="cxcmd:select ~sel &amp; ##selected">select ~sel &amp; ##selected</a></div></div>31473 atoms, 31085 bonds, 193 pseudobonds, 5083 residues, 6 models selected<br>
8186<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #9/L:422-423 toAtoms #3:61,62</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #9/L:422-423 toAtoms #3:61,62">align #9/L:422-423 toAtoms #3:61,62</a></div></div>RMSD between 16 atom pairs is 2.679 angstroms<br>
8187<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/S:25-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/S:25-84">select #9/S:25-84</a></div></div>393 atoms, 400 bonds, 49 residues, 1 model selected<br>
8188<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/L:25-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/L:25-84">select #9/L:25-84</a></div></div>450 atoms, 461 bonds, 60 residues, 1 model selected<br>
8189<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/L:27-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/L:27-84">select #9/L:27-84</a></div></div>432 atoms, 442 bonds, 58 residues, 1 model selected<br>
8190<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/L:27-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/L:27-84">select #9/L:27-84</a></div></div>432 atoms, 442 bonds, 58 residues, 1 model selected<br>
8191<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime">color sel lime</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/Y:63-121</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/Y:63-121">select #7/Y:63-121</a></div></div>434 atoms, 443 bonds, 59 residues, 1 model selected<br>
8192<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/Y:72-121</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/Y:72-121">select #7/Y:72-121</a></div></div>354 atoms, 358 bonds, 50 residues, 1 model selected<br>
8193<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #3">combine #3</a></div></div>Associated copy of BFd (2fdn) chain M to BFd (2fdn), chain M with 0 mismatches<br>
8194Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M, PSI_BFd_SF4_opt.pdb #4/F, copy of BFd (2fdn) #11/M<br>
8195<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #11/M to #7/Y &amp; sel pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #11/M to #7/Y &amp; sel pairing ss">matchmaker #11/M to #7/Y &amp; sel pairing ss</a></div></div>
8196 <table border=1 cellpadding=4 cellspacing=0>
8197 <tr>
8198 <th colspan="2">Parameters</th>
8199 </tr>
8200 <tr>
8201 <td>Chain pairing</td>
8202 <td>ss</td>
8203 </tr>
8204 <tr>
8205 <td>Alignment algorithm</td>
8206 <td>Needleman-Wunsch</td>
8207 </tr>
8208 <tr>
8209 <td>Similarity matrix</td>
8210 <td>BLOSUM-62</td>
8211 </tr>
8212
8213 <tr>
8214 <td>SS fraction</td>
8215 <td>0.3</td>
8216 </tr>
8217 <tr>
8218 <td>Gap open (HH/SS/other)</td>
8219 <td>18/18/6</td>
8220 </tr>
8221 <tr>
8222 <td>Gap extend</td>
8223 <td>1</td>
8224 </tr>
8225 <tr>
8226 <td>SS matrix</td>
8227 <td>
8228 <table>
8229 <tr>
8230 <th></th> <th>H</th> <th>S</th> <th>O</th>
8231 </tr>
8232 <tr>
8233 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
8234 </tr>
8235 <tr>
8236 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
8237 </tr>
8238 <tr>
8239 <th>O</th> <td></td> <td></td> <td align="right">4</td>
8240 </tr>
8241 </table>
8242 </td>
8243 </tr>
8244
8245 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
8246 </table>
8247 <br/>Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with copy of BFd (2fdn), chain M (#11), sequence alignment score = 86.5<br>
8248RMSD between 25 pruned atom pairs is 1.276 angstroms; (across all 42 pairs: 3.792)<br>
8249<br>
8250<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/L:25-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/L:25-84">select #9/L:25-84</a></div></div>450 atoms, 461 bonds, 60 residues, 1 model selected<br>
8251<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #9/L &amp; sel to #11/M pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #9/L &amp; sel to #11/M pairing ss">matchmaker #9/L &amp; sel to #11/M pairing ss</a></div></div>
8252 <table border=1 cellpadding=4 cellspacing=0>
8253 <tr>
8254 <th colspan="2">Parameters</th>
8255 </tr>
8256 <tr>
8257 <td>Chain pairing</td>
8258 <td>ss</td>
8259 </tr>
8260 <tr>
8261 <td>Alignment algorithm</td>
8262 <td>Needleman-Wunsch</td>
8263 </tr>
8264 <tr>
8265 <td>Similarity matrix</td>
8266 <td>BLOSUM-62</td>
8267 </tr>
8268
8269 <tr>
8270 <td>SS fraction</td>
8271 <td>0.3</td>
8272 </tr>
8273 <tr>
8274 <td>Gap open (HH/SS/other)</td>
8275 <td>18/18/6</td>
8276 </tr>
8277 <tr>
8278 <td>Gap extend</td>
8279 <td>1</td>
8280 </tr>
8281 <tr>
8282 <td>SS matrix</td>
8283 <td>
8284 <table>
8285 <tr>
8286 <th></th> <th>H</th> <th>S</th> <th>O</th>
8287 </tr>
8288 <tr>
8289 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
8290 </tr>
8291 <tr>
8292 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
8293 </tr>
8294 <tr>
8295 <th>O</th> <td></td> <td></td> <td align="right">4</td>
8296 </tr>
8297 </table>
8298 </td>
8299 </tr>
8300
8301 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
8302 </table>
8303 <br/>Matchmaker copy of BFd (2fdn), chain M (#11) with 1hfe, chain L (#9), sequence alignment score = 104.3<br>
8304RMSD between 43 pruned atom pairs is 1.236 angstroms; (across all 55 pairs: 2.501)<br>
8305<br>
8306<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3:61/11:61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3:61/11:61">select #3:61/11:61</a></div></div>8 atoms, 12 bonds, 1 residue, 1 model selected<br>
8307<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3:61#11:61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3:61#11:61">select #3:61#11:61</a></div></div>16 atoms, 24 bonds, 2 residues, 2 models selected<br>
8308<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cornflower blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cornflower blue">color sel cornflower blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/L:25-84</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/L:25-84">select #9/L:25-84</a></div></div>450 atoms, 461 bonds, 60 residues, 1 model selected<br>
8309<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #9/L &amp; sel to #3/M pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #9/L &amp; sel to #3/M pairing ss">matchmaker #9/L &amp; sel to #3/M pairing ss</a></div></div>
8310 <table border=1 cellpadding=4 cellspacing=0>
8311 <tr>
8312 <th colspan="2">Parameters</th>
8313 </tr>
8314 <tr>
8315 <td>Chain pairing</td>
8316 <td>ss</td>
8317 </tr>
8318 <tr>
8319 <td>Alignment algorithm</td>
8320 <td>Needleman-Wunsch</td>
8321 </tr>
8322 <tr>
8323 <td>Similarity matrix</td>
8324 <td>BLOSUM-62</td>
8325 </tr>
8326
8327 <tr>
8328 <td>SS fraction</td>
8329 <td>0.3</td>
8330 </tr>
8331 <tr>
8332 <td>Gap open (HH/SS/other)</td>
8333 <td>18/18/6</td>
8334 </tr>
8335 <tr>
8336 <td>Gap extend</td>
8337 <td>1</td>
8338 </tr>
8339 <tr>
8340 <td>SS matrix</td>
8341 <td>
8342 <table>
8343 <tr>
8344 <th></th> <th>H</th> <th>S</th> <th>O</th>
8345 </tr>
8346 <tr>
8347 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
8348 </tr>
8349 <tr>
8350 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
8351 </tr>
8352 <tr>
8353 <th>O</th> <td></td> <td></td> <td align="right">4</td>
8354 </tr>
8355 </table>
8356 </td>
8357 </tr>
8358
8359 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
8360 </table>
8361 <br/>Matchmaker BFd (2fdn), chain M (#3) with 1hfe, chain L (#9), sequence alignment score = 104.3<br>
8362RMSD between 43 pruned atom pairs is 1.232 angstroms; (across all 55 pairs: 2.484)<br>
8363<br>
8364<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #8/A to #9/L pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #8/A to #9/L pairing ss">matchmaker #8/A to #9/L pairing ss</a></div></div>
8365 <table border=1 cellpadding=4 cellspacing=0>
8366 <tr>
8367 <th colspan="2">Parameters</th>
8368 </tr>
8369 <tr>
8370 <td>Chain pairing</td>
8371 <td>ss</td>
8372 </tr>
8373 <tr>
8374 <td>Alignment algorithm</td>
8375 <td>Needleman-Wunsch</td>
8376 </tr>
8377 <tr>
8378 <td>Similarity matrix</td>
8379 <td>BLOSUM-62</td>
8380 </tr>
8381
8382 <tr>
8383 <td>SS fraction</td>
8384 <td>0.3</td>
8385 </tr>
8386 <tr>
8387 <td>Gap open (HH/SS/other)</td>
8388 <td>18/18/6</td>
8389 </tr>
8390 <tr>
8391 <td>Gap extend</td>
8392 <td>1</td>
8393 </tr>
8394 <tr>
8395 <td>SS matrix</td>
8396 <td>
8397 <table>
8398 <tr>
8399 <th></th> <th>H</th> <th>S</th> <th>O</th>
8400 </tr>
8401 <tr>
8402 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
8403 </tr>
8404 <tr>
8405 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
8406 </tr>
8407 <tr>
8408 <th>O</th> <td></td> <td></td> <td align="right">4</td>
8409 </tr>
8410 </table>
8411 </td>
8412 </tr>
8413
8414 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
8415 </table>
8416 <br/>Matchmaker 1hfe, chain L (#9) with fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#8), sequence alignment score = 2066.5<br>
8417RMSD between 390 pruned atom pairs is 0.207 angstroms; (across all 396 pairs: 1.636)<br>
8418<br>
8419<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/S</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/S">select #9/S</a></div></div>860 atoms, 733 bonds, 1 pseudobond, 235 residues, 2 models selected<br>
8420<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!9 &amp; sel) cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!9 &amp; sel) cyan">color (#!9 &amp; sel) cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8:467-477</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8:467-477">select #8:467-477</a></div></div>92 atoms, 96 bonds, 11 residues, 1 model selected<br>
8421<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #8">select add #8</a></div></div>3677 atoms, 3770 bonds, 477 residues, 1 model selected<br>
8422<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #8">select subtract #8</a></div></div>Nothing selected<br>
8423<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #8 models">show #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #9-10</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #9-10">close #9-10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/FDH TUM/AF3 FdhF_HycB complex/fold_clj_fdhf_hycb_D8GNT2_ptm80_iptm_67/fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/FDH TUM/AF3 FdhF_HycB complex/fold_clj_fdhf_hycb_D8GNT2_ptm80_iptm_67/fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/FDH TUM/AF3 FdhF_HycB complex/fold_clj_fdhf_hycb_D8GNT2_ptm80_iptm_67/fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
8424 <thead>
8425 <tr>
8426 <th colspan="2">Chain information for fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif #9</th>
8427 </tr>
8428 <tr>
8429 <th>Chain</th>
8430 <th>Description</th>
8431
8432 </tr>
8433 </thead>
8434 <tbody>
8435 <tr>
8436 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9/A:1-709">A</a></td>
8437 <td><a title="Show sequence" href="cxcmd:sequence chain #9/A">.</a></td>
8438
8439 </tr>
8440 <tr>
8441 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9/B:1-188">B</a></td>
8442 <td><a title="Show sequence" href="cxcmd:sequence chain #9/B">.</a></td>
8443
8444 </tr>
8445 </tbody>
8446</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #8 models">hide #8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view">view</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9:59-150 &amp;:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9:59-150 &amp;:Cys">select #9:59-150 &amp;:Cys</a></div></div>78 atoms, 65 bonds, 13 residues, 1 model selected<br>
8447<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9:59-140 &amp;:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9:59-140 &amp;:Cys">select #9:59-140 &amp;:Cys</a></div></div>66 atoms, 55 bonds, 11 residues, 1 model selected<br>
8448<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/B:59-140 &amp;:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/B:59-140 &amp;:Cys">select #9/B:59-140 &amp;:Cys</a></div></div>48 atoms, 40 bonds, 8 residues, 1 model selected<br>
8449<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #9/B &amp; sel to #11/M pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #9/B &amp; sel to #11/M pairing ss">matchmaker #9/B &amp; sel to #11/M pairing ss</a></div></div>
8450 <table border=1 cellpadding=4 cellspacing=0>
8451 <tr>
8452 <th colspan="2">Parameters</th>
8453 </tr>
8454 <tr>
8455 <td>Chain pairing</td>
8456 <td>ss</td>
8457 </tr>
8458 <tr>
8459 <td>Alignment algorithm</td>
8460 <td>Needleman-Wunsch</td>
8461 </tr>
8462 <tr>
8463 <td>Similarity matrix</td>
8464 <td>BLOSUM-62</td>
8465 </tr>
8466
8467 <tr>
8468 <td>SS fraction</td>
8469 <td>0.3</td>
8470 </tr>
8471 <tr>
8472 <td>Gap open (HH/SS/other)</td>
8473 <td>18/18/6</td>
8474 </tr>
8475 <tr>
8476 <td>Gap extend</td>
8477 <td>1</td>
8478 </tr>
8479 <tr>
8480 <td>SS matrix</td>
8481 <td>
8482 <table>
8483 <tr>
8484 <th></th> <th>H</th> <th>S</th> <th>O</th>
8485 </tr>
8486 <tr>
8487 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
8488 </tr>
8489 <tr>
8490 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
8491 </tr>
8492 <tr>
8493 <th>O</th> <td></td> <td></td> <td align="right">4</td>
8494 </tr>
8495 </table>
8496 </td>
8497 </tr>
8498
8499 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
8500 </table>
8501 <br/>Matchmaker copy of BFd (2fdn), chain M (#11) with fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif, chain B (#9), sequence alignment score = 46<br>
8502RMSD between 8 pruned atom pairs is 0.685 angstroms; (across all 8 pairs: 0.685)<br>
8503<br>
8504<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view">view</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/B:112-137</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/B:112-137">select #9/B:112-137</a></div></div>195 atoms, 196 bonds, 26 residues, 1 model selected<br>
8505<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/B:59-140 &amp;:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/B:59-140 &amp;:Cys">select #9/B:59-140 &amp;:Cys</a></div></div>48 atoms, 40 bonds, 8 residues, 1 model selected<br>
8506<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Mon Oct 14 21:44:01 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
8507<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #5.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #5.1 models">hide #5.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #6 models">hide #6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #9 models">hide #9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdHyd_PSI.opt.pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdHyd_PSI.opt.pdb">open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdHyd_PSI.opt.pdb</a></div></div><table border=1 cellpadding=4 cellspacing=0>
8508 <thead>
8509 <tr>
8510 <th colspan="2">Chain information for DdHyd_PSI.opt.pdb #10</th>
8511 </tr>
8512 <tr>
8513 <th>Chain</th>
8514 <th>Description</th>
8515
8516 </tr>
8517 </thead>
8518 <tbody>
8519 <tr>
8520 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10/?:1-2238">?</a></td>
8521 <td><a title="Show sequence" href="cxcmd:sequence chain #10/?">No description available</a></td>
8522
8523 </tr>
8524 </tbody>
8525</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!10 to #4 showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!10 to #4 showAlignment true">matchmaker #!10 to #4 showAlignment true</a></div></div>
8526 <table border=1 cellpadding=4 cellspacing=0>
8527 <tr>
8528 <th colspan="2">Parameters</th>
8529 </tr>
8530 <tr>
8531 <td>Chain pairing</td>
8532 <td>bb</td>
8533 </tr>
8534 <tr>
8535 <td>Alignment algorithm</td>
8536 <td>Needleman-Wunsch</td>
8537 </tr>
8538 <tr>
8539 <td>Similarity matrix</td>
8540 <td>BLOSUM-62</td>
8541 </tr>
8542
8543 <tr>
8544 <td>SS fraction</td>
8545 <td>0.3</td>
8546 </tr>
8547 <tr>
8548 <td>Gap open (HH/SS/other)</td>
8549 <td>18/18/6</td>
8550 </tr>
8551 <tr>
8552 <td>Gap extend</td>
8553 <td>1</td>
8554 </tr>
8555 <tr>
8556 <td>SS matrix</td>
8557 <td>
8558 <table>
8559 <tr>
8560 <th></th> <th>H</th> <th>S</th> <th>O</th>
8561 </tr>
8562 <tr>
8563 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
8564 </tr>
8565 <tr>
8566 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
8567 </tr>
8568 <tr>
8569 <th>O</th> <td></td> <td></td> <td align="right">4</td>
8570 </tr>
8571 </table>
8572 </td>
8573 </tr>
8574
8575 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
8576 </table>
8577 <br/>Matchmaker PSI_BFd_SF4_opt.pdb, chain A (#4) with DdHyd_PSI.opt.pdb, chain (blank) (#10), sequence alignment score = 3958.5<br>
8578Alignment identifier is 2<br>
8579Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 2<br>
8580Hiding conservation header for alignment 2<br>
8581Chains used in RMSD evaluation for alignment 2: PSI_BFd_SF4_opt.pdb #4/A, DdHyd_PSI.opt.pdb #10/?<br>
8582Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 2<br>
8583RMSD between 743 pruned atom pairs is 0.000 angstroms; (across all 743 pairs: 0.000)<br>
8584<br>
8585<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #10 atoms :1-743,2239 atoms :744-1476 atoms :1477-1556,2240-2241 atoms :1557-1699 atoms :1700-1765 atoms :1766-2238,2242-2244</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #10 atoms :1-743,2239 atoms :744-1476 atoms :1477-1556,2240-2241 atoms :1557-1699 atoms :1700-1765 atoms :1766-2238,2242-2244">split #10 atoms :1-743,2239 atoms :744-1476 atoms :1477-1556,2240-2241 atoms :1557-1699 atoms :1700-1765 atoms :1766-2238,2242-2244</a></div></div>Split DdHyd_PSI.opt.pdb (#10) into 6 models<br>
8586<table border=1 cellpadding=4 cellspacing=0>
8587 <thead>
8588 <tr>
8589 <th colspan="2">Chain information for DdHyd_PSI.opt.pdb 1 #10.1</th>
8590 </tr>
8591 <tr>
8592 <th>Chain</th>
8593 <th>Description</th>
8594
8595 </tr>
8596 </thead>
8597 <tbody>
8598 <tr>
8599 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10.1/?:1-743">?</a></td>
8600 <td><a title="Show sequence" href="cxcmd:sequence chain #10.1/?">No description available</a></td>
8601
8602 </tr>
8603 </tbody>
8604</table><br/><table border=1 cellpadding=4 cellspacing=0>
8605 <thead>
8606 <tr>
8607 <th colspan="2">Chain information for DdHyd_PSI.opt.pdb 2 #10.2</th>
8608 </tr>
8609 <tr>
8610 <th>Chain</th>
8611 <th>Description</th>
8612
8613 </tr>
8614 </thead>
8615 <tbody>
8616 <tr>
8617 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10.2/?:744-1476">?</a></td>
8618 <td><a title="Show sequence" href="cxcmd:sequence chain #10.2/?">No description available</a></td>
8619
8620 </tr>
8621 </tbody>
8622</table><br/><table border=1 cellpadding=4 cellspacing=0>
8623 <thead>
8624 <tr>
8625 <th colspan="2">Chain information for DdHyd_PSI.opt.pdb 3 #10.3</th>
8626 </tr>
8627 <tr>
8628 <th>Chain</th>
8629 <th>Description</th>
8630
8631 </tr>
8632 </thead>
8633 <tbody>
8634 <tr>
8635 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10.3/?:1477-1556">?</a></td>
8636 <td><a title="Show sequence" href="cxcmd:sequence chain #10.3/?">No description available</a></td>
8637
8638 </tr>
8639 </tbody>
8640</table><br/><table border=1 cellpadding=4 cellspacing=0>
8641 <thead>
8642 <tr>
8643 <th colspan="2">Chain information for DdHyd_PSI.opt.pdb 4 #10.4</th>
8644 </tr>
8645 <tr>
8646 <th>Chain</th>
8647 <th>Description</th>
8648
8649 </tr>
8650 </thead>
8651 <tbody>
8652 <tr>
8653 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10.4/?:1557-1699">?</a></td>
8654 <td><a title="Show sequence" href="cxcmd:sequence chain #10.4/?">No description available</a></td>
8655
8656 </tr>
8657 </tbody>
8658</table><br/><table border=1 cellpadding=4 cellspacing=0>
8659 <thead>
8660 <tr>
8661 <th colspan="2">Chain information for DdHyd_PSI.opt.pdb 5 #10.5</th>
8662 </tr>
8663 <tr>
8664 <th>Chain</th>
8665 <th>Description</th>
8666
8667 </tr>
8668 </thead>
8669 <tbody>
8670 <tr>
8671 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10.5/?:1700-1765">?</a></td>
8672 <td><a title="Show sequence" href="cxcmd:sequence chain #10.5/?">No description available</a></td>
8673
8674 </tr>
8675 </tbody>
8676</table><br/><table border=1 cellpadding=4 cellspacing=0>
8677 <thead>
8678 <tr>
8679 <th colspan="2">Chain information for DdHyd_PSI.opt.pdb 6 #10.6</th>
8680 </tr>
8681 <tr>
8682 <th>Chain</th>
8683 <th>Description</th>
8684
8685 </tr>
8686 </thead>
8687 <tbody>
8688 <tr>
8689 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10.6/?:1766-2238">?</a></td>
8690 <td><a title="Show sequence" href="cxcmd:sequence chain #10.6/?">No description available</a></td>
8691
8692 </tr>
8693 </tbody>
8694</table><br/>Associated DdHyd_PSI.opt.pdb 1 (10.1) chain (blank) to PSI_BFd_SF4_opt.pdb, chain A with 0 mismatches<br>
8695Associated DdHyd_PSI.opt.pdb 2 (10.2) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8696Associated DdHyd_PSI.opt.pdb 3 (10.3) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8697Associated DdHyd_PSI.opt.pdb 4 (10.4) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8698Associated DdHyd_PSI.opt.pdb 5 (10.5) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8699Associated DdHyd_PSI.opt.pdb 6 (10.6) chain (blank) to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8700Traceback (most recent call last):<br>
8701&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py&quot;, line 149, in invoke<br>
8702&nbsp;&nbsp;&nbsp;&nbsp;return self._func(self._name, data)<br>
8703&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
8704&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py&quot;, line 427, in &lt;lambda&gt;<br>
8705&nbsp;&nbsp;&nbsp;&nbsp;self.associate([s for s in models if isinstance(s, AtomicStructure)], force=False))<br>
8706&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
8707&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py&quot;, line 394, in associate<br>
8708&nbsp;&nbsp;&nbsp;&nbsp;self._notify_observers(note_name, note_data)<br>
8709&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py&quot;, line 826, in _notify_observers<br>
8710&nbsp;&nbsp;&nbsp;&nbsp;self._notify_rmsd_change()<br>
8711&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py&quot;, line 835, in _notify_rmsd_change<br>
8712&nbsp;&nbsp;&nbsp;&nbsp;self._notify_observers(self.NOTE_RMSD_UPDATE, None)<br>
8713&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py&quot;, line 823, in _notify_observers<br>
8714&nbsp;&nbsp;&nbsp;&nbsp;recipient.alignment_notification(note_name, note_data)<br>
8715&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_headers/rmsd.py&quot;, line 52, in alignment_notification<br>
8716&nbsp;&nbsp;&nbsp;&nbsp;self.reevaluate()<br>
8717&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_headers/rmsd.py&quot;, line 126, in reevaluate<br>
8718&nbsp;&nbsp;&nbsp;&nbsp;new_eval_chains = self.alignment.rmsd_chains<br>
8719&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
8720&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py&quot;, line 670, in rmsd_chains<br>
8721&nbsp;&nbsp;&nbsp;&nbsp;rmsd = self._eval_rmsd([c1, c2])<br>
8722&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^<br>
8723&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py&quot;, line 769, in _eval_rmsd<br>
8724&nbsp;&nbsp;&nbsp;&nbsp;for coords in self._gather_coords(chains, pa_name):<br>
8725&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
8726&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/alignment.py&quot;, line 794, in _gather_coords<br>
8727&nbsp;&nbsp;&nbsp;&nbsp;pa = r.find_atom(pa_name)<br>
8728&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^<br>
8729&nbsp;&nbsp;File &quot;atomic_cpp/cymol.pyx&quot;, line 1651, in chimerax.atomic.cymol.CyResidue.find_atom<br>
8730RuntimeError: Residue already deleted<br>
8731<br/>Error processing trigger "add models":<br>RuntimeError: Residue already deleted<br><br> File "atomic_cpp/cymol.pyx", line 1651, in chimerax.atomic.cymol.CyResidue.find_atom<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10.1 models">hide #!10.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #10.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #10.2 models">hide #10.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10.3 models">hide #!10.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #10.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #10.4 models">hide #10.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #10.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #10.5 models">hide #10.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10.6 models">hide #!10.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10.1 models">show #!10.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10.1 models">hide #!10.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #10.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #10.2 models">show #10.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10.1 models">show #!10.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #10.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #10.2 models">hide #10.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10.1 models">hide #!10.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10.1 models">show #!10.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #10.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #10.2 models">show #10.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10.3 models">show #!10.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #10.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #10.4 models">show #10.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10.3 models">hide #!10.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #10.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #10.2 models">hide #10.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10.1 models">hide #!10.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #10.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #10.4 models">hide #10.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #10.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #10.5 models">show #10.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #10.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #10.5 models">hide #10.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10.6 models">show #!10.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #10.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #10.2 models">show #10.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10.1 models">show #!10.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10.3 models">show #!10.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #10.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #10.4 models">show #10.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #10.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #10.5 models">show #10.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Change Chain IDs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Change Chain IDs&quot;">ui tool show &quot;Change Chain IDs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10.1">select add #10.1</a></div></div>11635 atoms, 11818 bonds, 18 pseudobonds, 752 residues, 3 models selected<br>
8732<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel A</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel A">changechains sel A</a></div></div><font color="crimson"><b>Cannot reassign chain ID to only part of polymeric chain (fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif #9/B)<br>
8733</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10.1">select add #10.1</a></div></div>11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected<br>
8734<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel A</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel A">changechains sel A</a></div></div>Chain IDs of 744 residues changed<br>
8735<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #10.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #10.1">select subtract #10.1</a></div></div>Nothing selected<br>
8736<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10.2">select add #10.2</a></div></div>11513 atoms, 11725 bonds, 733 residues, 1 model selected<br>
8737<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel B</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel B">changechains sel B</a></div></div>Chain IDs of 733 residues changed<br>
8738<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #10.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #10.2">select subtract #10.2</a></div></div>Nothing selected<br>
8739<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10.3">select add #10.3</a></div></div>1222 atoms, 1219 bonds, 36 pseudobonds, 82 residues, 2 models selected<br>
8740<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel C</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel C">changechains sel C</a></div></div>Chain IDs of 82 residues changed<br>
8741<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #10.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #10.3">select subtract #10.3</a></div></div>Nothing selected<br>
8742<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10.4">select add #10.4</a></div></div>2277 atoms, 2308 bonds, 143 residues, 1 model selected<br>
8743<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel D</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel D">changechains sel D</a></div></div>Chain IDs of 143 residues changed<br>
8744<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #10.4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #10.4">select subtract #10.4</a></div></div>Nothing selected<br>
8745<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10.5">select add #10.5</a></div></div>1059 atoms, 1071 bonds, 66 residues, 1 model selected<br>
8746<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel E</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel E">changechains sel E</a></div></div>Chain IDs of 66 residues changed<br>
8747<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10.6">select add #10.6</a></div></div>8232 atoms, 8313 bonds, 54 pseudobonds, 542 residues, 3 models selected<br>
8748<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #10.5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #10.5">select subtract #10.5</a></div></div>7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected<br>
8749<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/changechains.html">changechains</a> sel F</div><div class="cxcmd_as_cmd"><a href="cxcmd:changechains sel F">changechains sel F</a></div></div>Chain IDs of 476 residues changed<br>
8750<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10">select add #10</a></div></div>34831 atoms, 35343 bonds, 108 pseudobonds, 2244 residues, 10 models selected<br>
8751<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel bychain</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel bychain">color sel bychain</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #10.1#10.2#10.3#10.4#10.5#10.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #10.1#10.2#10.3#10.4#10.5#10.6">combine #10.1#10.2#10.3#10.4#10.5#10.6</a></div></div>Associated combination chain A to PSI_BFd_SF4_opt.pdb, chain A with 0 mismatches<br>
8752Associated combination chain B to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8753Associated combination chain F to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8754Associated combination chain D to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8755Associated combination chain C to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8756Associated combination chain E to DdHyd_PSI.opt.pdb, chain (blank) with 0 mismatches<br>
8757<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #12 &quot;DdHyd_PSI.opt.pdb split to chains&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #12 &quot;DdHyd_PSI.opt.pdb split to chains&quot;">rename #12 &quot;DdHyd_PSI.opt.pdb split to chains&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #10">close #10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #12 id #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #12 id #10">rename #12 id #10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10/A-E">select #10/A-E</a></div></div>27658 atoms, 28101 bonds, 54 pseudobonds, 1768 residues, 2 models selected<br>
8758<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Clashes</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Clashes">ui tool show Clashes</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">clashes</a> sel restrict #10/F resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:clashes sel restrict #10/F resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true">clashes sel restrict #10/F resSeparation 5 interModel false intraMol false color #fffb00 reveal true log true</a></div></div><pre>Allowed overlap: 0.6
8759H-bond overlap reduction: 0.4
8760Ignore clashes between atoms separated by 4 bonds or less
8761Ignore clashes between atoms in residues less than 5 apart in sequence
8762Detect intra-residue clashes: False
8763Detect intra-molecule clashes: False
8764
87650 clashes
8766atom1 atom2 overlap distance
8767</pre><br/>No clashes<br>
8768<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Contacts</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Contacts">ui tool show Contacts</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10/A-E &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10/A-E &amp;~H">select #10/A-E &amp;~H</a></div></div>14013 atoms, 14456 bonds, 54 pseudobonds, 1768 residues, 2 models selected<br>
8769<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/clashes.html">contacts</a> sel restrict &quot;#10/F &amp;~H&quot; resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:contacts sel restrict &quot;#10/F &amp;~H&quot; resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 reveal true log true">contacts sel restrict &quot;#10/F &amp;~H&quot; resSeparation 5 interModel false intraMol false color #ff85ff radius 0.2 reveal true log true</a></div></div><pre>Allowed overlap: -0.4
8770H-bond overlap reduction: 0.4
8771Ignore contacts between atoms separated by 4 bonds or less
8772Ignore contacts between atoms in residues less than 5 apart in sequence
8773Detect intra-residue contacts: False
8774Detect intra-molecule contacts: False
8775
877661 contacts
8777 atom1 atom2 overlap distance
8778DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F GLU 1794 C 0.260 3.065
8779DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1 DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 CA 0.258 2.922
8780DdHyd_PSI.opt.pdb split to chains #10/E ALA 1728 CB DdHyd_PSI.opt.pdb split to chains #10/F THR 1767 CG2 0.154 3.246
8781DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 N 0.146 3.104
8782DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 OE1 DdHyd_PSI.opt.pdb split to chains #10/F PRO 1816 CB 0.120 3.060
8783DdHyd_PSI.opt.pdb split to chains #10/C ILE 1487 O DdHyd_PSI.opt.pdb split to chains #10/F PRO 1841 CB 0.119 3.061
8784DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F TYR 2235 C 0.116 3.209
8785DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 CG 0.093 3.232
8786DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1 DdHyd_PSI.opt.pdb split to chains #10/F LEU 1769 C 0.079 3.246
8787DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CA 0.072 3.253
8788DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 CG DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N 0.044 3.281
8789DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 N 0.010 3.315
8790DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE DdHyd_PSI.opt.pdb split to chains #10/F TYR 2235 O -0.010 3.190
8791DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1 DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 C -0.035 3.215
8792DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2 DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 CB -0.041 3.366
8793DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O -0.057 2.762
8794DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O -0.077 3.257
8795DdHyd_PSI.opt.pdb split to chains #10/C ARG 1494 NH2 DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 NE2 -0.098 3.348
8796DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH1 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2 -0.100 2.805
8797DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 CZ DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2 -0.106 3.286
8798DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE DdHyd_PSI.opt.pdb split to chains #10/F TYR 2235 C -0.107 3.507
8799DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ DdHyd_PSI.opt.pdb split to chains #10/F LEU 1769 C -0.117 3.517
8800DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1 -0.124 2.829
8801DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2 -0.130 2.835
8802DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 OE1 -0.134 2.839
8803DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F GLY 1795 N -0.145 3.395
8804DdHyd_PSI.opt.pdb split to chains #10/D VAL 1666 CG1 DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 O -0.150 3.330
8805DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CA -0.155 3.555
8806DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1 DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N -0.157 2.862
8807DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2 DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 CA -0.160 3.485
8808DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1 DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O -0.161 2.866
8809DdHyd_PSI.opt.pdb split to chains #10/C LYS 1512 CE DdHyd_PSI.opt.pdb split to chains #10/F TYR 2157 OH -0.167 3.367
8810DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2 DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 O -0.168 2.873
8811DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F GLU 1794 O -0.177 2.882
8812DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD2 DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N -0.197 2.902
8813DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1 DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 N -0.199 3.449
8814DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F GLU 1794 CB -0.209 3.534
8815DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 N DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 O -0.210 2.915
8816DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 OE1 DdHyd_PSI.opt.pdb split to chains #10/F PRO 1816 CG -0.212 3.392
8817DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CD -0.217 3.542
8818DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 CB DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 ND2 -0.237 3.562
8819DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2 DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 C -0.249 3.574
8820DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 CA -0.265 3.665
8821DdHyd_PSI.opt.pdb split to chains #10/C LYS 1512 CD DdHyd_PSI.opt.pdb split to chains #10/F TYR 2157 OH -0.269 3.469
8822DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD1 -0.279 2.984
8823DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NE DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 CA -0.285 3.610
8824DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2 DdHyd_PSI.opt.pdb split to chains #10/F GLY 1770 N -0.292 3.542
8825DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 CG DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1 -0.295 3.475
8826DdHyd_PSI.opt.pdb split to chains #10/D VAL 1666 O DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 O -0.301 3.261
8827DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 CG DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 CA -0.304 3.704
8828DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2 DdHyd_PSI.opt.pdb split to chains #10/F LEU 1769 C -0.317 3.642
8829DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 CZ DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O -0.322 3.502
8830DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 CG DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 C -0.340 3.740
8831DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 CD DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 CA -0.345 3.745
8832DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ DdHyd_PSI.opt.pdb split to chains #10/F THR 1767 OG1 -0.349 3.074
8833DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 CE DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 N -0.360 3.685
8834DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F PRO 2236 CG -0.363 3.688
8835DdHyd_PSI.opt.pdb split to chains #10/E GLN 1731 CB DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 NZ -0.363 3.688
8836DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F GLY 1795 CA -0.364 3.689
8837DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 CG DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 CG2 -0.368 3.768
8838DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 C -0.398 3.723
8839</pre><br/>61 contacts<br>
8840<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #10.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #10.3 models">hide #10.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff restrict #10/F interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff restrict #10/F interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff restrict #10/F interModel false intraMol false intraRes false reveal true log true</a></div></div>Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.pdb split to chains #10/A CYF 575 SG<br>
8841Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.pdb split to chains #10/A CYF 575 SG<br>
8842<br>
8843[Repeated 1 time(s)]<p style="color:darkorange">Skipped 2 atom(s) with bad connectivities; see log for details<br>
8844</p><pre>Finding intramodel H-bonds
8845Constraints relaxed by 0.4 angstroms and 20 degrees
8846Models used:
8847 10 DdHyd_PSI.opt.pdb split to chains
8848
884913 H-bonds
8850H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8851DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 NH2 DdHyd_PSI.opt.pdb split to chains #10/F GLU 1814 OE1 DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 HH21 3.498 2.750
8852DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2 DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 O DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 HE21 2.873 2.126
8853DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1 DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 HZ2 2.829 1.880
8854DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 OE1 DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ2 2.839 1.911
8855DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ1 2.762 1.871
8856DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 N DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 O DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 H3 2.915 1.906
8857DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1 DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH11 2.866 1.886
8858DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2 DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH21 3.207 2.381
8859DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH1 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2 DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH12 2.805 1.855
8860DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD1 DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22 2.984 2.083
8861DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2 DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22 2.835 1.934
8862DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1 DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1 2.862 2.132
8863DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD2 DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1 2.902 1.907
8864</pre><br/>13 hydrogen bonds found<br>
8865<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10/A-E">select #10/A-E</a></div></div>27658 atoms, 28101 bonds, 54 pseudobonds, 1768 residues, 2 models selected<br>
8866<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff restrict #10/F interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff restrict #10/F interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff restrict #10/F interModel false intraMol false intraRes false reveal true log true</a></div></div>Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.pdb split to chains #10/A CYF 575 SG<br>
8867Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.pdb split to chains #10/A CYF 575 SG<br>
8868<br>
8869[Repeated 1 time(s)]<p style="color:darkorange">Skipped 2 atom(s) with bad connectivities; see log for details<br>
8870</p><pre>Finding intramodel H-bonds
8871Constraints relaxed by 0.4 angstroms and 20 degrees
8872Models used:
8873 10 DdHyd_PSI.opt.pdb split to chains
8874
887513 H-bonds
8876H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
8877DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 NH2 DdHyd_PSI.opt.pdb split to chains #10/F GLU 1814 OE1 DdHyd_PSI.opt.pdb split to chains #10/A ARG 27 HH21 3.498 2.750
8878DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 NE2 DdHyd_PSI.opt.pdb split to chains #10/F CYF 1799 O DdHyd_PSI.opt.pdb split to chains #10/C GLN 1491 HE21 2.873 2.126
8879DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 NZ DdHyd_PSI.opt.pdb split to chains #10/F ASN 1843 OD1 DdHyd_PSI.opt.pdb split to chains #10/C LYS 1510 HZ2 2.829 1.880
8880DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F GLN 1804 OE1 DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ2 2.839 1.911
8881DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 NZ DdHyd_PSI.opt.pdb split to chains #10/F PRO 2234 O DdHyd_PSI.opt.pdb split to chains #10/D LYS 1665 HZ1 2.762 1.871
8882DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 N DdHyd_PSI.opt.pdb split to chains #10/F LYS 2032 O DdHyd_PSI.opt.pdb split to chains #10/E PRO 1700 H3 2.915 1.906
8883DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH1 DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH11 2.866 1.886
8884DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 NH2 DdHyd_PSI.opt.pdb split to chains #10/F VAL 1768 O DdHyd_PSI.opt.pdb split to chains #10/E ARG 1706 HH21 3.207 2.381
8885DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH1 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2 DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH12 2.805 1.855
8886DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD1 DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22 2.984 2.083
8887DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 NH2 DdHyd_PSI.opt.pdb split to chains #10/F ASP 1792 OD2 DdHyd_PSI.opt.pdb split to chains #10/E ARG 1742 HH22 2.835 1.934
8888DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD1 DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1 2.862 2.132
8889DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 N DdHyd_PSI.opt.pdb split to chains #10/E ASP 1730 OD2 DdHyd_PSI.opt.pdb split to chains #10/F ILE 1766 H1 2.902 1.907
8890</pre><br/>13 hydrogen bonds found<br>
8891<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10/A-F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10/A-F">select #10/A-F</a></div></div>34831 atoms, 35343 bonds, 182 pseudobonds, 2244 residues, 4 models selected<br>
8892<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #10.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #10.1 models">hide #10.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><span style="color:white; background-color:crimson;">bonds #10:2239-2244@F4@F2</span></div><font color="crimson"><b>Unknown command: bonds #10:2239-2244@F4@F2</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F4@F2</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F4@F2">bond #10:2239-2244@F4@F2</a></div></div>Created 6 bonds<br>
8893<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10:2239-2244</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10:2239-2244">select #10:2239-2244</a></div></div>48 atoms, 6 bonds, 108 pseudobonds, 6 residues, 2 models selected<br>
8894<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 48 atom styles<br>
8895<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html#~bond">~bond</a> #10:2239-2244@F4@F2</div><div class="cxcmd_as_cmd"><a href="cxcmd:~bond #10:2239-2244@F4@F2">~bond #10:2239-2244@F4@F2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html#~bond">~bond</a> #10:2239-2244@F4@S1</div><div class="cxcmd_as_cmd"><a href="cxcmd:~bond #10:2239-2244@F4@S1">~bond #10:2239-2244@F4@S1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F4@S1</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F4@S1">bond #10:2239-2244@F4@S1</a></div></div>Created 6 bonds<br>
8896<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F3@S1</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F3@S1">bond #10:2239-2244@F3@S1</a></div></div>Created 6 bonds<br>
8897<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F3@S2</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F3@S2">bond #10:2239-2244@F3@S2</a></div></div>Created 6 bonds<br>
8898<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F4@S2</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F4@S2">bond #10:2239-2244@F4@S2</a></div></div>Created 6 bonds<br>
8899<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F3@S4</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F3@S4">bond #10:2239-2244@F3@S4</a></div></div>Created 6 bonds<br>
8900<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F2@S4</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F2@S4">bond #10:2239-2244@F2@S4</a></div></div>Created 6 bonds<br>
8901<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F2@S1</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F2@S1">bond #10:2239-2244@F2@S1</a></div></div>Created 6 bonds<br>
8902<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F2@S3</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F2@S3">bond #10:2239-2244@F2@S3</a></div></div>Created 6 bonds<br>
8903<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F4@S3</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F4@S3">bond #10:2239-2244@F4@S3</a></div></div>Created 6 bonds<br>
8904<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F1@S2</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F1@S2">bond #10:2239-2244@F1@S2</a></div></div>Created 6 bonds<br>
8905<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F1@S3</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F1@S3">bond #10:2239-2244@F1@S3</a></div></div>Created 6 bonds<br>
8906<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/bond.html">bond</a> #10:2239-2244@F1@S4</div><div class="cxcmd_as_cmd"><a href="cxcmd:bond #10:2239-2244@F1@S4">bond #10:2239-2244@F1@S4</a></div></div>Created 6 bonds<br>
8907<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10:SF4">select #10:SF4</a></div></div>48 atoms, 72 bonds, 108 pseudobonds, 6 residues, 2 models selected<br>
8908<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 48 atom styles<br>
8909<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10:SF4 &amp;Fe</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10:SF4 &amp;Fe">select #10:SF4 &amp;Fe</a></div></div>24 atoms, 36 pseudobonds, 6 residues, 2 models selected<br>
8910<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 24 atom styles<br>
8911<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10">select #10</a></div></div>34831 atoms, 35415 bonds, 183 pseudobonds, 2244 residues, 5 models selected<br>
8912<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd PSI-BFd AMBER opt.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd PSI-BFd AMBER opt.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd PSI-BFd AMBER opt.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Mon Oct 21 23:18:11 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
8913<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb&quot; models #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb&quot; models #4">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb&quot; models #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html#session">close session</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:close session">close session</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdHyd_PSI.opt.chains.pdb &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdHyd_PSI.opt.chains.pdb &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb&quot;">open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdHyd_PSI.opt.chains.pdb &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
8914 <thead>
8915 <tr>
8916 <th colspan="2">Chain information for DdHyd_PSI.opt.chains.pdb #1</th>
8917 </tr>
8918 <tr>
8919 <th>Chain</th>
8920 <th>Description</th>
8921
8922 </tr>
8923 </thead>
8924 <tbody>
8925 <tr>
8926 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #1/A:1-743">A</a></td>
8927 <td><a title="Show sequence" href="cxcmd:sequence chain #1/A">No description available</a></td>
8928
8929 </tr>
8930 <tr>
8931 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #1/B:744-1476">B</a></td>
8932 <td><a title="Show sequence" href="cxcmd:sequence chain #1/B">No description available</a></td>
8933
8934 </tr>
8935 <tr>
8936 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #1/C:1477-1556">C</a></td>
8937 <td><a title="Show sequence" href="cxcmd:sequence chain #1/C">No description available</a></td>
8938
8939 </tr>
8940 <tr>
8941 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #1/D:1557-1699">D</a></td>
8942 <td><a title="Show sequence" href="cxcmd:sequence chain #1/D">No description available</a></td>
8943
8944 </tr>
8945 <tr>
8946 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #1/E:1700-1765">E</a></td>
8947 <td><a title="Show sequence" href="cxcmd:sequence chain #1/E">No description available</a></td>
8948
8949 </tr>
8950 <tr>
8951 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #1/F:1766-2238">F</a></td>
8952 <td><a title="Show sequence" href="cxcmd:sequence chain #1/F">No description available</a></td>
8953
8954 </tr>
8955 </tbody>
8956</table><br/><table border=1 cellpadding=4 cellspacing=0>
8957 <thead>
8958 <tr>
8959 <th colspan="2">Chain information for PSI_BFD_SF4_opt_chains.pdb #2</th>
8960 </tr>
8961 <tr>
8962 <th>Chain</th>
8963 <th>Description</th>
8964
8965 </tr>
8966 </thead>
8967 <tbody>
8968 <tr>
8969 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/A:1-743">A</a></td>
8970 <td><a title="Show sequence" href="cxcmd:sequence chain #2/A">No description available</a></td>
8971
8972 </tr>
8973 <tr>
8974 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/B:1-733">B</a></td>
8975 <td><a title="Show sequence" href="cxcmd:sequence chain #2/B">No description available</a></td>
8976
8977 </tr>
8978 <tr>
8979 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/C:1-80">C</a></td>
8980 <td><a title="Show sequence" href="cxcmd:sequence chain #2/C">No description available</a></td>
8981
8982 </tr>
8983 <tr>
8984 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/D:1-143">D</a></td>
8985 <td><a title="Show sequence" href="cxcmd:sequence chain #2/D">No description available</a></td>
8986
8987 </tr>
8988 <tr>
8989 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/E:1-66">E</a></td>
8990 <td><a title="Show sequence" href="cxcmd:sequence chain #2/E">No description available</a></td>
8991
8992 </tr>
8993 <tr>
8994 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #2/F:1-61">F</a></td>
8995 <td><a title="Show sequence" href="cxcmd:sequence chain #2/F">No description available</a></td>
8996
8997 </tr>
8998 </tbody>
8999</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select protein">select protein</a></div></div>63258 atoms, 64292 bonds, 4064 residues, 2 models selected<br>
9000<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel bychain</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel bychain">color sel bychain</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#~select">~select</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:~select">~select</a></div></div>Nothing selected<br>
9001<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color byhetero">color byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Tue Oct 22 09:43:01 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
9002<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1 id #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1 id #3">rename #1 id #3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 id #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 id #1">rename #2 id #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 id #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 id #2">rename #3 id #2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb</div><div class="cxcmd_as_cmd"><a href="cxcmd:open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb">open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb</a></div></div><table border=1 cellpadding=4 cellspacing=0>
9003 <thead>
9004 <tr>
9005 <th colspan="2">Chain information for ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb #3</th>
9006 </tr>
9007 <tr>
9008 <th>Chain</th>
9009 <th>Description</th>
9010
9011 </tr>
9012 </thead>
9013 <tbody>
9014 <tr>
9015 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3/A:1-743">A</a></td>
9016 <td><a title="Show sequence" href="cxcmd:sequence chain #3/A">No description available</a></td>
9017
9018 </tr>
9019 <tr>
9020 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3/B:1-733">B</a></td>
9021 <td><a title="Show sequence" href="cxcmd:sequence chain #3/B">No description available</a></td>
9022
9023 </tr>
9024 <tr>
9025 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3/C:1-80">C</a></td>
9026 <td><a title="Show sequence" href="cxcmd:sequence chain #3/C">No description available</a></td>
9027
9028 </tr>
9029 <tr>
9030 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3/D:1-143">D</a></td>
9031 <td><a title="Show sequence" href="cxcmd:sequence chain #3/D">No description available</a></td>
9032
9033 </tr>
9034 <tr>
9035 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3/E:1-66">E</a></td>
9036 <td><a title="Show sequence" href="cxcmd:sequence chain #3/E">No description available</a></td>
9037
9038 </tr>
9039 <tr>
9040 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3/F:1-188">F</a></td>
9041 <td><a title="Show sequence" href="cxcmd:sequence chain #3/F">No description available</a></td>
9042
9043 </tr>
9044 <tr>
9045 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3/G:1-709">G</a></td>
9046 <td><a title="Show sequence" href="cxcmd:sequence chain #3/G">No description available</a></td>
9047
9048 </tr>
9049 </tbody>
9050</table><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3 &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3 &amp;protein">select #3 &amp;protein</a></div></div>34578 atoms, 35179 bonds, 2662 residues, 1 model selected<br>
9051<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/Y:1183-1187,1200</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/Y:1183-1187,1200">select #3/Y:1183-1187,1200</a></div></div>41 atoms, 12 bonds, 72 pseudobonds, 6 residues, 2 models selected<br>
9052<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 41 atom styles<br>
9053<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/Z:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/Z:SF4">select #3/Z:SF4</a></div></div>24 atoms, 54 pseudobonds, 3 residues, 2 models selected<br>
9054<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3 </div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3 ">select #3 </a></div></div>34737 atoms, 35295 bonds, 130 pseudobonds, 2673 residues, 2 models selected<br>
9055<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel bychain</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel bychain">color sel bychain</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #13/Y:1188-1189</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #13/Y:1188-1189">select #13/Y:1188-1189</a></div></div>Nothing selected<br>
9056<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/Y:1188-1189</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/Y:1188-1189">select #3/Y:1188-1189</a></div></div>94 atoms, 104 bonds, 2 residues, 1 model selected<br>
9057<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel magenta</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel magenta">color sel magenta</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Tue Oct 22 11:39:31 2024 &mdash;&mdash;&mdash;</p></details>opened ChimeraX session<br>
9058<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #3">select add #3</a></div></div>34737 atoms, 35295 bonds, 130 pseudobonds, 2673 residues, 2 models selected<br>
9059<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #3">select subtract #3</a></div></div>Nothing selected<br>
9060<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd PSI-FdhF.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Tue Oct 22 11:40:52 2024 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
9061<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 2fdn</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 2fdn">open 2fdn</a></div></div><i>2fdn</i> title:<br><b>2[4FE-4S] ferredoxin from clostridium acidi-urici</b> <a href="cxcmd:log metadata #4">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
9062 <thead>
9063 <tr>
9064 <th colspan="3">Chain information for 2fdn #4</th>
9065 </tr>
9066 <tr>
9067 <th>Chain</th>
9068 <th>Description</th>
9069 <th>UniProt</th>
9070 </tr>
9071 </thead>
9072 <tbody>
9073 <tr>
9074 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4/A:1-55">A</a></td>
9075 <td><a title="Show sequence" href="cxcmd:sequence chain #4/A">FERREDOXIN</a></td>
9076 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P00198 from uniprot associate #4/A">FER_CLOAC</a> <a title="Select sequence" href="cxcmd:select #4/A:1-55">1-55</a></td>
9077 </tr>
9078 </tbody>
9079</table><br/><table border=1 cellpadding=4 cellspacing=0>
9080 <thead>
9081 <tr>
9082 <th>Non-standard residues in 2fdn #4</th>
9083 </tr>
9084 </thead>
9085 <tbody>
9086 <tr>
9087 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
9088 </tr>
9089 </tbody>
9090</table><br/>74 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!4 to #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!4 to #1">matchmaker #!4 to #1</a></div></div>
9091 <table border=1 cellpadding=4 cellspacing=0>
9092 <tr>
9093 <th colspan="2">Parameters</th>
9094 </tr>
9095 <tr>
9096 <td>Chain pairing</td>
9097 <td>bb</td>
9098 </tr>
9099 <tr>
9100 <td>Alignment algorithm</td>
9101 <td>Needleman-Wunsch</td>
9102 </tr>
9103 <tr>
9104 <td>Similarity matrix</td>
9105 <td>BLOSUM-62</td>
9106 </tr>
9107
9108 <tr>
9109 <td>SS fraction</td>
9110 <td>0.3</td>
9111 </tr>
9112 <tr>
9113 <td>Gap open (HH/SS/other)</td>
9114 <td>18/18/6</td>
9115 </tr>
9116 <tr>
9117 <td>Gap extend</td>
9118 <td>1</td>
9119 </tr>
9120 <tr>
9121 <td>SS matrix</td>
9122 <td>
9123 <table>
9124 <tr>
9125 <th></th> <th>H</th> <th>S</th> <th>O</th>
9126 </tr>
9127 <tr>
9128 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
9129 </tr>
9130 <tr>
9131 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
9132 </tr>
9133 <tr>
9134 <th>O</th> <td></td> <td></td> <td align="right">4</td>
9135 </tr>
9136 </table>
9137 </td>
9138 </tr>
9139
9140 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
9141 </table>
9142 <br/>Matchmaker PSI_BFD_SF4_opt_chains.pdb, chain F (#1) with 2fdn, chain A (#4), sequence alignment score = 115.9<br>
9143RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs: 3.340)<br>
9144<br>
9145<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/A-E">select #1/A-E</a></div></div>27634 atoms, 28101 bonds, 1765 residues, 1 model selected<br>
9146<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X">select #1/X</a></div></div>40 atoms, 90 pseudobonds, 5 residues, 2 models selected<br>
9147<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/undo.html">undo</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:undo">undo</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X:1829-1831</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X:1829-1831">select #1/X:1829-1831</a></div></div>24 atoms, 54 pseudobonds, 3 residues, 2 models selected<br>
9148<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X:1827-1828</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X:1827-1828">select #1/X:1827-1828</a></div></div>16 atoms, 36 pseudobonds, 2 residues, 2 models selected<br>
9149<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 16 atom styles<br>
9150<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:Cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:Cys">select #1/F:Cys</a></div></div>Nothing selected<br>
9151<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:Cyf</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:Cyf">select #1/F:Cyf</a></div></div>80 atoms, 72 bonds, 8 residues, 1 model selected<br>
9152<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 80 atom styles<br>
9153<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select H">select H</a></div></div>45159 atoms, 5877 residues, 4 models selected<br>
9154<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!1 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!1 atoms">hide sel &amp; #!1 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X:1827-1828</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X:1827-1828">select #1/X:1827-1828</a></div></div>16 atoms, 36 pseudobonds, 2 residues, 2 models selected<br>
9155<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 16 atom styles<br>
9156<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4:61-62</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4:61-62">select #4:61-62</a></div></div>16 atoms, 24 bonds, 2 residues, 1 model selected<br>
9157<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 16 atom styles<br>
9158<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #4.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #4.1 models">hide #4.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!4 to #1 showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!4 to #1 showAlignment true">matchmaker #!4 to #1 showAlignment true</a></div></div>
9159 <table border=1 cellpadding=4 cellspacing=0>
9160 <tr>
9161 <th colspan="2">Parameters</th>
9162 </tr>
9163 <tr>
9164 <td>Chain pairing</td>
9165 <td>bb</td>
9166 </tr>
9167 <tr>
9168 <td>Alignment algorithm</td>
9169 <td>Needleman-Wunsch</td>
9170 </tr>
9171 <tr>
9172 <td>Similarity matrix</td>
9173 <td>BLOSUM-62</td>
9174 </tr>
9175
9176 <tr>
9177 <td>SS fraction</td>
9178 <td>0.3</td>
9179 </tr>
9180 <tr>
9181 <td>Gap open (HH/SS/other)</td>
9182 <td>18/18/6</td>
9183 </tr>
9184 <tr>
9185 <td>Gap extend</td>
9186 <td>1</td>
9187 </tr>
9188 <tr>
9189 <td>SS matrix</td>
9190 <td>
9191 <table>
9192 <tr>
9193 <th></th> <th>H</th> <th>S</th> <th>O</th>
9194 </tr>
9195 <tr>
9196 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
9197 </tr>
9198 <tr>
9199 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
9200 </tr>
9201 <tr>
9202 <th>O</th> <td></td> <td></td> <td align="right">4</td>
9203 </tr>
9204 </table>
9205 </td>
9206 </tr>
9207
9208 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
9209 </table>
9210 <br/>Matchmaker PSI_BFD_SF4_opt_chains.pdb, chain F (#1) with 2fdn, chain A (#4), sequence alignment score = 115.9<br>
9211Alignment identifier is 1<br>
9212Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
9213Hiding conservation header for alignment 1<br>
9214Chains used in RMSD evaluation for alignment 1: PSI_BFD_SF4_opt_chains.pdb #1/F, 2fdn #4/A<br>
9215Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
9216RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs: 3.340)<br>
9217<br>
9218<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:3">select #1/F:3</a></div></div>14 atoms, 14 bonds, 1 residue, 1 model selected<br>
9219<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:3-8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:3-8">select #1/F:3-8</a></div></div>96 atoms, 96 bonds, 6 residues, 1 model selected<br>
9220<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:3">select #1/F:3</a></div></div>14 atoms, 14 bonds, 1 residue, 1 model selected<br>
9221<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:3-8 #4/A:3-8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:3-8 #4/A:3-8">select #1/F:3-8 #4/A:3-8</a></div></div>168 atoms, 167 bonds, 12 residues, 2 models selected<br>
9222MatchMaker Alignment [ID: 1] region chain F..chain A [3-8] RMSD: 6.436<br>
9223<br>
9224<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:9">select #1/F:9</a></div></div>15 atoms, 14 bonds, 1 residue, 1 model selected<br>
9225<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:9">select #1/F:9</a></div></div>15 atoms, 14 bonds, 1 residue, 1 model selected<br>
9226<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:25</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:25">select #4/A:25</a></div></div>6 atoms, 5 bonds, 1 residue, 1 model selected<br>
9227<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:27-34 #4/A:25-29</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:27-34 #4/A:25-29">select #1/F:27-34 #4/A:25-29</a></div></div>160 atoms, 159 bonds, 13 residues, 2 models selected<br>
9228MatchMaker Alignment [ID: 1] region chain F..chain A [27-34] RMSD: 4.473<br>
9229<br>
9230<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:48</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:48">select #4/A:48</a></div></div>14 atoms, 14 bonds, 1 residue, 1 model selected<br>
9231<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:53-61 #4/A:48-55</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:53-61 #4/A:48-55">select #1/F:53-61 #4/A:48-55</a></div></div>240 atoms, 242 bonds, 17 residues, 2 models selected<br>
9232MatchMaker Alignment [ID: 1] region chain F..chain A [53-62] RMSD: 5.761<br>
9233<br>
9234<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel &amp; #!4 byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel &amp; #!4 byhetero">color sel &amp; #!4 byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #!4 byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color #!4 byhetero">color #!4 byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:3">select #1/F:3</a></div></div>14 atoms, 14 bonds, 1 residue, 1 model selected<br>
9235<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:3-9 #4/A:3-8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:3-9 #4/A:3-8">select #1/F:3-9 #4/A:3-8</a></div></div>183 atoms, 182 bonds, 13 residues, 2 models selected<br>
9236MatchMaker Alignment [ID: 1] region chain F..chain A [3-9] RMSD: 6.436<br>
9237<br>
9238<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel &amp; #!4 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel &amp; #!4 atoms">show sel &amp; #!4 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel &amp; #!4 stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel &amp; #!4 stick">style sel &amp; #!4 stick</a></div></div>Changed 72 atom styles<br>
9239<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-2,8-24,30-47</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-2,8-24,30-47">select #4/A:1-2,8-24,30-47</a></div></div>447 atoms, 448 bonds, 37 residues, 1 model selected<br>
9240<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-55 &amp;~:1-2,8-24,30-47</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-55 &amp;~:1-2,8-24,30-47">select #4/A:1-55 &amp;~:1-2,8-24,30-47</a></div></div>205 atoms, 204 bonds, 18 residues, 1 model selected<br>
9241<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select H">select H</a></div></div>45159 atoms, 5877 residues, 4 models selected<br>
9242<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!4 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!4 atoms">hide sel &amp; #!4 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-55 &amp;~:1-2,8-24,30-47</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-55 &amp;~:1-2,8-24,30-47">select #4/A:1-55 &amp;~:1-2,8-24,30-47</a></div></div>205 atoms, 204 bonds, 18 residues, 1 model selected<br>
9243<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:3">select #1/F:3</a></div></div>14 atoms, 14 bonds, 1 residue, 1 model selected<br>
9244<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:3-9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:3-9">select #1/F:3-9</a></div></div>111 atoms, 111 bonds, 7 residues, 1 model selected<br>
9245<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-55 &amp;~:1-2,8-24,30-47#1/F:3-9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-55 &amp;~:1-2,8-24,30-47#1/F:3-9">select #4/A:1-55 &amp;~:1-2,8-24,30-47#1/F:3-9</a></div></div>205 atoms, 204 bonds, 18 residues, 1 model selected<br>
9246<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-55 &amp;~:1-2,8-24,30-47 |#1/F:3-9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-55 &amp;~:1-2,8-24,30-47 |#1/F:3-9">select #4/A:1-55 &amp;~:1-2,8-24,30-47 |#1/F:3-9</a></div></div>205 atoms, 209 bonds, 18 residues, 1 model selected<br>
9247<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:3-9,27-34,53-61</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:3-9,27-34,53-61">select #1/F:3-9,27-34,53-61</a></div></div>368 atoms, 369 bonds, 24 residues, 1 model selected<br>
9248<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 368 atom styles<br>
9249<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select H">select H</a></div></div>45159 atoms, 5877 residues, 4 models selected<br>
9250<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!1,4 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!1,4 atoms">hide sel &amp; #!1,4 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 5877 items<br>
9251<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> @N,O</div><div class="cxcmd_as_cmd"><a href="cxcmd:select @N,O">select @N,O</a></div></div>13656 atoms, 6875 residues, 4 models selected<br>
9252<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!1,4 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!1,4 atoms">hide sel &amp; #!1,4 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:1-2,8-24,30-47</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:1-2,8-24,30-47">select #4/A:1-2,8-24,30-47</a></div></div>447 atoms, 448 bonds, 37 residues, 1 model selected<br>
9253<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light slate gray</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light slate gray">color sel light slate gray</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel steel blue">color sel steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel olive drab</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel olive drab">color sel olive drab</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel steel blue">color sel steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs&quot;">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sat Sep 13 22:23:04 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
9254<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/A-E</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/A-E">select #1/A-E</a></div></div>27634 atoms, 28101 bonds, 1765 residues, 1 model selected<br>
9255<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel cartoons">show sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X:1827-1828</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X:1827-1828">select #1/X:1827-1828</a></div></div>16 atoms, 36 pseudobonds, 2 residues, 2 models selected<br>
9256<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X">select #1/X</a></div></div>40 atoms, 90 pseudobonds, 5 residues, 2 models selected<br>
9257<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F">select #1/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
9258<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true">hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true</a></div></div>Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG<br>
9259Wrong number of grandchild atoms for phi/psi acceptor PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG<br>
9260<br>
9261[Repeated 1 time(s)]<p style="color:#ffb961">Skipped 2 atom(s) with bad connectivities; see log for details<br>
9262</p><pre>Finding intramodel H-bonds
9263Constraints relaxed by 0.4 angstroms and 20 degrees
9264Models used:
9265 1 PSI_BFD_SF4_opt_chains.pdb
9266
926719 H-bonds
9268H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9269PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1 PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11 2.760 1.842
9270PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1 PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21 2.719 1.800
9271PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1 3.148 2.456
9272PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2 PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2 2.746 1.778
9273PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11 2.812 1.825
9274PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11 3.358 2.560
9275PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22 2.780 1.765
9276PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1 2.917 2.045
9277PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1 PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2 2.737 1.813
9278PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1 PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE 2.875 1.950
9279PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12 2.980 2.103
9280PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22 2.848 1.943
9281PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1 PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21 2.738 1.784
9282PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2 PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1 2.666 1.685
9283PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2 PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22 3.598 2.755
9284PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE 2.902 1.898
9285PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1 PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12 2.894 1.970
9286PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2 PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21 3.324 2.539
9287PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2 PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22 2.784 1.818
9288</pre><br/>19 hydrogen bonds found<br>
9289<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 31 atom styles<br>
9290<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff showDist true interModel false intraMol false intraRes false select true reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true reveal true log true">hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true reveal true log true</a></div></div>Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG<br>
9291Wrong number of grandchild atoms for phi/psi acceptor PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG<br>
9292<br>
9293[Repeated 1 time(s)]<p style="color:#ffb961">Skipped 2 atom(s) with bad connectivities; see log for details<br>
9294</p><pre>Finding intramodel H-bonds
9295Constraints relaxed by 0.4 angstroms and 20 degrees
9296Models used:
9297 1 PSI_BFD_SF4_opt_chains.pdb
9298
929919 H-bonds
9300H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9301PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1 PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11 2.760 1.842
9302PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1 PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21 2.719 1.800
9303PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1 3.148 2.456
9304PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2 PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2 2.746 1.778
9305PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11 2.812 1.825
9306PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11 3.358 2.560
9307PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22 2.780 1.765
9308PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1 2.917 2.045
9309PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1 PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2 2.737 1.813
9310PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1 PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE 2.875 1.950
9311PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12 2.980 2.103
9312PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22 2.848 1.943
9313PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1 PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21 2.738 1.784
9314PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2 PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1 2.666 1.685
9315PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2 PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22 3.598 2.755
9316PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE 2.902 1.898
9317PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1 PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12 2.894 1.970
9318PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2 PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21 3.324 2.539
9319PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2 PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22 2.784 1.818
9320</pre><br/>19 hydrogen bonds found<br>
9321<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F">select #1/F</a></div></div>841 atoms, 848 bonds, 61 residues, 1 model selected<br>
9322<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff showDist true interModel false intraMol false intraRes false select true reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true reveal true log true">hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true reveal true log true</a></div></div>Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG<br>
9323Wrong number of grandchild atoms for phi/psi acceptor PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG<br>
9324<br>
9325[Repeated 1 time(s)]<p style="color:#ffb961">Skipped 2 atom(s) with bad connectivities; see log for details<br>
9326</p><pre>Finding intramodel H-bonds
9327Constraints relaxed by 0.4 angstroms and 20 degrees
9328Models used:
9329 1 PSI_BFD_SF4_opt_chains.pdb
9330
933119 H-bonds
9332H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9333PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1 PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11 2.760 1.842
9334PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1 PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21 2.719 1.800
9335PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1 3.148 2.456
9336PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2 PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2 2.746 1.778
9337PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11 2.812 1.825
9338PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11 3.358 2.560
9339PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22 2.780 1.765
9340PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1 2.917 2.045
9341PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1 PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2 2.737 1.813
9342PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1 PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE 2.875 1.950
9343PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12 2.980 2.103
9344PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22 2.848 1.943
9345PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1 PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21 2.738 1.784
9346PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2 PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1 2.666 1.685
9347PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2 PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22 3.598 2.755
9348PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE 2.902 1.898
9349PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1 PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12 2.894 1.970
9350PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2 PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21 3.324 2.539
9351PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2 PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22 2.784 1.818
9352</pre><br/>19 hydrogen bonds found<br>
9353<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff showDist true interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false reveal true log true</a></div></div>Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG<br>
9354Wrong number of grandchild atoms for phi/psi acceptor PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG<br>
9355<br>
9356[Repeated 1 time(s)]<p style="color:#ffb961">Skipped 2 atom(s) with bad connectivities; see log for details<br>
9357</p><pre>Finding intramodel H-bonds
9358Constraints relaxed by 0.4 angstroms and 20 degrees
9359Models used:
9360 1 PSI_BFD_SF4_opt_chains.pdb
9361
936219 H-bonds
9363H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9364PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1 PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH11 2.760 1.842
9365PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD1 PSI_BFD_SF4_opt_chains.pdb #1/A ARG 27 HH21 2.719 1.800
9366PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 O PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ1 3.148 2.456
9367PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 NZ PSI_BFD_SF4_opt_chains.pdb #1/F ASP 30 OD2 PSI_BFD_SF4_opt_chains.pdb #1/A LYS 31 HZ2 2.746 1.778
9368PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE1 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11 2.812 1.825
9369PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH11 3.358 2.560
9370PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 17 OE2 PSI_BFD_SF4_opt_chains.pdb #1/C ARG 18 HH22 2.780 1.765
9371PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ PSI_BFD_SF4_opt_chains.pdb #1/F PRO 18 O PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ1 2.917 2.045
9372PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 NZ PSI_BFD_SF4_opt_chains.pdb #1/F GLU 19 OE1 PSI_BFD_SF4_opt_chains.pdb #1/D LYS 109 HZ2 2.737 1.813
9373PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NE PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1 PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HE 2.875 1.950
9374PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH1 PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH12 2.980 2.103
9375PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F ALA 7 O PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH22 2.848 1.943
9376PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 NH2 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE1 PSI_BFD_SF4_opt_chains.pdb #1/E ARG 43 HH21 2.738 1.784
9377PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F GLU 9 OE2 PSI_BFD_SF4_opt_chains.pdb #1/E THR 54 HG1 2.666 1.685
9378PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 ND2 PSI_BFD_SF4_opt_chains.pdb #1/F PRO 53 O PSI_BFD_SF4_opt_chains.pdb #1/E ASN 56 HD22 3.598 2.755
9379PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NE PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HE 2.902 1.898
9380PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH1 PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH12 2.894 1.970
9381PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2 PSI_BFD_SF4_opt_chains.pdb #1/A THR 28 OG1 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH21 3.324 2.539
9382PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 NH2 PSI_BFD_SF4_opt_chains.pdb #1/A ASP 34 OD2 PSI_BFD_SF4_opt_chains.pdb #1/F ARG 32 HH22 2.784 1.818
9383</pre><br/>19 hydrogen bonds found<br>
9384<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/A:27,28,31,34/C:18/D:109/E:43,54,56</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/A:27,28,31,34/C:18/D:109/E:43,54,56">select #1/A:27,28,31,34/C:18/D:109/E:43,54,56</a></div></div>170 atoms, 162 bonds, 9 residues, 1 model selected<br>
9385<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &amp;~H">select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &amp;~H</a></div></div>81 atoms, 73 bonds, 9 residues, 1 model selected<br>
9386<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 81 atom styles<br>
9387<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.2.1 models">hide #1.2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X:1829-1831</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X:1829-1831">select #1/X:1829-1831</a></div></div>24 atoms, 54 pseudobonds, 3 residues, 2 models selected<br>
9388<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 24 atom styles<br>
9389<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 24 atom styles<br>
9390<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X:1829-1831 &amp;S</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X:1829-1831 &amp;S">select #1/X:1829-1831 &amp;S</a></div></div>12 atoms, 3 residues, 1 model selected<br>
9391<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel gold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel gold">color sel gold</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel goldenrod</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel goldenrod">color sel goldenrod</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel gold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel gold">color sel gold</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel green yellow</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel green yellow">color sel green yellow</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel yellow green</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel yellow green">color sel yellow green</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel green yellow</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel green yellow">color sel green yellow</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel pale goldenrod</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel pale goldenrod">color sel pale goldenrod</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel wheat</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel wheat">color sel wheat</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel beige</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel beige">color sel beige</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light goldenrod yellow</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light goldenrod yellow">color sel light goldenrod yellow</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Graphics/Designs/BFD design on PSI H-bonds.png&quot; width 1800 height 1355 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Graphics/Designs/BFD design on PSI H-bonds.png&quot; width 1800 height 1355 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Graphics/Designs/BFD design on PSI H-bonds.png&quot; width 1800 height 1355 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs&quot;">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> zoom1</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name zoom1">view name zoom1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/A &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/A &amp;protein">select #1/A &amp;protein</a></div></div>11579 atoms, 11778 bonds, 743 residues, 1 model selected<br>
9392<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel thistle target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel thistle target c">color sel thistle target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lavender target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lavender target c">color sel lavender target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light pink target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light pink target c">color sel light pink target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel thistle target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel thistle target c">color sel thistle target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel plum target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel plum target c">color sel plum target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/B &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/B &amp;protein">select #1/B &amp;protein</a></div></div>11513 atoms, 11725 bonds, 733 residues, 1 model selected<br>
9393<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light pink target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light pink target c">color sel light pink target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/C &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/C &amp;protein">select #1/C &amp;protein</a></div></div>1206 atoms, 1219 bonds, 80 residues, 1 model selected<br>
9394<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel pale green target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel pale green target c">color sel pale green target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel dark sea green target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel dark sea green target c">color sel dark sea green target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/C &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/C &amp;protein">select #1/C &amp;protein</a></div></div>1206 atoms, 1219 bonds, 80 residues, 1 model selected<br>
9395<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel dark gray target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel dark gray target c">color sel dark gray target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel gray target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel gray target c">color sel gray target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel teal target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel teal target c">color sel teal target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel green target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel green target c">color sel green target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel maroon target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel maroon target c">color sel maroon target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel dark salmon target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel dark salmon target c">color sel dark salmon target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel dark goldenrod target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel dark goldenrod target c">color sel dark goldenrod target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel brown target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel brown target c">color sel brown target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/D &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/D &amp;protein">select #1/D &amp;protein</a></div></div>2277 atoms, 2308 bonds, 143 residues, 1 model selected<br>
9396<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel dark khaki target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel dark khaki target c">color sel dark khaki target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel wheat target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel wheat target c">color sel wheat target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel peach puff target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel peach puff target c">color sel peach puff target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel pale goldenrod target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel pale goldenrod target c">color sel pale goldenrod target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light salmon target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light salmon target c">color sel light salmon target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel burly wood target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel burly wood target c">color sel burly wood target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/E &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/E &amp;protein">select #1/E &amp;protein</a></div></div>1059 atoms, 1071 bonds, 66 residues, 1 model selected<br>
9397<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> zoom1</div><div class="cxcmd_as_cmd"><a href="cxcmd:view zoom1">view zoom1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> zoom2</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name zoom2">view name zoom2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/E &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/E &amp;protein">select #1/E &amp;protein</a></div></div>1059 atoms, 1071 bonds, 66 residues, 1 model selected<br>
9398<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel sandy brown target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel sandy brown target c">color sel sandy brown target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel peach puff target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel peach puff target c">color sel peach puff target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light salmon target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light salmon target c">color sel light salmon target c</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel sandy brown target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel sandy brown target c">color sel sandy brown target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light salmon target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light salmon target c">color sel light salmon target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> zoom2</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name zoom2">view name zoom2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:17-18</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:17-18">select #1/F:17-18</a></div></div>29 atoms, 29 bonds, 2 residues, 1 model selected<br>
9399<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:17-18 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:17-18 &amp;~H">select #1/F:17-18 &amp;~H</a></div></div>16 atoms, 16 bonds, 2 residues, 1 model selected<br>
9400<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 16 atom styles<br>
9401<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:17-19 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:17-19 &amp;~H">select #1/F:17-19 &amp;~H</a></div></div>25 atoms, 25 bonds, 3 residues, 1 model selected<br>
9402<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 25 atom styles<br>
9403<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/C</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/C">select #1/C</a></div></div>1206 atoms, 1219 bonds, 80 residues, 1 model selected<br>
9404<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/C &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/C &amp;protein">select #1/C &amp;protein</a></div></div>1206 atoms, 1219 bonds, 80 residues, 1 model selected<br>
9405<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel brown target ac</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel brown target ac">color sel brown target ac</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel orange red target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel orange red target c">color sel orange red target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel dark orange target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel dark orange target c">color sel dark orange target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel coral target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel coral target c">color sel coral target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel chocolate target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel chocolate target c">color sel chocolate target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &amp;~H">select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &amp;~H</a></div></div>81 atoms, 73 bonds, 9 residues, 1 model selected<br>
9406<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel steel blue target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel steel blue target c">color sel steel blue target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel steel blue target ac</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel steel blue target ac">color sel steel blue target ac</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel medium orchid target ac</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel medium orchid target ac">color sel medium orchid target ac</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel medium purple target ac</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel medium purple target ac">color sel medium purple target ac</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> Hbonding sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen Hbonding sel">name frozen Hbonding sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel medium violet red target ac</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel medium violet red target ac">color sel medium violet red target ac</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel deep pink target ac</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel deep pink target ac">color sel deep pink target ac</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/E &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/E &amp;protein">select #1/E &amp;protein</a></div></div>1059 atoms, 1071 bonds, 66 residues, 1 model selected<br>
9407<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel bisque target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel bisque target c">color sel bisque target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel pink target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel pink target c">color sel pink target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel peach puff target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel peach puff target c">color sel peach puff target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/C &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/C &amp;protein">select #1/C &amp;protein</a></div></div>1206 atoms, 1219 bonds, 80 residues, 1 model selected<br>
9408<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel wheat target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel wheat target c">color sel wheat target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel burly wood target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel burly wood target c">color sel burly wood target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel tan target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel tan target c">color sel tan target c</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/D &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/D &amp;protein">select #1/D &amp;protein</a></div></div>2277 atoms, 2308 bonds, 143 residues, 1 model selected<br>
9409<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel burly wood target c</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel burly wood target c">color sel burly wood target c</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F:9,17-19 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F:9,17-19 &amp;~H">select #1/F:9,17-19 &amp;~H</a></div></div>34 atoms, 33 bonds, 4 residues, 1 model selected<br>
9410<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> zoom2</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name zoom2">view name zoom2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs&quot;">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Sun Sep 14 07:49:27 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
9411<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/A:393</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/A:393">select #1/A:393</a></div></div>16 atoms, 15 bonds, 1 residue, 1 model selected<br>
9412<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A">select #2/A</a></div></div>11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected<br>
9413<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><a href="help:user/commands/color.html">color</a> #2/A <span style="background-color:crimson;">DDA0DD target c </span></div><font color="crimson"><b>Expected a color or one of &#x27;byatom&#x27;, &#x27;bychain&#x27;, &#x27;byelement&#x27;, &#x27;byhetero&#x27;, &#x27;byidentity&#x27;, &#x27;bymodel&#x27;, &#x27;bynucleotide&#x27;, &#x27;bypolymer&#x27;, &#x27;fromatoms&#x27;, &#x27;fromcartoons&#x27;, &#x27;fromribbons&#x27;, or &#x27;random&#x27; or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/A #DDA0DD target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/A #DDA0DD target c ">color #2/A #DDA0DD target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/B:393</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/B:393">select #1/B:393</a></div></div>20 atoms, 20 bonds, 1 residue, 1 model selected<br>
9414<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/B #FFB6C1 target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/B #FFB6C1 target c ">color #2/B #FFB6C1 target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/C:40</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/C:40">select #1/C:40</a></div></div>11 atoms, 10 bonds, 1 residue, 1 model selected<br>
9415<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/C #D2B48C target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/C #D2B48C target c ">color #2/C #D2B48C target c </a></div></div><div class="cxcmd"><a href="help:user/commands/view.html">view</a> <span style="background-color:crimson;">session_start</span></div><font color="crimson"><b>Expected an objects specifier or a view name or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#list">view list</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view list">view list</a></div></div>Named views: <a href="cxcmd:view session-start">session-start</a>, <a href="cxcmd:view zoom1">zoom1</a>, <a href="cxcmd:view zoom2">zoom2</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view session-start">view session-start</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/D:40</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/D:40">select #1/D:40</a></div></div>14 atoms, 14 bonds, 1 residue, 1 model selected<br>
9416<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/D:40</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/D:40">select #2/D:40</a></div></div>Nothing selected<br>
9417<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#list">view list</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view list">view list</a></div></div>Named views: <a href="cxcmd:view session-start">session-start</a>, <a href="cxcmd:view zoom1">zoom1</a>, <a href="cxcmd:view zoom2">zoom2</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view session-start">view session-start</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/D:40</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/D:40">select #1/D:40</a></div></div>14 atoms, 14 bonds, 1 residue, 1 model selected<br>
9418<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/D #DEB887 target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/D #DEB887 target c ">color #2/D #DEB887 target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/E:40</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/E:40">select #1/E:40</a></div></div>16 atoms, 15 bonds, 1 residue, 1 model selected<br>
9419<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/D #FFDAB9 target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/D #FFDAB9 target c ">color #2/D #FFDAB9 target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/D #DEB887 target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/D #DEB887 target c ">color #2/D #DEB887 target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/E #FFDAB9 target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/E #FFDAB9 target c ">color #2/E #FFDAB9 target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X:1829@S1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X:1829@S1">select #1/X:1829@S1</a></div></div>1 atom, 1 residue, 1 model selected<br>
9420<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:2239-2241</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:2239-2241">select #2:2239-2241</a></div></div>24 atoms, 54 pseudobonds, 3 residues, 2 models selected<br>
9421<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:2239-2241 &amp;S</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:2239-2241 &amp;S">select #2:2239-2241 &amp;S</a></div></div>12 atoms, 3 residues, 1 model selected<br>
9422<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/X:1829@S1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/X:1829@S1">select #1/X:1829@S1</a></div></div>1 atom, 1 residue, 1 model selected<br>
9423<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:2239-2241 &amp;S</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:2239-2241 &amp;S">select #2:2239-2241 &amp;S</a></div></div>12 atoms, 3 residues, 1 model selected<br>
9424<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2:2239-2241 &amp;S #FAFAD2</div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2:2239-2241 &amp;S #FAFAD2">color #2:2239-2241 &amp;S #FAFAD2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view session-start">view session-start</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> viewH2ase</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name viewH2ase">view name viewH2ase</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 1hfe</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 1hfe">open 1hfe</a></div></div><i>1hfe</i> title:<br><b>1.6 A resolution structure of the Fe-ONLY hydrogenase from desulfovibrio desulfuricans</b> <a href="cxcmd:log metadata #5">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
9425 <thead>
9426 <tr>
9427 <th colspan="3">Chain information for 1hfe #5</th>
9428 </tr>
9429 <tr>
9430 <th>Chain</th>
9431 <th>Description</th>
9432 <th>UniProt</th>
9433 </tr>
9434 </thead>
9435 <tbody>
9436 <tr>
9437 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/L:2-398">L</a> <a title="Select chain" href="cxcmd:select #5/M:2-398">M</a></td>
9438 <td><a title="Show sequence" href="cxcmd:sequence chain #5/L#5/M">PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))</a></td>
9439 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07598 from uniprot associate #5/L,M">PHFL_DESVH</a> <a title="Select sequence" href="cxcmd:select #5/L,M:1-421">1-421</a></td>
9440 </tr>
9441 <tr>
9442 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/S:36-123">S</a> <a title="Select chain" href="cxcmd:select #5/T:36-123">T</a></td>
9443 <td><a title="Show sequence" href="cxcmd:sequence chain #5/S#5/T">PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))</a></td>
9444 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07603 from uniprot associate #5/S,T">PHFS_DESVH</a> <a title="Select sequence" href="cxcmd:select #5/S,T:1-123">1-123</a></td>
9445 </tr>
9446 </tbody>
9447</table><br/><table border=1 cellpadding=4 cellspacing=0>
9448 <thead>
9449 <tr>
9450 <th>Non-standard residues in 1hfe #5</th>
9451 </tr>
9452 </thead>
9453 <tbody>
9454 <tr>
9455 <td><a title="select residue" href="cxcmd:sel :CMO">CMO</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CMO">carbon monoxide</a></td>
9456 </tr>
9457 <tr>
9458 <td><a title="select residue" href="cxcmd:sel :CYN">CYN</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CYN">cyanide ion</a></td>
9459 </tr>
9460 <tr>
9461 <td><a title="select residue" href="cxcmd:sel :CYS">CYS</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CYS">cysteine</a></td>
9462 </tr>
9463 <tr>
9464 <td><a title="select residue" href="cxcmd:sel :FE2">FE2</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/FE2">Fe (II) ion</a></td>
9465 </tr>
9466 <tr>
9467 <td><a title="select residue" href="cxcmd:sel :PDT">PDT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PDT">1,3-propanedithiol</a></td>
9468 </tr>
9469 <tr>
9470 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
9471 </tr>
9472 <tr>
9473 <td><a title="select residue" href="cxcmd:sel :ZN">ZN</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/ZN">zinc ion</a></td>
9474 </tr>
9475 </tbody>
9476</table><br/><table border=1 cellpadding=4 cellspacing=0>
9477<tr><th colspan=3>1hfe mmCIF Assemblies
9478<tr><td><a title="Generate assembly" href="cxcmd:sym #5 assembly 1 ; view">1</a><td>author_and_software_defined_assembly
9479<tr><td><a title="Generate assembly" href="cxcmd:sym #5 assembly 2 ; view">2</a><td>author_and_software_defined_assembly
9480<tr><td><a title="Generate assembly" href="cxcmd:sym #5 assembly 3 ; view">3</a><td>software_defined_assembly
9481</table><br/>351 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!5 to #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!5 to #2">matchmaker #!5 to #2</a></div></div>
9482 <table border=1 cellpadding=4 cellspacing=0>
9483 <tr>
9484 <th colspan="2">Parameters</th>
9485 </tr>
9486 <tr>
9487 <td>Chain pairing</td>
9488 <td>bb</td>
9489 </tr>
9490 <tr>
9491 <td>Alignment algorithm</td>
9492 <td>Needleman-Wunsch</td>
9493 </tr>
9494 <tr>
9495 <td>Similarity matrix</td>
9496 <td>BLOSUM-62</td>
9497 </tr>
9498
9499 <tr>
9500 <td>SS fraction</td>
9501 <td>0.3</td>
9502 </tr>
9503 <tr>
9504 <td>Gap open (HH/SS/other)</td>
9505 <td>18/18/6</td>
9506 </tr>
9507 <tr>
9508 <td>Gap extend</td>
9509 <td>1</td>
9510 </tr>
9511 <tr>
9512 <td>SS matrix</td>
9513 <td>
9514 <table>
9515 <tr>
9516 <th></th> <th>H</th> <th>S</th> <th>O</th>
9517 </tr>
9518 <tr>
9519 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
9520 </tr>
9521 <tr>
9522 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
9523 </tr>
9524 <tr>
9525 <th>O</th> <td></td> <td></td> <td align="right">4</td>
9526 </tr>
9527 </table>
9528 </td>
9529 </tr>
9530
9531 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
9532 </table>
9533 <br/>Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5), sequence alignment score = 1795.1<br>
9534RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs: 2.105)<br>
9535<br>
9536<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/M/T</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/M/T">select #5/M/T</a></div></div>4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected<br>
9537<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L/S</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L/S">select #5/L/S</a></div></div>4358 atoms, 3871 bonds, 19 pseudobonds, 1080 residues, 2 models selected<br>
9538<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/M/T</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/M/T">select #5/M/T</a></div></div>4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected<br>
9539<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/S</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/S">select #5/S</a></div></div>860 atoms, 733 bonds, 1 pseudobond, 235 residues, 2 models selected<br>
9540<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> (#!5 &amp; sel) orange</div><div class="cxcmd_as_cmd"><a href="cxcmd:color (#!5 &amp; sel) orange">color (#!5 &amp; sel) orange</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2157</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2157">select #2/F:2157</a></div></div>21 atoms, 21 bonds, 1 residue, 1 model selected<br>
9541<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2157-2238</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2157-2238">select #2/F:2157-2238</a></div></div>1309 atoms, 1329 bonds, 82 residues, 1 model selected<br>
9542<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel steel blue">color sel steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel slate gray</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel slate gray">color sel slate gray</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light slate gray</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light slate gray">color sel light slate gray</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel steel blue">color sel steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light steel blue">color sel light steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2150-2151</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2150-2151">select #2/F:2150-2151</a></div></div>14 atoms, 13 bonds, 2 residues, 1 model selected<br>
9543<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:386</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:386">select #5:386</a></div></div>8 atoms, 6 bonds, 2 residues, 1 model selected<br>
9544<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:388</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:388">select #5:388</a></div></div>18 atoms, 16 bonds, 2 residues, 1 model selected<br>
9545<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2152-2153</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2152-2153">select #2/F:2152-2153</a></div></div>22 atoms, 21 bonds, 2 residues, 1 model selected<br>
9546<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2152-2156</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2152-2156">select #2/F:2152-2156</a></div></div>65 atoms, 65 bonds, 5 residues, 1 model selected<br>
9547<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:388-390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:388-390">select #2/F:388-390</a></div></div>Nothing selected<br>
9548<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:388-390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:388-390">select #5/L:388-390</a></div></div>23 atoms, 23 bonds, 3 residues, 1 model selected<br>
9549<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel orange</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel orange">color sel orange</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel orange red</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel orange red">color sel orange red</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:388-397</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:388-397">select #5/L:388-397</a></div></div>71 atoms, 72 bonds, 10 residues, 1 model selected<br>
9550<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel orange</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel orange">color sel orange</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/M:43-123</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/M:43-123">select #5/M:43-123</a></div></div>607 atoms, 624 bonds, 81 residues, 1 model selected<br>
9551<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light steel blue">color sel light steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/S:43-123</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/S:43-123">select #5/S:43-123</a></div></div>651 atoms, 670 bonds, 81 residues, 1 model selected<br>
9552<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light steel blue">color sel light steel blue</a></div></div><div class="cxcmd"><a href="help:user/commands/select.html">select</a> <span style="background-color:crimson;">#5/:15-30,35-52,58-387,396-477</span></div><font color="crimson"><b>Expected an objects specifier or a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:15-30,35-52,58-387,396-477</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:15-30,35-52,58-387,396-477">select #5/L:15-30,35-52,58-387,396-477</a></div></div>2866 atoms, 2890 bonds, 18 pseudobonds, 423 residues, 2 models selected<br>
9553<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><a href="help:user/commands/select.html">select</a> #5/L:1-400 <span style="background-color:crimson;">&amp;~15-30,35-52,58-387,396-477</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:1-400 &amp;~:15-30,35-52,58-387,396-477</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:1-400 &amp;~:15-30,35-52,58-387,396-477">select #5/L:1-400 &amp;~:15-30,35-52,58-387,396-477</a></div></div>240 atoms, 241 bonds, 30 residues, 1 model selected<br>
9554<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> viewH2ase</div><div class="cxcmd_as_cmd"><a href="cxcmd:view viewH2ase">view viewH2ase</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1766-1776</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1766-1776">select #2/F:1766-1776</a></div></div>160 atoms, 160 bonds, 11 residues, 1 model selected<br>
9555<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1766-1775</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1766-1775">select #2/F:1766-1775</a></div></div>146 atoms, 146 bonds, 10 residues, 1 model selected<br>
9556<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1766-1775,1792-1795,1814-1821</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1766-1775,1792-1795,1814-1821">select #2/F:1766-1775,1792-1795,1814-1821</a></div></div>293 atoms, 293 bonds, 22 residues, 1 model selected<br>
9557<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel cyan</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel cyan">color sel cyan</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> viewH2ase</div><div class="cxcmd_as_cmd"><a href="cxcmd:view viewH2ase">view viewH2ase</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F &amp;protein">select #2/F &amp;protein</a></div></div>7149 atoms, 7242 bonds, 473 residues, 1 model selected<br>
9558<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff showDist true interModel false intraMol false intraRes false reveal true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false reveal true log true">hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false reveal true log true</a></div></div>Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A CYF 575 SG<br>
9559Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb #2/A CYF 575 SG<br>
9560<br>
9561[Repeated 1 time(s)]<p style="color:#ffb961">Skipped 2 atom(s) with bad connectivities; see log for details<br>
9562</p><pre>Finding intramodel H-bonds
9563Constraints relaxed by 0.4 angstroms and 20 degrees
9564Models used:
9565 2 DdHyd_PSI.opt.chains.pdb
9566
956713 H-bonds
9568H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9569DdHyd_PSI.opt.chains.pdb #2/A ARG 27 NH2 DdHyd_PSI.opt.chains.pdb #2/F GLU 1814 OE1 DdHyd_PSI.opt.chains.pdb #2/A ARG 27 HH21 3.498 2.750
9570DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 NE2 DdHyd_PSI.opt.chains.pdb #2/F CYF 1799 O DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 HE21 2.873 2.126
9571DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 NZ DdHyd_PSI.opt.chains.pdb #2/F ASN 1843 OD1 DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 HZ2 2.829 1.880
9572DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ DdHyd_PSI.opt.chains.pdb #2/F GLN 1804 OE1 DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ2 2.839 1.911
9573DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ DdHyd_PSI.opt.chains.pdb #2/F PRO 2234 O DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ1 2.762 1.871
9574DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 N DdHyd_PSI.opt.chains.pdb #2/F LYS 2032 O DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 H3 2.915 1.906
9575DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH1 DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH11 2.866 1.886
9576DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH2 DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH21 3.207 2.381
9577DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH1 DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2 DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH12 2.805 1.855
9578DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2 DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD1 DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22 2.984 2.083
9579DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2 DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2 DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22 2.835 1.934
9580DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD1 DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1 2.862 2.132
9581DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD2 DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1 2.902 1.907
9582</pre><br/>13 hydrogen bonds found<br>
9583<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F &amp;protein">select #2/F &amp;protein</a></div></div>7149 atoms, 7242 bonds, 473 residues, 1 model selected<br>
9584<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2 &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2 &amp;protein">select #2 &amp;protein</a></div></div>34783 atoms, 35343 bonds, 13 pseudobonds, 2238 residues, 2 models selected<br>
9585<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 34783 atom styles<br>
9586<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730">select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730</a></div></div>161 atoms, 154 bonds, 8 residues, 1 model selected<br>
9587<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel deep pink</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel deep pink">color sel deep pink</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2 &amp;H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2 &amp;H">select #2 &amp;H</a></div></div>17179 atoms, 2238 residues, 1 model selected<br>
9588<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true">hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true</a></div></div>Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A CYF 575 SG<br>
9589Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb #2/A CYF 575 SG<br>
9590<br>
9591[Repeated 1 time(s)]<p style="color:#ffb961">Skipped 2 atom(s) with bad connectivities; see log for details<br>
9592</p><pre>Finding intramodel H-bonds
9593Constraints relaxed by 0.4 angstroms and 20 degrees
9594Models used:
9595 2 DdHyd_PSI.opt.chains.pdb
9596
95970 H-bonds
9598H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9599</pre><br/>0 hydrogen bonds found<br>
9600<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F &amp;protein">select #2/F &amp;protein</a></div></div>7149 atoms, 7242 bonds, 473 residues, 1 model selected<br>
9601<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> H-Bonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show H-Bonds">ui tool show H-Bonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/hbonds.html">hbonds</a> sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true</div><div class="cxcmd_as_cmd"><a href="cxcmd:hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true">hbonds sel color #0096ff showDist true interModel false intraMol false intraRes false select true log true</a></div></div>Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A CYF 575 SG<br>
9602Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb #2/A CYF 575 SG<br>
9603<br>
9604[Repeated 1 time(s)]<p style="color:#ffb961">Skipped 2 atom(s) with bad connectivities; see log for details<br>
9605</p><pre>Finding intramodel H-bonds
9606Constraints relaxed by 0.4 angstroms and 20 degrees
9607Models used:
9608 2 DdHyd_PSI.opt.chains.pdb
9609
961013 H-bonds
9611H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
9612DdHyd_PSI.opt.chains.pdb #2/A ARG 27 NH2 DdHyd_PSI.opt.chains.pdb #2/F GLU 1814 OE1 DdHyd_PSI.opt.chains.pdb #2/A ARG 27 HH21 3.498 2.750
9613DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 NE2 DdHyd_PSI.opt.chains.pdb #2/F CYF 1799 O DdHyd_PSI.opt.chains.pdb #2/C GLN 1491 HE21 2.873 2.126
9614DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 NZ DdHyd_PSI.opt.chains.pdb #2/F ASN 1843 OD1 DdHyd_PSI.opt.chains.pdb #2/C LYS 1510 HZ2 2.829 1.880
9615DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ DdHyd_PSI.opt.chains.pdb #2/F GLN 1804 OE1 DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ2 2.839 1.911
9616DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 NZ DdHyd_PSI.opt.chains.pdb #2/F PRO 2234 O DdHyd_PSI.opt.chains.pdb #2/D LYS 1665 HZ1 2.762 1.871
9617DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 N DdHyd_PSI.opt.chains.pdb #2/F LYS 2032 O DdHyd_PSI.opt.chains.pdb #2/E PRO 1700 H3 2.915 1.906
9618DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH1 DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH11 2.866 1.886
9619DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 NH2 DdHyd_PSI.opt.chains.pdb #2/F VAL 1768 O DdHyd_PSI.opt.chains.pdb #2/E ARG 1706 HH21 3.207 2.381
9620DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH1 DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2 DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH12 2.805 1.855
9621DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2 DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD1 DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22 2.984 2.083
9622DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 NH2 DdHyd_PSI.opt.chains.pdb #2/F ASP 1792 OD2 DdHyd_PSI.opt.chains.pdb #2/E ARG 1742 HH22 2.835 1.934
9623DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD1 DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1 2.862 2.132
9624DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 N DdHyd_PSI.opt.chains.pdb #2/E ASP 1730 OD2 DdHyd_PSI.opt.chains.pdb #2/F ILE 1766 H1 2.902 1.907
9625</pre><br/>13 hydrogen bonds found<br>
9626<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.2.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.2.1 models">hide #2.2.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/E #FFDAB9 target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/E #FFDAB9 target c ">color #2/E #FFDAB9 target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/D #DEB887 target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/D #DEB887 target c ">color #2/D #DEB887 target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/C #D2B48C target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/C #D2B48C target c ">color #2/C #D2B48C target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#list">view list</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view list">view list</a></div></div>Named views: <a href="cxcmd:view session-start">session-start</a>, <a href="cxcmd:view viewH2ase">viewH2ase</a>, <a href="cxcmd:view zoom1">zoom1</a>, <a href="cxcmd:view zoom2">zoom2</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view session-start">view session-start</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> #2/A #DDA0DD target c </div><div class="cxcmd_as_cmd"><a href="cxcmd:color #2/A #DDA0DD target c ">color #2/A #DDA0DD target c </a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> viewH2aseHbonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name viewH2aseHbonds">view name viewH2aseHbonds</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Mon Sep 15 19:12:58 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
9627<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> viewH2aseHbonds</div><div class="cxcmd_as_cmd"><a href="cxcmd:view viewH2aseHbonds">view viewH2aseHbonds</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd Hbonds.png&quot; width 1800 height 1358 supersample 3 transparentBackground true</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd Hbonds.png&quot; width 1800 height 1358 supersample 3 transparentBackground true">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd Hbonds.png&quot; width 1800 height 1358 supersample 3 transparentBackground true</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730">select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730</a></div></div>161 atoms, 154 bonds, 8 residues, 1 model selected<br>
9628<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/name.html#frozen">name frozen</a> HbondingDdH sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:name frozen HbondingDdH sel">name frozen HbondingDdH sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Mon Sep 15 20:51:36 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
9629<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1766-1775,1792-1795,1814-1821 &amp;H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1766-1775,1792-1795,1814-1821 &amp;H">select #2/F:1766-1775,1792-1795,1814-1821 &amp;H</a></div></div>139 atoms, 22 residues, 1 model selected<br>
9630<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1766-1775,1792-1795,1814-1821 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1766-1775,1792-1795,1814-1821 &amp;~H">select #2/F:1766-1775,1792-1795,1814-1821 &amp;~H</a></div></div>154 atoms, 154 bonds, 22 residues, 1 model selected<br>
9631<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1766-1775,1792-1795,1814-1821,2151-2156 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1766-1775,1792-1795,1814-1821,2151-2156 &amp;~H">select #2/F:1766-1775,1792-1795,1814-1821,2151-2156 &amp;~H</a></div></div>196 atoms, 196 bonds, 28 residues, 1 model selected<br>
9632<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1766-1775,1792-1795,1814-1821,2152-2156 &amp;~H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1766-1775,1792-1795,1814-1821,2152-2156 &amp;~H">select #2/F:1766-1775,1792-1795,1814-1821,2152-2156 &amp;~H</a></div></div>192 atoms, 192 bonds, 27 residues, 1 model selected<br>
9633<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view session-start">view session-start</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Mon Sep 15 21:24:55 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
9634<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/C-F &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/C-F &amp;protein">select #2/C-F &amp;protein</a></div></div>11691 atoms, 11840 bonds, 12 pseudobonds, 762 residues, 2 models selected<br>
9635<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
9636Assigning partial charges to residue CYF (net charge -1) with am1-bcc method<br>
9637Running ANTECHAMBER command: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n<br>
9638(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.in.mol2); atoms read (25), bonds read (24).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 102; net charge: -1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.10.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
9639Coulombic values for DdHyd_PSI.opt.chains.pdb_C SES surface #2.3: minimum, -22.19, mean -4.05, maximum 8.43<br>
9640Coulombic values for DdHyd_PSI.opt.chains.pdb_D SES surface #2.4: minimum, -10.22, mean 2.11, maximum 15.27<br>
9641Coulombic values for DdHyd_PSI.opt.chains.pdb_E SES surface #2.5: minimum, -11.34, mean 1.57, maximum 12.31<br>
9642Coulombic values for DdHyd_PSI.opt.chains.pdb_F SES surface #2.6: minimum, -23.25, mean -3.85, maximum 11.53<br>
9643<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> coulSide</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name coulSide">view name coulSide</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/A-B &amp;protein</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/A-B &amp;protein">select #2/A-B &amp;protein</a></div></div>23092 atoms, 23503 bonds, 1476 residues, 1 model selected<br>
9644<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/coulombic.html">coulombic</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:coulombic sel">coulombic sel</a></div></div>Using Amber 20 recommended default charges and atom types for standard residues<br>
9645Assigning partial charges to residue CYF (net charge -1) with am1-bcc method<br>
9646Running ANTECHAMBER command: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek qm_theory=&#x27;AM1&#x27;, -i /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.in.mol2 -fi mol2 -o /var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n<br>
9647(CYF) <code></code><br/>(CYF) <code>Welcome to antechamber 20.0: molecular input file processor.</code><br/>(CYF) <code></code><br/>(CYF) <code>Info: Finished reading file (/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.in.mol2); atoms read (22), bonds read (21).</code><br/>(CYF) <code>Info: Determining atomic numbers from atomic symbols which are case sensitive.</code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac</code><br/>(CYF) <code></code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff</code><br/>(CYF) <code>Info: Total number of electrons: 94; net charge: -1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.10.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1</code><br/>(CYF) <code></code><br/>(CYF) <code>Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC</code><br/>(CYF) <code></code><br/>Charges for residue CYF determined<br>
9648Coulombic values for DdHyd_PSI.opt.chains.pdb_A SES surface #2.7: minimum, -12.58, mean -0.47, maximum 17.74<br>
9649Coulombic values for DdHyd_PSI.opt.chains.pdb_B SES surface #2.8: minimum, -15.68, mean -0.16, maximum 13.13<br>
9650<span style="color:blue">To also show corresponding color key, enter the above</span> <b>coulombic</b> <span style="color:blue">command and add</span> <i>key true</i><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.6 models">hide #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #5">combine #5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/L:CMO,CYN,PDT,FE2:424</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/L:CMO,CYN,PDT,FE2:424">select #6/L:CMO,CYN,PDT,FE2:424</a></div></div>23 atoms, 20 bonds, 4 pseudobonds, 8 residues, 2 models selected<br>
9651<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6 &amp;~/L:CMO,CYN,PDT,FE2:424</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6 &amp;~/L:CMO,CYN,PDT,FE2:424">select #6 &amp;~/L:CMO,CYN,PDT,FE2:424</a></div></div>8705 atoms, 7722 bonds, 29 pseudobonds, 2164 residues, 2 models selected<br>
9652<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#atoms">delete atoms</a> (#!6 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete atoms (#!6 &amp; sel)">delete atoms (#!6 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#bonds">delete bonds</a> (#!6 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete bonds (#!6 &amp; sel)">delete bonds (#!6 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/align.html">align</a> #6/L:424@FE4,S3,FE1,S2,S1,FE2,S4,FE3 toAtoms #2/F:2244@F4,S3,F1,S2,S1,F2,S4,F3</div><div class="cxcmd_as_cmd"><a href="cxcmd:align #6/L:424@FE4,S3,FE1,S2,S1,FE2,S4,FE3 toAtoms #2/F:2244@F4,S3,F1,S2,S1,F2,S4,F3">align #6/L:424@FE4,S3,FE1,S2,S1,FE2,S4,FE3 toAtoms #2/F:2244@F4,S3,F1,S2,S1,F2,S4,F3</a></div></div>RMSD between 8 atom pairs is 0.065 angstroms<br>
9653<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:CYF</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:CYF">select #2/F:CYF</a></div></div>120 atoms, 108 bonds, 12 residues, 1 model selected<br>
9654<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:CYF &amp;H</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:CYF &amp;H">select #2/F:CYF &amp;H</a></div></div>48 atoms, 12 residues, 1 model selected<br>
9655<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:SF4">select #2/F:SF4</a></div></div>24 atoms, 54 pseudobonds, 3 residues, 2 models selected<br>
9656<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 24 atom styles<br>
9657<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6:SF4">select #6:SF4</a></div></div>8 atoms, 12 bonds, 1 residue, 1 model selected<br>
9658<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:SF4">select #2/F:SF4</a></div></div>24 atoms, 54 pseudobonds, 3 residues, 2 models selected<br>
9659<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 24 atom styles<br>
9660<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6">select #6</a></div></div>23 atoms, 20 bonds, 4 pseudobonds, 8 residues, 2 models selected<br>
9661<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel maroon</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel maroon">color sel maroon</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 23 atom styles<br>
9662<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.6 models">show #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3 models">hide #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.4 models">hide #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.3 models">show #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.4 models">show #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.5 models">show #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design coulombic surfs.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design coulombic surfs.cxs&quot;">save &quot;/Users/drornoy/Dropbox/2024 NSF BSF Dror iron sulfu/Resubmission2025/Models and structures/PSI-DdHyd design coulombic surfs.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #1">close #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #4">close #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #6 &quot;Catalytic Site&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #6 &quot;Catalytic Site&quot;">rename #6 &quot;Catalytic Site&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #3">close #3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #5/L to #2/F pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #5/L to #2/F pairing ss showAlignment true">matchmaker #5/L to #2/F pairing ss showAlignment true</a></div></div>
9663 <table border=1 cellpadding=4 cellspacing=0>
9664 <tr>
9665 <th colspan="2">Parameters</th>
9666 </tr>
9667 <tr>
9668 <td>Chain pairing</td>
9669 <td>ss</td>
9670 </tr>
9671 <tr>
9672 <td>Alignment algorithm</td>
9673 <td>Needleman-Wunsch</td>
9674 </tr>
9675 <tr>
9676 <td>Similarity matrix</td>
9677 <td>BLOSUM-62</td>
9678 </tr>
9679
9680 <tr>
9681 <td>SS fraction</td>
9682 <td>0.3</td>
9683 </tr>
9684 <tr>
9685 <td>Gap open (HH/SS/other)</td>
9686 <td>18/18/6</td>
9687 </tr>
9688 <tr>
9689 <td>Gap extend</td>
9690 <td>1</td>
9691 </tr>
9692 <tr>
9693 <td>SS matrix</td>
9694 <td>
9695 <table>
9696 <tr>
9697 <th></th> <th>H</th> <th>S</th> <th>O</th>
9698 </tr>
9699 <tr>
9700 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
9701 </tr>
9702 <tr>
9703 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
9704 </tr>
9705 <tr>
9706 <th>O</th> <td></td> <td></td> <td align="right">4</td>
9707 </tr>
9708 </table>
9709 </td>
9710 </tr>
9711
9712 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
9713 </table>
9714 <br/>Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5), sequence alignment score = 1795.1<br>
9715Alignment identifier is 1<br>
9716Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
9717Hiding conservation header for alignment 1<br>
9718Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #2/F, 1hfe #5/L<br>
9719Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
9720RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs: 2.105)<br>
9721<br>
9722<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #5/L to #2/F pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #5/L to #2/F pairing ss showAlignment true">matchmaker #5/L to #2/F pairing ss showAlignment true</a></div></div>
9723 <table border=1 cellpadding=4 cellspacing=0>
9724 <tr>
9725 <th colspan="2">Parameters</th>
9726 </tr>
9727 <tr>
9728 <td>Chain pairing</td>
9729 <td>ss</td>
9730 </tr>
9731 <tr>
9732 <td>Alignment algorithm</td>
9733 <td>Needleman-Wunsch</td>
9734 </tr>
9735 <tr>
9736 <td>Similarity matrix</td>
9737 <td>BLOSUM-62</td>
9738 </tr>
9739
9740 <tr>
9741 <td>SS fraction</td>
9742 <td>0.3</td>
9743 </tr>
9744 <tr>
9745 <td>Gap open (HH/SS/other)</td>
9746 <td>18/18/6</td>
9747 </tr>
9748 <tr>
9749 <td>Gap extend</td>
9750 <td>1</td>
9751 </tr>
9752 <tr>
9753 <td>SS matrix</td>
9754 <td>
9755 <table>
9756 <tr>
9757 <th></th> <th>H</th> <th>S</th> <th>O</th>
9758 </tr>
9759 <tr>
9760 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
9761 </tr>
9762 <tr>
9763 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
9764 </tr>
9765 <tr>
9766 <th>O</th> <td></td> <td></td> <td align="right">4</td>
9767 </tr>
9768 </table>
9769 </td>
9770 </tr>
9771
9772 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
9773 </table>
9774 <br/>Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5), sequence alignment score = 1795.1<br>
9775Alignment identifier is 2<br>
9776Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 2<br>
9777Hiding conservation header for alignment 2<br>
9778Chains used in RMSD evaluation for alignment 2: DdHyd_PSI.opt.chains.pdb #2/F, 1hfe #5/L<br>
9779Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 2<br>
9780RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs: 2.105)<br>
9781<br>
9782<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3 models">hide #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.3 models">show #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.6 models">hide #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.7 models">hide #2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.8 models">hide #2.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.8 models">show #2.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.7 models">show #2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1812</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1812">select #2/F:1812</a></div></div>20 atoms, 20 bonds, 1 residue, 1 model selected<br>
9783<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1812-1820 #5/L:51-56</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1812-1820 #5/L:51-56">select #2/F:1812-1820 #5/L:51-56</a></div></div>164 atoms, 166 bonds, 15 residues, 2 models selected<br>
9784MatchMaker Alignment [ID: 2] region chain F..chain L [51-59] RMSD: 2.042<br>
9785<br>
9786<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1766</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1766">select #2/F:1766</a></div></div>21 atoms, 20 bonds, 1 residue, 1 model selected<br>
9787<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:1766-1773 #5/L:3-12</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:1766-1773 #5/L:3-12">select #2/F:1766-1773 #5/L:3-12</a></div></div>213 atoms, 212 bonds, 18 residues, 2 models selected<br>
9788MatchMaker Alignment [ID: 2] region chain F..chain L [3-12] RMSD: 8.370<br>
9789<br>
9790<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.6 models">show #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.6 models">hide #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:389</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:389">select #5/L:389</a></div></div>7 atoms, 7 bonds, 1 residue, 1 model selected<br>
9791<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:389-391</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:389-391">select #5/L:389-391</a></div></div>22 atoms, 22 bonds, 3 residues, 1 model selected<br>
9792<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2149</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2149">select #2/F:2149</a></div></div>7 atoms, 6 bonds, 1 residue, 1 model selected<br>
9793<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2149-2152</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2149-2152">select #2/F:2149-2152</a></div></div>28 atoms, 27 bonds, 4 residues, 1 model selected<br>
9794<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2152</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2152">select #2/F:2152</a></div></div>7 atoms, 6 bonds, 1 residue, 1 model selected<br>
9795<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2152-2153</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2152-2153">select #2/F:2152-2153</a></div></div>22 atoms, 21 bonds, 2 residues, 1 model selected<br>
9796<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2152</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2152">select #2/F:2152</a></div></div>7 atoms, 6 bonds, 1 residue, 1 model selected<br>
9797<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2152-2155</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2152-2155">select #2/F:2152-2155</a></div></div>50 atoms, 50 bonds, 4 residues, 1 model selected<br>
9798<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2152</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2152">select #2/F:2152</a></div></div>7 atoms, 6 bonds, 1 residue, 1 model selected<br>
9799<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2152-2156</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2152-2156">select #2/F:2152-2156</a></div></div>65 atoms, 65 bonds, 5 residues, 1 model selected<br>
9800<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #5/L to #2/F pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #5/L to #2/F pairing ss showAlignment true">matchmaker #5/L to #2/F pairing ss showAlignment true</a></div></div>
9801 <table border=1 cellpadding=4 cellspacing=0>
9802 <tr>
9803 <th colspan="2">Parameters</th>
9804 </tr>
9805 <tr>
9806 <td>Chain pairing</td>
9807 <td>ss</td>
9808 </tr>
9809 <tr>
9810 <td>Alignment algorithm</td>
9811 <td>Needleman-Wunsch</td>
9812 </tr>
9813 <tr>
9814 <td>Similarity matrix</td>
9815 <td>BLOSUM-62</td>
9816 </tr>
9817
9818 <tr>
9819 <td>SS fraction</td>
9820 <td>0.3</td>
9821 </tr>
9822 <tr>
9823 <td>Gap open (HH/SS/other)</td>
9824 <td>18/18/6</td>
9825 </tr>
9826 <tr>
9827 <td>Gap extend</td>
9828 <td>1</td>
9829 </tr>
9830 <tr>
9831 <td>SS matrix</td>
9832 <td>
9833 <table>
9834 <tr>
9835 <th></th> <th>H</th> <th>S</th> <th>O</th>
9836 </tr>
9837 <tr>
9838 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
9839 </tr>
9840 <tr>
9841 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
9842 </tr>
9843 <tr>
9844 <th>O</th> <td></td> <td></td> <td align="right">4</td>
9845 </tr>
9846 </table>
9847 </td>
9848 </tr>
9849
9850 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
9851 </table>
9852 <br/>Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5), sequence alignment score = 1795.1<br>
9853Alignment identifier is 1<br>
9854Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
9855Hiding conservation header for alignment 1<br>
9856Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #2/F, 1hfe #5/L<br>
9857Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 1<br>
9858RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs: 2.105)<br>
9859<br>
9860<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/PSI-DdHyd design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/PSI-DdHyd design.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/PSI-DdHyd design.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Wed Sep 17 15:57:48 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
9861<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:2-3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:2-3">select #5/L:2-3</a></div></div>17 atoms, 16 bonds, 2 residues, 1 model selected<br>
9862<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:389</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:389">select #5/L:389</a></div></div>7 atoms, 7 bonds, 1 residue, 1 model selected<br>
9863<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:389-391</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:389-391">select #5/L:389-391</a></div></div>22 atoms, 22 bonds, 3 residues, 1 model selected<br>
9864<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2153</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2153">select #2/F:2153</a></div></div>15 atoms, 14 bonds, 1 residue, 1 model selected<br>
9865<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2/F:2153-2158</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2/F:2153-2158">select #2/F:2153-2158</a></div></div>96 atoms, 97 bonds, 6 residues, 1 model selected<br>
9866<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:388-389</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:388-389">select #5/L:388-389</a></div></div>16 atoms, 16 bonds, 2 residues, 1 model selected<br>
9867<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:389-398</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:389-398">select #5/L:389-398</a></div></div>63 atoms, 64 bonds, 10 residues, 1 model selected<br>
9868<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 3lx4</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 3lx4">open 3lx4</a></div></div>
9869<table border=1 cellpadding=4 cellspacing=0>
9870 <thead>
9871 <tr>
9872 <th colspan="2">Summary of feedback from opening 3lx4 fetched from pdb</th>
9873 </tr>
9874 </thead>
9875 <tbody>
9876 <tr>
9877 <td><i>note</i></td> <td style="background-color:Canvas">Fetching compressed mmCIF 3lx4 from http://files.rcsb.org/download/3lx4.cif</td> </tr>
9878 </tbody>
9879</table><br/><i>3lx4</i> title:<br><b>Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG)</b> <a href="cxcmd:log metadata #1">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
9880 <thead>
9881 <tr>
9882 <th colspan="3">Chain information for 3lx4 #1</th>
9883 </tr>
9884 <tr>
9885 <th>Chain</th>
9886 <th>Description</th>
9887 <th>UniProt</th>
9888 </tr>
9889 </thead>
9890 <tbody>
9891 <tr>
9892 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #1/A:25-450">A</a> <a title="Select chain" href="cxcmd:select #1/B:25-450">B</a></td>
9893 <td><a title="Show sequence" href="cxcmd:sequence chain #1/A#1/B">Fe-hydrogenase</a></td>
9894 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q9FYU1 from uniprot associate #1/A,B">Q9FYU1_CHLRE</a> <a title="Select sequence" href="cxcmd:select #1/A,B:17-457">17-457</a></td>
9895 </tr>
9896 </tbody>
9897</table><br/><table border=1 cellpadding=4 cellspacing=0>
9898 <thead>
9899 <tr>
9900 <th>Non-standard residues in 3lx4 #1</th>
9901 </tr>
9902 </thead>
9903 <tbody>
9904 <tr>
9905 <td><a title="select residue" href="cxcmd:sel :ACT">ACT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/ACT">acetate ion</a></td>
9906 </tr>
9907 <tr>
9908 <td><a title="select residue" href="cxcmd:sel :CL">CL</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CL">chloride ion</a></td>
9909 </tr>
9910 <tr>
9911 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
9912 </tr>
9913 </tbody>
9914</table><br/><table border=1 cellpadding=4 cellspacing=0>
9915<tr><th colspan=3>3lx4 mmCIF Assemblies
9916<tr><td><a title="Generate assembly" href="cxcmd:sym #1 assembly 1 ; view">1</a><td>author_and_software_defined_assembly
9917<tr><td><a title="Generate assembly" href="cxcmd:sym #1 assembly 2 ; view">2</a><td>author_and_software_defined_assembly
9918</table><br/>32 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!1 to #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!1 to #2">matchmaker #!1 to #2</a></div></div>
9919 <table border=1 cellpadding=4 cellspacing=0>
9920 <tr>
9921 <th colspan="2">Parameters</th>
9922 </tr>
9923 <tr>
9924 <td>Chain pairing</td>
9925 <td>bb</td>
9926 </tr>
9927 <tr>
9928 <td>Alignment algorithm</td>
9929 <td>Needleman-Wunsch</td>
9930 </tr>
9931 <tr>
9932 <td>Similarity matrix</td>
9933 <td>BLOSUM-62</td>
9934 </tr>
9935
9936 <tr>
9937 <td>SS fraction</td>
9938 <td>0.3</td>
9939 </tr>
9940 <tr>
9941 <td>Gap open (HH/SS/other)</td>
9942 <td>18/18/6</td>
9943 </tr>
9944 <tr>
9945 <td>Gap extend</td>
9946 <td>1</td>
9947 </tr>
9948 <tr>
9949 <td>SS matrix</td>
9950 <td>
9951 <table>
9952 <tr>
9953 <th></th> <th>H</th> <th>S</th> <th>O</th>
9954 </tr>
9955 <tr>
9956 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
9957 </tr>
9958 <tr>
9959 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
9960 </tr>
9961 <tr>
9962 <th>O</th> <td></td> <td></td> <td align="right">4</td>
9963 </tr>
9964 </table>
9965 </td>
9966 </tr>
9967
9968 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
9969 </table>
9970 <br/>Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 3lx4, chain B (#1), sequence alignment score = 861.9<br>
9971RMSD between 264 pruned atom pairs is 1.082 angstroms; (across all 356 pairs: 3.848)<br>
9972<br>
9973<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.8 models">hide #2.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.7 models">hide #2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.6 models">show #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.6 models">hide #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.7 models">show #2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.7 models">hide #2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3 models">hide #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.4 models">hide #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.5 models">hide #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.6 models">show #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.6 models">hide #2.6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.5 models">show #2.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.4 models">show #2.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.3 models">show #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.3 models">hide #2.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.7 models">show #2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.8 models">show #2.8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/A">select #1/A</a></div></div>3460 atoms, 3157 bonds, 7 pseudobonds, 774 residues, 3 models selected<br>
9974<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #5/S #5/T</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #5/S #5/T">sequence chain #5/S #5/T</a></div></div>Alignment identifier is 2<br>
9975<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/S-T:38</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/S-T:38">select #5/S-T:38</a></div></div>18 atoms, 16 bonds, 2 residues, 1 model selected<br>
9976<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/S-T:38-45</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/S-T:38-45">select #5/S-T:38-45</a></div></div>140 atoms, 140 bonds, 16 residues, 1 model selected<br>
9977<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/S-T:46</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/S-T:46">select #5/S-T:46</a></div></div>22 atoms, 20 bonds, 2 residues, 1 model selected<br>
9978<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/S-T:46-51</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/S-T:46-51">select #5/S-T:46-51</a></div></div>100 atoms, 100 bonds, 12 residues, 1 model selected<br>
9979<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/S-T:38</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/S-T:38">select #5/S-T:38</a></div></div>18 atoms, 16 bonds, 2 residues, 1 model selected<br>
9980<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/S-T:38-45</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/S-T:38-45">select #5/S-T:38-45</a></div></div>140 atoms, 140 bonds, 16 residues, 1 model selected<br>
9981<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:2-14</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:2-14">select #5/L:2-14</a></div></div>115 atoms, 116 bonds, 13 residues, 1 model selected<br>
9982<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:2-14,31-34,53-57</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:2-14,31-34,53-57">select #5/L:2-14,31-34,53-57</a></div></div>183 atoms, 183 bonds, 22 residues, 1 model selected<br>
9983<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:2-14,31-34,53-57,388-397</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:2-14,31-34,53-57,388-397">select #5/L:2-14,31-34,53-57,388-397</a></div></div>254 atoms, 255 bonds, 32 residues, 1 model selected<br>
9984<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel alice blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel alice blue">color sel alice blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel sky blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel sky blue">color sel sky blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light sky blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light sky blue">color sel light sky blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light blue">color sel light blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel pale turquoise</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel pale turquoise">color sel pale turquoise</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light steel blue">color sel light steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel pale turquoise</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel pale turquoise">color sel pale turquoise</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel wheat</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel wheat">color sel wheat</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel gainsboro</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel gainsboro">color sel gainsboro</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel powder blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel powder blue">color sel powder blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel pale turquoise</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel pale turquoise">color sel pale turquoise</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:2-14,31-34,53-57,388-397/S:36-42</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:2-14,31-34,53-57,388-397/S:36-42">select #5/L:2-14,31-34,53-57,388-397/S:36-42</a></div></div>316 atoms, 317 bonds, 39 residues, 1 model selected<br>
9985<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/L:2-14,31-34,53-57,388-397/S:36-41</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/L:2-14,31-34,53-57,388-397/S:36-41">select #5/L:2-14,31-34,53-57,388-397/S:36-41</a></div></div>304 atoms, 304 bonds, 38 residues, 1 model selected<br>
9986<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot;">save &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #1">close #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1 id 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1 id 1">rename #1 id 1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 id 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 id 1">rename #2 id 1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1 id 2</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1 id 2">rename #1 id 2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2#6 id #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2#6 id #1">rename #2#6 id #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1 DdHyd_PSI</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1 DdHyd_PSI">rename #1 DdHyd_PSI</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #5 id #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #5 id #2">rename #5 id #2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1.2 models">show #!1.2 models</a></div></div><div class="cxcmd"><a href="help:user/commands/combine.html">combine</a> #1 <span style="background-color:crimson;">copy t</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #1">combine #1</a></div></div>Associated combination chain F to chain F with 0 mismatches<br>
9987Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #1.1/F, 1hfe #2/L, combination #3/F<br>
9988<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3.1 models">hide #3.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3.1 models">show #3.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3.1 models">hide #3.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3.2 models">hide #3.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/split.html">split</a> #3 chains</div><div class="cxcmd_as_cmd"><a href="cxcmd:split #3 chains">split #3 chains</a></div></div>Split combination (#3) into 7 models<br>
9989<table border=1 cellpadding=4 cellspacing=0>
9990 <thead>
9991 <tr>
9992 <th colspan="2">Chain information for combination A #3.1</th>
9993 </tr>
9994 <tr>
9995 <th>Chain</th>
9996 <th>Description</th>
9997
9998 </tr>
9999 </thead>
10000 <tbody>
10001 <tr>
10002 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3.1/A:1-743">A</a></td>
10003 <td><a title="Show sequence" href="cxcmd:sequence chain #3.1/A">No description available</a></td>
10004
10005 </tr>
10006 </tbody>
10007</table><br/><table border=1 cellpadding=4 cellspacing=0>
10008 <thead>
10009 <tr>
10010 <th colspan="2">Chain information for combination B #3.2</th>
10011 </tr>
10012 <tr>
10013 <th>Chain</th>
10014 <th>Description</th>
10015
10016 </tr>
10017 </thead>
10018 <tbody>
10019 <tr>
10020 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3.2/B:744-1476">B</a></td>
10021 <td><a title="Show sequence" href="cxcmd:sequence chain #3.2/B">No description available</a></td>
10022
10023 </tr>
10024 </tbody>
10025</table><br/><table border=1 cellpadding=4 cellspacing=0>
10026 <thead>
10027 <tr>
10028 <th colspan="2">Chain information for combination C #3.3</th>
10029 </tr>
10030 <tr>
10031 <th>Chain</th>
10032 <th>Description</th>
10033
10034 </tr>
10035 </thead>
10036 <tbody>
10037 <tr>
10038 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3.3/C:1477-1556">C</a></td>
10039 <td><a title="Show sequence" href="cxcmd:sequence chain #3.3/C">No description available</a></td>
10040
10041 </tr>
10042 </tbody>
10043</table><br/><table border=1 cellpadding=4 cellspacing=0>
10044 <thead>
10045 <tr>
10046 <th colspan="2">Chain information for combination D #3.4</th>
10047 </tr>
10048 <tr>
10049 <th>Chain</th>
10050 <th>Description</th>
10051
10052 </tr>
10053 </thead>
10054 <tbody>
10055 <tr>
10056 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3.4/D:1557-1699">D</a></td>
10057 <td><a title="Show sequence" href="cxcmd:sequence chain #3.4/D">No description available</a></td>
10058
10059 </tr>
10060 </tbody>
10061</table><br/><table border=1 cellpadding=4 cellspacing=0>
10062 <thead>
10063 <tr>
10064 <th colspan="2">Chain information for combination E #3.5</th>
10065 </tr>
10066 <tr>
10067 <th>Chain</th>
10068 <th>Description</th>
10069
10070 </tr>
10071 </thead>
10072 <tbody>
10073 <tr>
10074 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3.5/E:1700-1765">E</a></td>
10075 <td><a title="Show sequence" href="cxcmd:sequence chain #3.5/E">No description available</a></td>
10076
10077 </tr>
10078 </tbody>
10079</table><br/><table border=1 cellpadding=4 cellspacing=0>
10080 <thead>
10081 <tr>
10082 <th colspan="2">Chain information for combination F #3.6</th>
10083 </tr>
10084 <tr>
10085 <th>Chain</th>
10086 <th>Description</th>
10087
10088 </tr>
10089 </thead>
10090 <tbody>
10091 <tr>
10092 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3.6/F:1766-2238">F</a></td>
10093 <td><a title="Show sequence" href="cxcmd:sequence chain #3.6/F">No description available</a></td>
10094
10095 </tr>
10096 </tbody>
10097</table><br/>Associated combination F (3.6) chain F to chain F with 0 mismatches<br>
10098Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #1.1/F, 1hfe #2/L, combination F #3.6/F<br>
10099<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3.1 models">hide #!3.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3.2 models">hide #3.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3.3 models">hide #!3.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3.4 models">hide #3.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3.5 models">hide #3.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3.1-3.3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3.1-3.3">select #3.1-3.3</a></div></div>Nothing selected<br>
10100<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3.1">select #3.1</a></div></div>11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected<br>
10101<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3.1#3.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3.1#3.2">select #3.1#3.2</a></div></div>23100 atoms, 23503 bonds, 18 pseudobonds, 1477 residues, 3 models selected<br>
10102<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3.1#3.2#3.3#3.4#3.5 id #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3.1#3.2#3.3#3.4#3.5 id #4">rename #3.1#3.2#3.3#3.4#3.5 id #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.1.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.1.3 models">show #1.1.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.1.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.1.3 models">hide #1.1.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1/F">select #1/F</a></div></div>7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected<br>
10103<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1.1/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1.1/F">select #1.1/F</a></div></div>7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected<br>
10104<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #1.1/F</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #1.1/F">select #1.1/F</a></div></div>7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected<br>
10105<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#atoms">delete atoms</a> (#!1.1 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete atoms (#!1.1 &amp; sel)">delete atoms (#!1.1 &amp; sel)</a></div></div>Chains used in RMSD evaluation for alignment 1: 1hfe #2/L, combination F #3.6/F<br>
10106<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/delete.html#bonds">delete bonds</a> (#!1.1 &amp; sel)</div><div class="cxcmd_as_cmd"><a href="cxcmd:delete bonds (#!1.1 &amp; sel)">delete bonds (#!1.1 &amp; sel)</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1.1 models">hide #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1.1 models">show #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1.1 models">hide #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1.1 models">show #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #1.2</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #1.2">close #1.2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1.1 id #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1.1 id #1">rename #1.1 id #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1.1 id 1</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1.1 id 1">rename #1.1 id 1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/combine.html">combine</a> #1.1</div><div class="cxcmd_as_cmd"><a href="cxcmd:combine #1.1">combine #1.1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #5">close #5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1.1 models">hide #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1.1 models">show #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1 PSI</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1 PSI">rename #1 PSI</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #1.1 &quot;DdHyd_PSI.opt.chains no DdHyd&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #1.1 &quot;DdHyd_PSI.opt.chains no DdHyd&quot;">rename #1.1 &quot;DdHyd_PSI.opt.chains no DdHyd&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 id 6</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 id 6">rename #2 id 6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4.1 models">show #!4.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.2 models">show #4.2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4.3 models">show #!4.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.4 models">show #4.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #4.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #4.5 models">show #4.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #4">close #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3.6 DdHyd_PSI.opt.chains</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3.6 DdHyd_PSI.opt.chains">rename #3.6 DdHyd_PSI.opt.chains</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3.7 &quot;Catalytic site&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3.7 &quot;Catalytic site&quot;">rename #3.7 &quot;Catalytic site&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 id 2</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 id 2">rename #3 id 2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #6 id 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #6 id 3">rename #6 id 3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 DdHyd_PSI</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 DdHyd_PSI">rename #2 DdHyd_PSI</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 9gbu 9gnk</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 9gbu 9gnk">open 9gbu 9gnk</a></div></div>
10107<table border=1 cellpadding=4 cellspacing=0>
10108 <thead>
10109 <tr>
10110 <th colspan="2">Summary of feedback from opening 9gbu fetched from pdb</th>
10111 </tr>
10112 </thead>
10113 <tbody>
10114 <tr>
10115 <td><i>warnings</i></td> <td style="background-color:#ffb961">Atom HS2 is not in the residue template for 402 /A:505<br>Atom HS2 is not in the residue template for 402 /B:504</td> </tr>
10116 <tr>
10117 <td><i>notes</i></td> <td style="background-color:Canvas">Fetching compressed mmCIF 9gbu from http://files.rcsb.org/download/9gbu.cif<br>Fetching CCD MPD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif</td> </tr>
10118 </tbody>
10119</table><br/>
10120<table border=1 cellpadding=4 cellspacing=0>
10121 <thead>
10122 <tr>
10123 <th colspan="2">Summary of feedback from opening 9gnk fetched from pdb</th>
10124 </tr>
10125 </thead>
10126 <tbody>
10127 <tr>
10128 <td><i>warnings</i></td> <td style="background-color:#ffb961">Atom HS2 is not in the residue template for 402 /A:502<br>Atom H3 is not in the residue template for PG4 /A:512</td> </tr>
10129 <tr>
10130 <td><i>notes</i></td> <td style="background-color:Canvas">Fetching compressed mmCIF 9gnk from http://files.rcsb.org/download/9gnk.cif<br>Fetching CCD EPE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/EPE/EPE.cif<br>Fetching CCD PG4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PG4/PG4.cif</td> </tr>
10131 </tbody>
10132</table><br/><i>9gbu</i> title:<br><b>Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei</b> <a href="cxcmd:log metadata #4">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
10133 <thead>
10134 <tr>
10135 <th colspan="3">Chain information for 9gbu #4</th>
10136 </tr>
10137 <tr>
10138 <th>Chain</th>
10139 <th>Description</th>
10140 <th>UniProt</th>
10141 </tr>
10142 </thead>
10143 <tbody>
10144 <tr>
10145 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4/A:2-479">A</a> <a title="Select chain" href="cxcmd:select #4/B:2-481">B</a></td>
10146 <td><a title="Show sequence" href="cxcmd:sequence chain #4/A#4/B">Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit</a></td>
10147 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07598 from uniprot associate #4/A,B">PHFL_NITV2</a> <a title="Select sequence" href="cxcmd:select #4/A,B:1-389">1-389</a>, <a title="Show annotations" href="cxcmd:open P07603 from uniprot associate #4/A,B">PHFS_NITV2</a> <a title="Select sequence" href="cxcmd:select #4/A,B:403-480">403-480</a></td>
10148 </tr>
10149 </tbody>
10150</table><br/><table border=1 cellpadding=4 cellspacing=0>
10151 <thead>
10152 <tr>
10153 <th>Non-standard residues in 9gbu #4</th>
10154 </tr>
10155 </thead>
10156 <tbody>
10157 <tr>
10158 <td><a title="select residue" href="cxcmd:sel ::name=&quot;402&quot;">402</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/402">dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)</a></td>
10159 </tr>
10160 <tr>
10161 <td><a title="select residue" href="cxcmd:sel :MPD">MPD</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/MPD">(4S)-2-methyl-2,4-pentanediol</a></td>
10162 </tr>
10163 <tr>
10164 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
10165 </tr>
10166 </tbody>
10167</table><br/><table border=1 cellpadding=4 cellspacing=0>
10168<tr><th colspan=3>9gbu mmCIF Assemblies
10169<tr><td><a title="Generate assembly" href="cxcmd:sym #4 assembly 1 ; view">1</a><td>author_defined_assembly
10170<tr><td><a title="Generate assembly" href="cxcmd:sym #4 assembly 2 ; view">2</a><td>author_defined_assembly
10171</table><br/>166 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/><i>9gnk</i> title:<br><b>Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum</b> <a href="cxcmd:log metadata #5">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
10172 <thead>
10173 <tr>
10174 <th colspan="3">Chain information for 9gnk #5</th>
10175 </tr>
10176 <tr>
10177 <th>Chain</th>
10178 <th>Description</th>
10179 <th>UniProt</th>
10180 </tr>
10181 </thead>
10182 <tbody>
10183 <tr>
10184 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #5/A:2-486">A</a></td>
10185 <td><a title="Show sequence" href="cxcmd:sequence chain #5/A">Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit</a></td>
10186 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07598 from uniprot associate #5/A">PHFL_NITV2</a> <a title="Select sequence" href="cxcmd:select #5/A:1-390">1-390</a>, <a title="Show annotations" href="cxcmd:open P07603 from uniprot associate #5/A">PHFS_NITV2</a> <a title="Select sequence" href="cxcmd:select #5/A:404-482">404-482</a></td>
10187 </tr>
10188 </tbody>
10189</table><br/><table border=1 cellpadding=4 cellspacing=0>
10190 <thead>
10191 <tr>
10192 <th>Non-standard residues in 9gnk #5</th>
10193 </tr>
10194 </thead>
10195 <tbody>
10196 <tr>
10197 <td><a title="select residue" href="cxcmd:sel ::name=&quot;402&quot;">402</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/402">dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)</a></td>
10198 </tr>
10199 <tr>
10200 <td><a title="select residue" href="cxcmd:sel :CMO">CMO</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CMO">carbon monoxide</a></td>
10201 </tr>
10202 <tr>
10203 <td><a title="select residue" href="cxcmd:sel :EPE">EPE</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/EPE">4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid</a> (HEPES)</td>
10204 </tr>
10205 <tr>
10206 <td><a title="select residue" href="cxcmd:sel :PEG">PEG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PEG">di(hydroxyethyl)ether</a></td>
10207 </tr>
10208 <tr>
10209 <td><a title="select residue" href="cxcmd:sel :PG4">PG4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PG4">tetraethylene glycol</a></td>
10210 </tr>
10211 <tr>
10212 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
10213 </tr>
10214 </tbody>
10215</table><br/><table border=1 cellpadding=4 cellspacing=0>
10216<tr><th colspan=3>9gnk mmCIF Assemblies
10217<tr><td><a title="Generate assembly" href="cxcmd:sym #5 assembly 1 ; view">1</a><td>author_defined_assembly
10218</table><br/>200 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/>Associated 9gbu chain A to chain L with 31 mismatches<br>
10219Associated 9gbu chain B to chain L with 31 mismatches<br>
10220Associated 9gnk chain A to chain L with 29 mismatches<br>
10221Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains #2.6/F, 1hfe #3/L, 9gbu #4/B, 9gnk #5/A<br>
10222<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B">select #4/B</a></div></div>7543 atoms, 7548 bonds, 24 pseudobonds, 577 residues, 2 models selected<br>
10223<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!4-5 to #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!4-5 to #2.6">matchmaker #!4-5 to #2.6</a></div></div>
10224 <table border=1 cellpadding=4 cellspacing=0>
10225 <tr>
10226 <th colspan="2">Parameters</th>
10227 </tr>
10228 <tr>
10229 <td>Chain pairing</td>
10230 <td>bb</td>
10231 </tr>
10232 <tr>
10233 <td>Alignment algorithm</td>
10234 <td>Needleman-Wunsch</td>
10235 </tr>
10236 <tr>
10237 <td>Similarity matrix</td>
10238 <td>BLOSUM-62</td>
10239 </tr>
10240
10241 <tr>
10242 <td>SS fraction</td>
10243 <td>0.3</td>
10244 </tr>
10245 <tr>
10246 <td>Gap open (HH/SS/other)</td>
10247 <td>18/18/6</td>
10248 </tr>
10249 <tr>
10250 <td>Gap extend</td>
10251 <td>1</td>
10252 </tr>
10253 <tr>
10254 <td>SS matrix</td>
10255 <td>
10256 <table>
10257 <tr>
10258 <th></th> <th>H</th> <th>S</th> <th>O</th>
10259 </tr>
10260 <tr>
10261 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
10262 </tr>
10263 <tr>
10264 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
10265 </tr>
10266 <tr>
10267 <th>O</th> <td></td> <td></td> <td align="right">4</td>
10268 </tr>
10269 </table>
10270 </td>
10271 </tr>
10272
10273 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
10274 </table>
10275 <br/>Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 9gbu, chain A (#4), sequence alignment score = 2182.6<br>
10276RMSD between 454 pruned atom pairs is 0.553 angstroms; (across all 469 pairs: 1.405)<br>
10277<br>
10278Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 9gnk, chain A (#5), sequence alignment score = 2184.3<br>
10279RMSD between 453 pruned atom pairs is 0.534 angstroms; (across all 470 pairs: 1.482)<br>
10280<br>
10281Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains #2.6/F, 1hfe #3/L, 9gbu #4/A, 9gnk #5/A<br>
10282<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #3">select add #3</a></div></div>16271 atoms, 15290 bonds, 63 pseudobonds, 2749 residues, 4 models selected<br>
10283<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4">select add #4</a></div></div>23871 atoms, 22854 bonds, 87 pseudobonds, 3365 residues, 4 models selected<br>
10284<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #4">select subtract #4</a></div></div>8728 atoms, 7742 bonds, 39 pseudobonds, 2172 residues, 2 models selected<br>
10285<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #3">select subtract #3</a></div></div>Nothing selected<br>
10286<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5">select add #5</a></div></div>8157 atoms, 7706 bonds, 24 pseudobonds, 1040 residues, 2 models selected<br>
10287<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel sandy brown</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel sandy brown">color sel sandy brown</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel dark khaki</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel dark khaki">color sel dark khaki</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel plum</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel plum">color sel plum</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5">select subtract #5</a></div></div>Nothing selected<br>
10288<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :4O2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :4O2">select :4O2</a></div></div>Nothing selected<br>
10289<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :402">select :402</a></div></div>64 atoms, 61 bonds, 4 residues, 3 models selected<br>
10290<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:402">select #5:402</a></div></div>22 atoms, 21 bonds, 1 residue, 1 model selected<br>
10291<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> ::name=&quot;402&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:select ::name=&quot;402&quot;">select ::name=&quot;402&quot;</a></div></div>72 atoms, 48 bonds, 33 pseudobonds, 3 residues, 4 models selected<br>
10292<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :EPE,PEG,PG4,MPD</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :EPE,PEG,PG4,MPD">select :EPE,PEG,PG4,MPD</a></div></div>290 atoms, 278 bonds, 13 residues, 2 models selected<br>
10293<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!5 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!5 atoms">hide sel &amp; #!5 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :EPE,PEG,PG4,MPD,HOH</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :EPE,PEG,PG4,MPD,HOH">select :EPE,PEG,PG4,MPD,HOH</a></div></div>2233 atoms, 278 bonds, 1956 residues, 3 models selected<br>
10294<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!5 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!5 atoms">hide sel &amp; #!5 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #5/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #5/A">sequence chain #5/A</a></div></div>Alignment identifier is 5/A<br>
10295<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #4/A #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #4/A #4/B">sequence chain #4/A #4/B</a></div></div>Alignment identifier is 3<br>
10296<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:400</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:400">select #5/A:400</a></div></div>12 atoms, 11 bonds, 1 residue, 1 model selected<br>
10297<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:388</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:388">select #5/A:388</a></div></div>17 atoms, 16 bonds, 1 residue, 1 model selected<br>
10298<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:388-400</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:388-400">select #5/A:388-400</a></div></div>209 atoms, 210 bonds, 13 residues, 1 model selected<br>
10299<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:390">select #5/A:390</a></div></div>16 atoms, 15 bonds, 1 residue, 1 model selected<br>
10300<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:390-399</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:390-399">select #5/A:390-399</a></div></div>166 atoms, 166 bonds, 10 residues, 1 model selected<br>
10301<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A-B:402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A-B:402">select #4/A-B:402</a></div></div>22 atoms, 20 bonds, 2 residues, 1 model selected<br>
10302<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A-B:390-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A-B:390-402">select #4/A-B:390-402</a></div></div>440 atoms, 442 bonds, 26 residues, 1 model selected<br>
10303<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:404-405</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:404-405">select #5/A:404-405</a></div></div>36 atoms, 35 bonds, 2 residues, 1 model selected<br>
10304<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:390-405</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:390-405">select #5/A:390-405</a></div></div>277 atoms, 277 bonds, 16 residues, 1 model selected<br>
10305<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:390-391</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:390-391">select #5/A:390-391</a></div></div>32 atoms, 31 bonds, 2 residues, 1 model selected<br>
10306<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:390-404</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:390-404">select #5/A:390-404</a></div></div>253 atoms, 253 bonds, 15 residues, 1 model selected<br>
10307<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:390-404#4/A:390-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:390-404#4/A:390-402">select #5/A:390-404#4/A:390-402</a></div></div>473 atoms, 474 bonds, 28 residues, 2 models selected<br>
10308<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/A:390-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/A:390-402">select #4/A:390-402</a></div></div>220 atoms, 221 bonds, 13 residues, 1 model selected<br>
10309<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel sea green</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel sea green">color sel sea green</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5/A:390-404</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5/A:390-404">select #5/A:390-404</a></div></div>253 atoms, 253 bonds, 15 residues, 1 model selected<br>
10310<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel purple</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel purple">color sel purple</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot;">save &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Wed Oct 22 18:27:07 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
10311<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_model_0.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_model_0.cif&quot;">open &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_model_0.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
10312 <thead>
10313 <tr>
10314 <th colspan="2">Chain information for fold_ddhyab_model_0.cif #6</th>
10315 </tr>
10316 <tr>
10317 <th>Chain</th>
10318 <th>Description</th>
10319
10320 </tr>
10321 </thead>
10322 <tbody>
10323 <tr>
10324 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/A:1-474">A</a></td>
10325 <td><a title="Show sequence" href="cxcmd:sequence chain #6/A">.</a></td>
10326
10327 </tr>
10328 </tbody>
10329</table><br/>Associated fold_ddhyab_model_0.cif chain A to chain L with 27 mismatches<br>
10330Computing secondary structure<br>
10331<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #6 to #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #6 to #2.6">matchmaker #6 to #2.6</a></div></div>
10332 <table border=1 cellpadding=4 cellspacing=0>
10333 <tr>
10334 <th colspan="2">Parameters</th>
10335 </tr>
10336 <tr>
10337 <td>Chain pairing</td>
10338 <td>bb</td>
10339 </tr>
10340 <tr>
10341 <td>Alignment algorithm</td>
10342 <td>Needleman-Wunsch</td>
10343 </tr>
10344 <tr>
10345 <td>Similarity matrix</td>
10346 <td>BLOSUM-62</td>
10347 </tr>
10348
10349 <tr>
10350 <td>SS fraction</td>
10351 <td>0.3</td>
10352 </tr>
10353 <tr>
10354 <td>Gap open (HH/SS/other)</td>
10355 <td>18/18/6</td>
10356 </tr>
10357 <tr>
10358 <td>Gap extend</td>
10359 <td>1</td>
10360 </tr>
10361 <tr>
10362 <td>SS matrix</td>
10363 <td>
10364 <table>
10365 <tr>
10366 <th></th> <th>H</th> <th>S</th> <th>O</th>
10367 </tr>
10368 <tr>
10369 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
10370 </tr>
10371 <tr>
10372 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
10373 </tr>
10374 <tr>
10375 <th>O</th> <td></td> <td></td> <td align="right">4</td>
10376 </tr>
10377 </table>
10378 </td>
10379 </tr>
10380
10381 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
10382 </table>
10383 <br/>Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with fold_ddhyab_model_0.cif, chain A (#6), sequence alignment score = 2224.5<br>
10384RMSD between 456 pruned atom pairs is 0.436 angstroms; (across all 470 pairs: 1.221)<br>
10385<br>
10386<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;AlphaFold Error Plot&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;AlphaFold Error Plot&quot;">ui tool show &quot;AlphaFold Error Plot&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #6 file &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_full_data_0.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #6 file &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_full_data_0.json&quot;">alphafold pae #6 file &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_full_data_0.json&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#byattribute">color bfactor</a> #6 palette alphafold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color bfactor #6 palette alphafold">color bfactor #6 palette alphafold</a></div></div>3649 atoms, 474 residues, atom bfactor range 50.4 to 99<br>
10387<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot;">save &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking design.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Wed Oct 22 19:01:49 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
10388<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #6 models">hide #6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #6</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #6">close #6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5">select add #5</a></div></div>8157 atoms, 7706 bonds, 24 pseudobonds, 1040 residues, 2 models selected<br>
10389<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #5">select subtract #5</a></div></div>Nothing selected<br>
10390<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #5 id 9</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #5 id 9">rename #5 id 9</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #4 id 8</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #4 id 8">rename #4 id 8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 id 7</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 id 7">rename #3 id 7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;">save &quot;/Users/drornoy/OneDrive - Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
10391 <thead>
10392 <tr>
10393 <th colspan="2">Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3</th>
10394 </tr>
10395 <tr>
10396 <th>Chain</th>
10397 <th>Description</th>
10398
10399 </tr>
10400 </thead>
10401 <tbody>
10402 <tr>
10403 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #3/A:1-477">A</a></td>
10404 <td><a title="Show sequence" href="cxcmd:sequence chain #3/A">.</a></td>
10405
10406 </tr>
10407 </tbody>
10408</table><br/>Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to chain L with 25 mismatches<br>
10409Computing secondary structure<br>
10410<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #3 to #2.6 showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #3 to #2.6 showAlignment true">matchmaker #3 to #2.6 showAlignment true</a></div></div>
10411 <table border=1 cellpadding=4 cellspacing=0>
10412 <tr>
10413 <th colspan="2">Parameters</th>
10414 </tr>
10415 <tr>
10416 <td>Chain pairing</td>
10417 <td>bb</td>
10418 </tr>
10419 <tr>
10420 <td>Alignment algorithm</td>
10421 <td>Needleman-Wunsch</td>
10422 </tr>
10423 <tr>
10424 <td>Similarity matrix</td>
10425 <td>BLOSUM-62</td>
10426 </tr>
10427
10428 <tr>
10429 <td>SS fraction</td>
10430 <td>0.3</td>
10431 </tr>
10432 <tr>
10433 <td>Gap open (HH/SS/other)</td>
10434 <td>18/18/6</td>
10435 </tr>
10436 <tr>
10437 <td>Gap extend</td>
10438 <td>1</td>
10439 </tr>
10440 <tr>
10441 <td>SS matrix</td>
10442 <td>
10443 <table>
10444 <tr>
10445 <th></th> <th>H</th> <th>S</th> <th>O</th>
10446 </tr>
10447 <tr>
10448 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
10449 </tr>
10450 <tr>
10451 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
10452 </tr>
10453 <tr>
10454 <th>O</th> <td></td> <td></td> <td align="right">4</td>
10455 </tr>
10456 </table>
10457 </td>
10458 </tr>
10459
10460 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
10461 </table>
10462 <br/>Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3), sequence alignment score = 2230.1<br>
10463Alignment identifier is 4<br>
10464Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 4<br>
10465Hiding conservation header for alignment 4<br>
10466Chains used in RMSD evaluation for alignment 4: DdHyd_PSI.opt.chains #2.6/F, fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A<br>
10467Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 4<br>
10468RMSD between 456 pruned atom pairs is 0.422 angstroms; (across all 470 pairs: 1.377)<br>
10469<br>
10470<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;AlphaFold Error Plot&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;AlphaFold Error Plot&quot;">ui tool show &quot;AlphaFold Error Plot&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #3 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_full_data_0.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #3 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_full_data_0.json&quot;">alphafold pae #3 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/DdH2ase Single Chain/fold_ddh2ase_single_chain_chlamy_tdk_linker/fold_ddh2ase_single_chain_chlamy_tdk_linker_full_data_0.json&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#byattribute">color bfactor</a> #3 palette alphafold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color bfactor #3 palette alphafold">color bfactor #3 palette alphafold</a></div></div>3677 atoms, 477 residues, atom bfactor range 44.8 to 99<br>
10471<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #3">select add #3</a></div></div>3677 atoms, 3770 bonds, 477 residues, 1 model selected<br>
10472<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #3">select subtract #3</a></div></div>Nothing selected<br>
10473<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 3lx4</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 3lx4">open 3lx4</a></div></div><i>3lx4</i> title:<br><b>Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG)</b> <a href="cxcmd:log metadata #4">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
10474 <thead>
10475 <tr>
10476 <th colspan="3">Chain information for 3lx4 #4</th>
10477 </tr>
10478 <tr>
10479 <th>Chain</th>
10480 <th>Description</th>
10481 <th>UniProt</th>
10482 </tr>
10483 </thead>
10484 <tbody>
10485 <tr>
10486 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #4/A:25-450">A</a> <a title="Select chain" href="cxcmd:select #4/B:25-450">B</a></td>
10487 <td><a title="Show sequence" href="cxcmd:sequence chain #4/A#4/B">Fe-hydrogenase</a></td>
10488 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open Q9FYU1 from uniprot associate #4/A,B">Q9FYU1_CHLRE</a> <a title="Select sequence" href="cxcmd:select #4/A,B:17-457">17-457</a></td>
10489 </tr>
10490 </tbody>
10491</table><br/><table border=1 cellpadding=4 cellspacing=0>
10492 <thead>
10493 <tr>
10494 <th>Non-standard residues in 3lx4 #4</th>
10495 </tr>
10496 </thead>
10497 <tbody>
10498 <tr>
10499 <td><a title="select residue" href="cxcmd:sel :ACT">ACT</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/ACT">acetate ion</a></td>
10500 </tr>
10501 <tr>
10502 <td><a title="select residue" href="cxcmd:sel :CL">CL</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CL">chloride ion</a></td>
10503 </tr>
10504 <tr>
10505 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
10506 </tr>
10507 </tbody>
10508</table><br/><table border=1 cellpadding=4 cellspacing=0>
10509<tr><th colspan=3>3lx4 mmCIF Assemblies
10510<tr><td><a title="Generate assembly" href="cxcmd:sym #4 assembly 1 ; view">1</a><td>author_and_software_defined_assembly
10511<tr><td><a title="Generate assembly" href="cxcmd:sym #4 assembly 2 ; view">2</a><td>author_and_software_defined_assembly
10512</table><br/>32 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :SF4">select :SF4</a></div></div>192 atoms, 216 bonds, 108 pseudobonds, 24 residues, 9 models selected<br>
10513<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #4/A to #2.6/F pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #4/A to #2.6/F pairing ss showAlignment true">matchmaker #4/A to #2.6/F pairing ss showAlignment true</a></div></div>
10514 <table border=1 cellpadding=4 cellspacing=0>
10515 <tr>
10516 <th colspan="2">Parameters</th>
10517 </tr>
10518 <tr>
10519 <td>Chain pairing</td>
10520 <td>ss</td>
10521 </tr>
10522 <tr>
10523 <td>Alignment algorithm</td>
10524 <td>Needleman-Wunsch</td>
10525 </tr>
10526 <tr>
10527 <td>Similarity matrix</td>
10528 <td>BLOSUM-62</td>
10529 </tr>
10530
10531 <tr>
10532 <td>SS fraction</td>
10533 <td>0.3</td>
10534 </tr>
10535 <tr>
10536 <td>Gap open (HH/SS/other)</td>
10537 <td>18/18/6</td>
10538 </tr>
10539 <tr>
10540 <td>Gap extend</td>
10541 <td>1</td>
10542 </tr>
10543 <tr>
10544 <td>SS matrix</td>
10545 <td>
10546 <table>
10547 <tr>
10548 <th></th> <th>H</th> <th>S</th> <th>O</th>
10549 </tr>
10550 <tr>
10551 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
10552 </tr>
10553 <tr>
10554 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
10555 </tr>
10556 <tr>
10557 <th>O</th> <td></td> <td></td> <td align="right">4</td>
10558 </tr>
10559 </table>
10560 </td>
10561 </tr>
10562
10563 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
10564 </table>
10565 <br/>Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 3lx4, chain A (#4), sequence alignment score = 854.7<br>
10566Alignment identifier is 2<br>
10567Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 2<br>
10568Hiding conservation header for alignment 2<br>
10569Chains used in RMSD evaluation for alignment 2: DdHyd_PSI.opt.chains #2.6/F, 3lx4 #4/A<br>
10570Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 2<br>
10571RMSD between 265 pruned atom pairs is 1.087 angstroms; (across all 356 pairs: 3.844)<br>
10572<br>
10573<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #4 &quot;CrHydA1 3lx4&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #4 &quot;CrHydA1 3lx4&quot;">rename #4 &quot;CrHydA1 3lx4&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #7 &quot;DdHydAHydB 1hfe&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #7 &quot;DdHydAHydB 1hfe&quot;">rename #7 &quot;DdHydAHydB 1hfe&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/B">select #3/B</a></div></div>Nothing selected<br>
10574<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/B">select #4/B</a></div></div>3507 atoms, 3157 bonds, 7 pseudobonds, 821 residues, 3 models selected<br>
10575<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #8">close #8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #9">close #9</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #7 id 5</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #7 id 5">rename #7 id 5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 8ru6</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 8ru6">open 8ru6</a></div></div>
10576<table border=1 cellpadding=4 cellspacing=0>
10577 <thead>
10578 <tr>
10579 <th colspan="2">Summary of feedback from opening 8ru6 fetched from pdb</th>
10580 </tr>
10581 </thead>
10582 <tbody>
10583 <tr>
10584 <td><i>warning</i></td> <td style="background-color:#ffb961">Atom HS1 is not in the residue template for MHX /B:508</td> </tr>
10585 </tbody>
10586</table><br/><i>8ru6</i> title:<br><b>Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 4 amino acid linker peptide derived from CpI of Clostridium pasteurianum</b> <a href="cxcmd:log metadata #6">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
10587 <thead>
10588 <tr>
10589 <th colspan="3">Chain information for 8ru6 #6</th>
10590 </tr>
10591 <tr>
10592 <th>Chain</th>
10593 <th>Description</th>
10594 <th>UniProt</th>
10595 </tr>
10596 </thead>
10597 <tbody>
10598 <tr>
10599 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #6/B:3-486">B</a></td>
10600 <td><a title="Show sequence" href="cxcmd:sequence chain #6/B">Periplasmic [Fe] hydrogenase large subunit,CpI,Periplasmic [Fe] hydrogenase small subunit</a></td>
10601 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07598 from uniprot associate #6/B">PHFL_DESVH</a> <a title="Select sequence" href="cxcmd:select #6/B:1-392">1-392</a>, <a title="Show annotations" href="cxcmd:open P29166 from uniprot associate #6/B">PHF1_CLOPA</a> <a title="Select sequence" href="cxcmd:select #6/B:393-396">393-396</a>, <a title="Show annotations" href="cxcmd:open P07603 from uniprot associate #6/B">PHFS_DESVH</a> <a title="Select sequence" href="cxcmd:select #6/B:397-481">397-481</a></td>
10602 </tr>
10603 </tbody>
10604</table><br/><table border=1 cellpadding=4 cellspacing=0>
10605 <thead>
10606 <tr>
10607 <th>Non-standard residues in 8ru6 #6</th>
10608 </tr>
10609 </thead>
10610 <tbody>
10611 <tr>
10612 <td><a title="select residue" href="cxcmd:sel :MHX">MHX</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/MHX">Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster (-CO form)</a></td>
10613 </tr>
10614 <tr>
10615 <td><a title="select residue" href="cxcmd:sel :PG4">PG4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PG4">tetraethylene glycol</a></td>
10616 </tr>
10617 <tr>
10618 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
10619 </tr>
10620 </tbody>
10621</table><br/>147 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/>Associated 8ru6 chain B to chain L with 25 mismatches<br>
10622<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #6/B to #3/A pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #6/B to #3/A pairing ss showAlignment true">matchmaker #6/B to #3/A pairing ss showAlignment true</a></div></div>
10623 <table border=1 cellpadding=4 cellspacing=0>
10624 <tr>
10625 <th colspan="2">Parameters</th>
10626 </tr>
10627 <tr>
10628 <td>Chain pairing</td>
10629 <td>ss</td>
10630 </tr>
10631 <tr>
10632 <td>Alignment algorithm</td>
10633 <td>Needleman-Wunsch</td>
10634 </tr>
10635 <tr>
10636 <td>Similarity matrix</td>
10637 <td>BLOSUM-62</td>
10638 </tr>
10639
10640 <tr>
10641 <td>SS fraction</td>
10642 <td>0.3</td>
10643 </tr>
10644 <tr>
10645 <td>Gap open (HH/SS/other)</td>
10646 <td>18/18/6</td>
10647 </tr>
10648 <tr>
10649 <td>Gap extend</td>
10650 <td>1</td>
10651 </tr>
10652 <tr>
10653 <td>SS matrix</td>
10654 <td>
10655 <table>
10656 <tr>
10657 <th></th> <th>H</th> <th>S</th> <th>O</th>
10658 </tr>
10659 <tr>
10660 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
10661 </tr>
10662 <tr>
10663 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
10664 </tr>
10665 <tr>
10666 <th>O</th> <td></td> <td></td> <td align="right">4</td>
10667 </tr>
10668 </table>
10669 </td>
10670 </tr>
10671
10672 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
10673 </table>
10674 <br/>Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with 8ru6, chain B (#6), sequence alignment score = 2480.9<br>
10675Alignment identifier is 3<br>
10676Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 3<br>
10677Hiding conservation header for alignment 3<br>
10678Chains used in RMSD evaluation for alignment 3: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, 8ru6 #6/B<br>
10679Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 3<br>
10680RMSD between 471 pruned atom pairs is 0.353 angstroms; (across all 475 pairs: 0.476)<br>
10681<br>
10682<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #6 &quot;DdHydAB_L1 8ru6&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #6 &quot;DdHydAB_L1 8ru6&quot;">rename #6 &quot;DdHydAB_L1 8ru6&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 9gnk</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 9gnk">open 9gnk</a></div></div>
10683<table border=1 cellpadding=4 cellspacing=0>
10684 <thead>
10685 <tr>
10686 <th colspan="2">Summary of feedback from opening 9gnk fetched from pdb</th>
10687 </tr>
10688 </thead>
10689 <tbody>
10690 <tr>
10691 <td><i>warnings</i></td> <td style="background-color:#ffb961">Atom HS2 is not in the residue template for 402 /A:502<br>Atom H3 is not in the residue template for PG4 /A:512</td> </tr>
10692 </tbody>
10693</table><br/><i>9gnk</i> title:<br><b>Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum</b> <a href="cxcmd:log metadata #7">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
10694 <thead>
10695 <tr>
10696 <th colspan="3">Chain information for 9gnk #7</th>
10697 </tr>
10698 <tr>
10699 <th>Chain</th>
10700 <th>Description</th>
10701 <th>UniProt</th>
10702 </tr>
10703 </thead>
10704 <tbody>
10705 <tr>
10706 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #7/A:2-486">A</a></td>
10707 <td><a title="Show sequence" href="cxcmd:sequence chain #7/A">Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit</a></td>
10708 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07598 from uniprot associate #7/A">PHFL_NITV2</a> <a title="Select sequence" href="cxcmd:select #7/A:1-390">1-390</a>, <a title="Show annotations" href="cxcmd:open P07603 from uniprot associate #7/A">PHFS_NITV2</a> <a title="Select sequence" href="cxcmd:select #7/A:404-482">404-482</a></td>
10709 </tr>
10710 </tbody>
10711</table><br/><table border=1 cellpadding=4 cellspacing=0>
10712 <thead>
10713 <tr>
10714 <th>Non-standard residues in 9gnk #7</th>
10715 </tr>
10716 </thead>
10717 <tbody>
10718 <tr>
10719 <td><a title="select residue" href="cxcmd:sel ::name=&quot;402&quot;">402</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/402">dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)</a></td>
10720 </tr>
10721 <tr>
10722 <td><a title="select residue" href="cxcmd:sel :CMO">CMO</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/CMO">carbon monoxide</a></td>
10723 </tr>
10724 <tr>
10725 <td><a title="select residue" href="cxcmd:sel :EPE">EPE</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/EPE">4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid</a> (HEPES)</td>
10726 </tr>
10727 <tr>
10728 <td><a title="select residue" href="cxcmd:sel :PEG">PEG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PEG">di(hydroxyethyl)ether</a></td>
10729 </tr>
10730 <tr>
10731 <td><a title="select residue" href="cxcmd:sel :PG4">PG4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/PG4">tetraethylene glycol</a></td>
10732 </tr>
10733 <tr>
10734 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
10735 </tr>
10736 </tbody>
10737</table><br/><table border=1 cellpadding=4 cellspacing=0>
10738<tr><th colspan=3>9gnk mmCIF Assemblies
10739<tr><td><a title="Generate assembly" href="cxcmd:sym #7 assembly 1 ; view">1</a><td>author_defined_assembly
10740</table><br/>200 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/>Associated 9gnk chain A to chain L with 29 mismatches<br>
10741<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #7/A to #3/A pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #7/A to #3/A pairing ss showAlignment true">matchmaker #7/A to #3/A pairing ss showAlignment true</a></div></div>
10742 <table border=1 cellpadding=4 cellspacing=0>
10743 <tr>
10744 <th colspan="2">Parameters</th>
10745 </tr>
10746 <tr>
10747 <td>Chain pairing</td>
10748 <td>ss</td>
10749 </tr>
10750 <tr>
10751 <td>Alignment algorithm</td>
10752 <td>Needleman-Wunsch</td>
10753 </tr>
10754 <tr>
10755 <td>Similarity matrix</td>
10756 <td>BLOSUM-62</td>
10757 </tr>
10758
10759 <tr>
10760 <td>SS fraction</td>
10761 <td>0.3</td>
10762 </tr>
10763 <tr>
10764 <td>Gap open (HH/SS/other)</td>
10765 <td>18/18/6</td>
10766 </tr>
10767 <tr>
10768 <td>Gap extend</td>
10769 <td>1</td>
10770 </tr>
10771 <tr>
10772 <td>SS matrix</td>
10773 <td>
10774 <table>
10775 <tr>
10776 <th></th> <th>H</th> <th>S</th> <th>O</th>
10777 </tr>
10778 <tr>
10779 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
10780 </tr>
10781 <tr>
10782 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
10783 </tr>
10784 <tr>
10785 <th>O</th> <td></td> <td></td> <td align="right">4</td>
10786 </tr>
10787 </table>
10788 </td>
10789 </tr>
10790
10791 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
10792 </table>
10793 <br/>Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with 9gnk, chain A (#7), sequence alignment score = 2461.4<br>
10794Alignment identifier is 5<br>
10795Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 5<br>
10796Hiding conservation header for alignment 5<br>
10797Chains used in RMSD evaluation for alignment 5: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, 9gnk #7/A<br>
10798Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 5<br>
10799RMSD between 469 pruned atom pairs is 0.373 angstroms; (across all 476 pairs: 0.928)<br>
10800<br>
10801<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 9gbu</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 9gbu">open 9gbu</a></div></div>
10802<table border=1 cellpadding=4 cellspacing=0>
10803 <thead>
10804 <tr>
10805 <th colspan="2">Summary of feedback from opening 9gbu fetched from pdb</th>
10806 </tr>
10807 </thead>
10808 <tbody>
10809 <tr>
10810 <td><i>warnings</i></td> <td style="background-color:#ffb961">Atom HS2 is not in the residue template for 402 /A:505<br>Atom HS2 is not in the residue template for 402 /B:504</td> </tr>
10811 </tbody>
10812</table><br/><i>9gbu</i> title:<br><b>Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from a group A1 type [FeFe]-hydrogenase of Solobacterium moorei</b> <a href="cxcmd:log metadata #8">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
10813 <thead>
10814 <tr>
10815 <th colspan="3">Chain information for 9gbu #8</th>
10816 </tr>
10817 <tr>
10818 <th>Chain</th>
10819 <th>Description</th>
10820 <th>UniProt</th>
10821 </tr>
10822 </thead>
10823 <tbody>
10824 <tr>
10825 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #8/A:2-479">A</a> <a title="Select chain" href="cxcmd:select #8/B:2-481">B</a></td>
10826 <td><a title="Show sequence" href="cxcmd:sequence chain #8/A#8/B">Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit</a></td>
10827 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07598 from uniprot associate #8/A,B">PHFL_NITV2</a> <a title="Select sequence" href="cxcmd:select #8/A,B:1-389">1-389</a>, <a title="Show annotations" href="cxcmd:open P07603 from uniprot associate #8/A,B">PHFS_NITV2</a> <a title="Select sequence" href="cxcmd:select #8/A,B:403-480">403-480</a></td>
10828 </tr>
10829 </tbody>
10830</table><br/><table border=1 cellpadding=4 cellspacing=0>
10831 <thead>
10832 <tr>
10833 <th>Non-standard residues in 9gbu #8</th>
10834 </tr>
10835 </thead>
10836 <tbody>
10837 <tr>
10838 <td><a title="select residue" href="cxcmd:sel ::name=&quot;402&quot;">402</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/402">dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)</a></td>
10839 </tr>
10840 <tr>
10841 <td><a title="select residue" href="cxcmd:sel :MPD">MPD</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/MPD">(4S)-2-methyl-2,4-pentanediol</a></td>
10842 </tr>
10843 <tr>
10844 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
10845 </tr>
10846 </tbody>
10847</table><br/><table border=1 cellpadding=4 cellspacing=0>
10848<tr><th colspan=3>9gbu mmCIF Assemblies
10849<tr><td><a title="Generate assembly" href="cxcmd:sym #8 assembly 1 ; view">1</a><td>author_defined_assembly
10850<tr><td><a title="Generate assembly" href="cxcmd:sym #8 assembly 2 ; view">2</a><td>author_defined_assembly
10851</table><br/>166 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/>Associated 9gbu chain A to chain L with 31 mismatches<br>
10852Associated 9gbu chain B to chain L with 31 mismatches<br>
10853<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #6/B to #3/A pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #6/B to #3/A pairing ss showAlignment true">matchmaker #6/B to #3/A pairing ss showAlignment true</a></div></div>
10854 <table border=1 cellpadding=4 cellspacing=0>
10855 <tr>
10856 <th colspan="2">Parameters</th>
10857 </tr>
10858 <tr>
10859 <td>Chain pairing</td>
10860 <td>ss</td>
10861 </tr>
10862 <tr>
10863 <td>Alignment algorithm</td>
10864 <td>Needleman-Wunsch</td>
10865 </tr>
10866 <tr>
10867 <td>Similarity matrix</td>
10868 <td>BLOSUM-62</td>
10869 </tr>
10870
10871 <tr>
10872 <td>SS fraction</td>
10873 <td>0.3</td>
10874 </tr>
10875 <tr>
10876 <td>Gap open (HH/SS/other)</td>
10877 <td>18/18/6</td>
10878 </tr>
10879 <tr>
10880 <td>Gap extend</td>
10881 <td>1</td>
10882 </tr>
10883 <tr>
10884 <td>SS matrix</td>
10885 <td>
10886 <table>
10887 <tr>
10888 <th></th> <th>H</th> <th>S</th> <th>O</th>
10889 </tr>
10890 <tr>
10891 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
10892 </tr>
10893 <tr>
10894 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
10895 </tr>
10896 <tr>
10897 <th>O</th> <td></td> <td></td> <td align="right">4</td>
10898 </tr>
10899 </table>
10900 </td>
10901 </tr>
10902
10903 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
10904 </table>
10905 <br/>Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with DdHydAB_L1 8ru6, chain B (#6), sequence alignment score = 2480.9<br>
10906Alignment identifier is 6<br>
10907Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 6<br>
10908Hiding conservation header for alignment 6<br>
10909Chains used in RMSD evaluation for alignment 6: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, DdHydAB_L1 8ru6 #6/B<br>
10910Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 6<br>
10911RMSD between 471 pruned atom pairs is 0.353 angstroms; (across all 475 pairs: 0.476)<br>
10912<br>
10913<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #8/A to #3/A pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #8/A to #3/A pairing ss showAlignment true">matchmaker #8/A to #3/A pairing ss showAlignment true</a></div></div>
10914 <table border=1 cellpadding=4 cellspacing=0>
10915 <tr>
10916 <th colspan="2">Parameters</th>
10917 </tr>
10918 <tr>
10919 <td>Chain pairing</td>
10920 <td>ss</td>
10921 </tr>
10922 <tr>
10923 <td>Alignment algorithm</td>
10924 <td>Needleman-Wunsch</td>
10925 </tr>
10926 <tr>
10927 <td>Similarity matrix</td>
10928 <td>BLOSUM-62</td>
10929 </tr>
10930
10931 <tr>
10932 <td>SS fraction</td>
10933 <td>0.3</td>
10934 </tr>
10935 <tr>
10936 <td>Gap open (HH/SS/other)</td>
10937 <td>18/18/6</td>
10938 </tr>
10939 <tr>
10940 <td>Gap extend</td>
10941 <td>1</td>
10942 </tr>
10943 <tr>
10944 <td>SS matrix</td>
10945 <td>
10946 <table>
10947 <tr>
10948 <th></th> <th>H</th> <th>S</th> <th>O</th>
10949 </tr>
10950 <tr>
10951 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
10952 </tr>
10953 <tr>
10954 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
10955 </tr>
10956 <tr>
10957 <th>O</th> <td></td> <td></td> <td align="right">4</td>
10958 </tr>
10959 </table>
10960 </td>
10961 </tr>
10962
10963 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
10964 </table>
10965 <br/>Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with 9gbu, chain A (#8), sequence alignment score = 2453.1<br>
10966Alignment identifier is 6<br>
10967Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 6<br>
10968Hiding conservation header for alignment 6<br>
10969Chains used in RMSD evaluation for alignment 6: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, 9gbu #8/A<br>
10970Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 6<br>
10971RMSD between 469 pruned atom pairs is 0.356 angstroms; (across all 475 pairs: 0.810)<br>
10972<br>
10973<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/B">select #8/B</a></div></div>7543 atoms, 7548 bonds, 24 pseudobonds, 577 residues, 2 models selected<br>
10974<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #7 &quot;DdHydAB_L2 9gnk&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #7 &quot;DdHydAB_L2 9gnk&quot;">rename #7 &quot;DdHydAB_L2 9gnk&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #8 &quot;DdHydAB_L3 9gbu&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #8 &quot;DdHydAB_L3 9gbu&quot;">rename #8 &quot;DdHydAB_L3 9gbu&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :PG4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :PG4">select :PG4</a></div></div>179 atoms, 172 bonds, 7 residues, 2 models selected<br>
10975<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!7 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!7 atoms">hide sel &amp; #!7 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :MPD</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :MPD">select :MPD</a></div></div>132 atoms, 126 bonds, 6 residues, 1 model selected<br>
10976<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :HOH</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :HOH">select :HOH</a></div></div>3198 atoms, 3198 residues, 5 models selected<br>
10977<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!7-8 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!7-8 atoms">hide sel &amp; #!7-8 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8">select #8</a></div></div>15143 atoms, 15112 bonds, 48 pseudobonds, 1193 residues, 2 models selected<br>
10978<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel plum</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel plum">color sel plum</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel magenta</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel magenta">color sel magenta</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :PG4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :PG4">select :PG4</a></div></div>179 atoms, 172 bonds, 7 residues, 2 models selected<br>
10979<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> :PG4,HOH</div><div class="cxcmd_as_cmd"><a href="cxcmd:select :PG4,HOH">select :PG4,HOH</a></div></div>3377 atoms, 172 bonds, 3205 residues, 5 models selected<br>
10980<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel &amp; #!4,6-8 atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel &amp; #!4,6-8 atoms">hide sel &amp; #!4,6-8 atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #4/A to #3/A pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #4/A to #3/A pairing ss showAlignment true">matchmaker #4/A to #3/A pairing ss showAlignment true</a></div></div>
10981 <table border=1 cellpadding=4 cellspacing=0>
10982 <tr>
10983 <th colspan="2">Parameters</th>
10984 </tr>
10985 <tr>
10986 <td>Chain pairing</td>
10987 <td>ss</td>
10988 </tr>
10989 <tr>
10990 <td>Alignment algorithm</td>
10991 <td>Needleman-Wunsch</td>
10992 </tr>
10993 <tr>
10994 <td>Similarity matrix</td>
10995 <td>BLOSUM-62</td>
10996 </tr>
10997
10998 <tr>
10999 <td>SS fraction</td>
11000 <td>0.3</td>
11001 </tr>
11002 <tr>
11003 <td>Gap open (HH/SS/other)</td>
11004 <td>18/18/6</td>
11005 </tr>
11006 <tr>
11007 <td>Gap extend</td>
11008 <td>1</td>
11009 </tr>
11010 <tr>
11011 <td>SS matrix</td>
11012 <td>
11013 <table>
11014 <tr>
11015 <th></th> <th>H</th> <th>S</th> <th>O</th>
11016 </tr>
11017 <tr>
11018 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
11019 </tr>
11020 <tr>
11021 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
11022 </tr>
11023 <tr>
11024 <th>O</th> <td></td> <td></td> <td align="right">4</td>
11025 </tr>
11026 </table>
11027 </td>
11028 </tr>
11029
11030 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
11031 </table>
11032 <br/>Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with CrHydA1 3lx4, chain A (#4), sequence alignment score = 943.4<br>
11033Alignment identifier is 2<br>
11034Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 2<br>
11035Hiding conservation header for alignment 2<br>
11036Chains used in RMSD evaluation for alignment 2: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, CrHydA1 3lx4 #4/A<br>
11037Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 2<br>
11038RMSD between 268 pruned atom pairs is 1.062 angstroms; (across all 361 pairs: 3.707)<br>
11039<br>
11040<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #4/A to #3/A pairing ss showAlignment true</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #4/A to #3/A pairing ss showAlignment true">matchmaker #4/A to #3/A pairing ss showAlignment true</a></div></div>
11041 <table border=1 cellpadding=4 cellspacing=0>
11042 <tr>
11043 <th colspan="2">Parameters</th>
11044 </tr>
11045 <tr>
11046 <td>Chain pairing</td>
11047 <td>ss</td>
11048 </tr>
11049 <tr>
11050 <td>Alignment algorithm</td>
11051 <td>Needleman-Wunsch</td>
11052 </tr>
11053 <tr>
11054 <td>Similarity matrix</td>
11055 <td>BLOSUM-62</td>
11056 </tr>
11057
11058 <tr>
11059 <td>SS fraction</td>
11060 <td>0.3</td>
11061 </tr>
11062 <tr>
11063 <td>Gap open (HH/SS/other)</td>
11064 <td>18/18/6</td>
11065 </tr>
11066 <tr>
11067 <td>Gap extend</td>
11068 <td>1</td>
11069 </tr>
11070 <tr>
11071 <td>SS matrix</td>
11072 <td>
11073 <table>
11074 <tr>
11075 <th></th> <th>H</th> <th>S</th> <th>O</th>
11076 </tr>
11077 <tr>
11078 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
11079 </tr>
11080 <tr>
11081 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
11082 </tr>
11083 <tr>
11084 <th>O</th> <td></td> <td></td> <td align="right">4</td>
11085 </tr>
11086 </table>
11087 </td>
11088 </tr>
11089
11090 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
11091 </table>
11092 <br/>Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#3) with CrHydA1 3lx4, chain A (#4), sequence alignment score = 943.4<br>
11093Alignment identifier is 7<br>
11094Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 7<br>
11095Hiding conservation header for alignment 7<br>
11096Chains used in RMSD evaluation for alignment 7: fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, CrHydA1 3lx4 #4/A<br>
11097Showing rmsd header (&quot;seq_rmsd&quot; residue attribute) for alignment 7<br>
11098RMSD between 268 pruned atom pairs is 1.062 angstroms; (across all 361 pairs: 3.707)<br>
11099<br>
11100<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:392">select #3/A:392</a></div></div>7 atoms, 6 bonds, 1 residue, 1 model selected<br>
11101<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:392-393 #4/A:391-392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:392-393 #4/A:391-392">select #3/A:392-393 #4/A:391-392</a></div></div>30 atoms, 28 bonds, 4 residues, 2 models selected<br>
11102MatchMaker Alignment [ID: 7] region chain A..chain A [451-452] RMSD: 1.147<br>
11103<br>
11104<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> All_H2ases</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name All_H2ases">view name All_H2ases</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:392">select #3/A:392</a></div></div>7 atoms, 6 bonds, 1 residue, 1 model selected<br>
11105<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:392-393 #4/A:391-392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:392-393 #4/A:391-392">select #3/A:392-393 #4/A:391-392</a></div></div>30 atoms, 28 bonds, 4 residues, 2 models selected<br>
11106MatchMaker Alignment [ID: 2] region chain A..chain A [451-452] RMSD: 1.147<br>
11107<br>
11108<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> All_H2ases</div><div class="cxcmd_as_cmd"><a href="cxcmd:view All_H2ases">view All_H2ases</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.6/F:2153-2156 #3/A:389-395</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.6/F:2153-2156 #3/A:389-395">select #2.6/F:2153-2156 #3/A:389-395</a></div></div>112 atoms, 112 bonds, 11 residues, 2 models selected<br>
11109MatchMaker Alignment [ID: 4] region chain F..chain A [392-398] RMSD: 7.546<br>
11110<br>
11111<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #1.1.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #1.1.3 models">show #1.1.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.1.3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.1.3 models">hide #1.1.3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> PsaC_interface</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name PsaC_interface">view name PsaC_interface</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures and designs/PSI_DdH2ase dock design with all single chains variants.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Wed Oct 29 10:26:11 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
11112<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1.1 models">hide #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1.1 models">show #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
11113 <thead>
11114 <tr>
11115 <th colspan="2">Chain information for HydAB_TD_linker_model.cif #9</th>
11116 </tr>
11117 <tr>
11118 <th>Chain</th>
11119 <th>Description</th>
11120
11121 </tr>
11122 </thead>
11123 <tbody>
11124 <tr>
11125 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9/A:1-477">A</a></td>
11126 <td><a title="Show sequence" href="cxcmd:sequence chain #9/A">.</a></td>
11127
11128 </tr>
11129 </tbody>
11130</table><br/><p style="color:#ffb961">No chain in structure corresponds to chain ID given in local score info (chain &#x27;B&#x27;)<br>
11131</p>Associated HydAB_TD_linker_model.cif chain A to chain L with 25 mismatches<br>
11132Associated HydAB_TD_linker_model.cif chain A to chain A with 0 mismatches<br>
11133[Repeated 4 time(s)]Computing secondary structure<br>
11134<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #9 HydAB_TD_linker_model_MSA.cif</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #9 HydAB_TD_linker_model_MSA.cif">rename #9 HydAB_TD_linker_model_MSA.cif</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
11135 <thead>
11136 <tr>
11137 <th colspan="2">Chain information for HydAB_TD_linker_model.cif #10</th>
11138 </tr>
11139 <tr>
11140 <th>Chain</th>
11141 <th>Description</th>
11142
11143 </tr>
11144 </thead>
11145 <tbody>
11146 <tr>
11147 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10/A:1-477">A</a></td>
11148 <td><a title="Show sequence" href="cxcmd:sequence chain #10/A">.</a></td>
11149
11150 </tr>
11151 </tbody>
11152</table><br/><p style="color:#ffb961">No chain in structure corresponds to chain ID given in local score info (chain &#x27;B&#x27;)<br>
11153</p>Associated HydAB_TD_linker_model.cif chain A to chain L with 25 mismatches<br>
11154Associated HydAB_TD_linker_model.cif chain A to chain A with 0 mismatches<br>
11155[Repeated 4 time(s)]Computing secondary structure<br>
11156<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #10 HydAB_TD_linker_model_noMSA.cif</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #10 HydAB_TD_linker_model_noMSA.cif">rename #10 HydAB_TD_linker_model_noMSA.cif</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> AlphaFold</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show AlphaFold">ui tool show AlphaFold</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;AlphaFold Error Plot&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;AlphaFold Error Plot&quot;">ui tool show &quot;AlphaFold Error Plot&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #9 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #9 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json&quot;">alphafold pae #9 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#byattribute">color bfactor</a> #9 palette alphafold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color bfactor #9 palette alphafold">color bfactor #9 palette alphafold</a></div></div>3720 atoms, 481 residues, atom bfactor range 41.5 to 99<br>
11157<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;AlphaFold Error Plot&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;AlphaFold Error Plot&quot;">ui tool show &quot;AlphaFold Error Plot&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json&quot;">alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#byattribute">color bfactor</a> #10 palette alphafold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color bfactor #10 palette alphafold">color bfactor #10 palette alphafold</a></div></div>3720 atoms, 481 residues, atom bfactor range 13.2 to 97<br>
11158<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;AlphaFold Error Plot&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;AlphaFold Error Plot&quot;">ui tool show &quot;AlphaFold Error Plot&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #9 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #9 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json&quot;">alphafold pae #9 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#byattribute">color bfactor</a> #9 palette alphafold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color bfactor #9 palette alphafold">color bfactor #9 palette alphafold</a></div></div>3720 atoms, 481 residues, atom bfactor range 41.5 to 99<br>
11159<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#byattribute">color bfactor</a> #9 palette alphafold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color bfactor #9 palette alphafold">color bfactor #9 palette alphafold</a></div></div>3720 atoms, 481 residues, atom bfactor range 41.5 to 99<br>
11160<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!9-10 to #2.6</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!9-10 to #2.6">matchmaker #!9-10 to #2.6</a></div></div>
11161 <table border=1 cellpadding=4 cellspacing=0>
11162 <tr>
11163 <th colspan="2">Parameters</th>
11164 </tr>
11165 <tr>
11166 <td>Chain pairing</td>
11167 <td>bb</td>
11168 </tr>
11169 <tr>
11170 <td>Alignment algorithm</td>
11171 <td>Needleman-Wunsch</td>
11172 </tr>
11173 <tr>
11174 <td>Similarity matrix</td>
11175 <td>BLOSUM-62</td>
11176 </tr>
11177
11178 <tr>
11179 <td>SS fraction</td>
11180 <td>0.3</td>
11181 </tr>
11182 <tr>
11183 <td>Gap open (HH/SS/other)</td>
11184 <td>18/18/6</td>
11185 </tr>
11186 <tr>
11187 <td>Gap extend</td>
11188 <td>1</td>
11189 </tr>
11190 <tr>
11191 <td>SS matrix</td>
11192 <td>
11193 <table>
11194 <tr>
11195 <th></th> <th>H</th> <th>S</th> <th>O</th>
11196 </tr>
11197 <tr>
11198 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
11199 </tr>
11200 <tr>
11201 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
11202 </tr>
11203 <tr>
11204 <th>O</th> <td></td> <td></td> <td align="right">4</td>
11205 </tr>
11206 </table>
11207 </td>
11208 </tr>
11209
11210 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
11211 </table>
11212 <br/>Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with HydAB_TD_linker_model_MSA.cif, chain A (#9), sequence alignment score = 2218.3<br>
11213RMSD between 458 pruned atom pairs is 0.496 angstroms; (across all 470 pairs: 1.251)<br>
11214<br>
11215Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with HydAB_TD_linker_model_noMSA.cif, chain A (#10), sequence alignment score = 1834.3<br>
11216RMSD between 35 pruned atom pairs is 1.452 angstroms; (across all 470 pairs: 19.133)<br>
11217<br>
11218<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #9">select add #9</a></div></div>3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected<br>
11219<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10">select add #10</a></div></div>7552 atoms, 7744 bonds, 22 pseudobonds, 973 residues, 6 models selected<br>
11220<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #10">select subtract #10</a></div></div>3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected<br>
11221<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #9">select subtract #9</a></div></div>112 atoms, 112 bonds, 11 residues, 2 models selected<br>
11222<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #9">select add #9</a></div></div>3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected<br>
11223<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10">select add #10</a></div></div>7552 atoms, 7744 bonds, 22 pseudobonds, 973 residues, 6 models selected<br>
11224<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel &amp; #!10 byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel &amp; #!10 byhetero">color sel &amp; #!10 byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel &amp; #!9-10 byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel &amp; #!9-10 byhetero">color sel &amp; #!9-10 byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #9">select subtract #9</a></div></div>3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected<br>
11225<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #10">select subtract #10</a></div></div>112 atoms, 112 bonds, 11 residues, 2 models selected<br>
11226<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #3">select add #3</a></div></div>3735 atoms, 3828 bonds, 481 residues, 2 models selected<br>
11227<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #3">select subtract #3</a></div></div>58 atoms, 58 bonds, 4 residues, 1 model selected<br>
11228<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#list">view list</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:view list">view list</a></div></div>Named views: <a href="cxcmd:view All_H2ases">All_H2ases</a>, <a href="cxcmd:view PsaC_interface">PsaC_interface</a>, <a href="cxcmd:view coulSide">coulSide</a>, <a href="cxcmd:view session-start">session-start</a>, <a href="cxcmd:view viewH2ase">viewH2ase</a>, <a href="cxcmd:view viewH2aseHbonds">viewH2aseHbonds</a>, <a href="cxcmd:view zoom1">zoom1</a>, <a href="cxcmd:view zoom2">zoom2</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> zoom1</div><div class="cxcmd_as_cmd"><a href="cxcmd:view zoom1">view zoom1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> zoom2</div><div class="cxcmd_as_cmd"><a href="cxcmd:view zoom2">view zoom2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9:392-393</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9:392-393">select #9:392-393</a></div></div>15 atoms, 14 bonds, 2 residues, 1 model selected<br>
11229<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 15 atom styles<br>
11230<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 15 atom styles<br>
11231<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Selection Inspector&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Selection Inspector&quot;">ui tool show &quot;Selection Inspector&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/setattr.html">setattr</a> sel r ribbon_hide_backbone false</div><div class="cxcmd_as_cmd"><a href="cxcmd:setattr sel r ribbon_hide_backbone false">setattr sel r ribbon_hide_backbone false</a></div></div>Assigning ribbon_hide_backbone attribute to 2 items<br>
11232<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 15 atom styles<br>
11233<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel ball">style sel ball</a></div></div>Changed 15 atom styles<br>
11234<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel stick">style sel stick</a></div></div>Changed 15 atom styles<br>
11235<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime target cspf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime target cspf">color sel lime target cspf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> linkerZoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name linkerZoom">view name linkerZoom</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/B:392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/B:392">select #6/B:392</a></div></div>14 atoms, 14 bonds, 1 residue, 1 model selected<br>
11236<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/B:392-398</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/B:392-398">select #6/B:392-398</a></div></div>123 atoms, 123 bonds, 7 residues, 1 model selected<br>
11237<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime target cspf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime target cspf">color sel lime target cspf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9:392-393</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9:392-393">select #9:392-393</a></div></div>15 atoms, 14 bonds, 2 residues, 1 model selected<br>
11238<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:391</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:391">select #7/A:391</a></div></div>16 atoms, 15 bonds, 1 residue, 1 model selected<br>
11239<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:391-398</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:391-398">select #7/A:391-398</a></div></div>134 atoms, 134 bonds, 8 residues, 1 model selected<br>
11240<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:397-398</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:397-398">select #7/A:397-398</a></div></div>37 atoms, 36 bonds, 2 residues, 1 model selected<br>
11241<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:391-398</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:391-398">select #7/A:391-398</a></div></div>134 atoms, 134 bonds, 8 residues, 1 model selected<br>
11242<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:399-400</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:399-400">select #7/A:399-400</a></div></div>28 atoms, 27 bonds, 2 residues, 1 model selected<br>
11243<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #7/A:391-400</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #7/A:391-400">select #7/A:391-400</a></div></div>162 atoms, 162 bonds, 10 residues, 1 model selected<br>
11244<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime target cspf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime target cspf">color sel lime target cspf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:390">select #8/A:390</a></div></div>24 atoms, 23 bonds, 1 residue, 1 model selected<br>
11245<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:390-400</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:390-400">select #8/A:390-400</a></div></div>194 atoms, 195 bonds, 11 residues, 1 model selected<br>
11246<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:390">select #8/A:390</a></div></div>24 atoms, 23 bonds, 1 residue, 1 model selected<br>
11247<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402">select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402</a></div></div>469 atoms, 470 bonds, 43 residues, 4 models selected<br>
11248MatchMaker Alignment [ID: 6] region chain A..chain A [390-402] RMSD: 30.556<br>
11249<br>
11250<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:399 #9/A:399 #10/A:399</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:399 #9/A:399 #10/A:399">select #3/A:399 #9/A:399 #10/A:399</a></div></div>24 atoms, 21 bonds, 3 residues, 3 models selected<br>
11251<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:399-400 #9/A:399-400 #10/A:399-400</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:399-400 #9/A:399-400 #10/A:399-400">select #3/A:399-400 #9/A:399-400 #10/A:399-400</a></div></div>57 atoms, 54 bonds, 6 residues, 3 models selected<br>
11252MatchMaker Alignment [ID: 6] region chain A [402-403] RMSD: 34.950<br>
11253<br>
11254<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:390">select #8/A:390</a></div></div>24 atoms, 23 bonds, 1 residue, 1 model selected<br>
11255<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402">select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402</a></div></div>469 atoms, 470 bonds, 43 residues, 4 models selected<br>
11256MatchMaker Alignment [ID: 6] region chain A..chain A [390-402] RMSD: 30.556<br>
11257<br>
11258<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:390">select #8/A:390</a></div></div>24 atoms, 23 bonds, 1 residue, 1 model selected<br>
11259<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402">select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402</a></div></div>469 atoms, 470 bonds, 43 residues, 4 models selected<br>
11260MatchMaker Alignment [ID: 6] region chain A..chain A [390-402] RMSD: 30.556<br>
11261<br>
11262<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:390">select #8/A:390</a></div></div>24 atoms, 23 bonds, 1 residue, 1 model selected<br>
11263<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:390-400</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:390-400">select #8/A:390-400</a></div></div>194 atoms, 195 bonds, 11 residues, 1 model selected<br>
11264<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8:390-399</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8:390-399">select #8:390-399</a></div></div>344 atoms, 346 bonds, 20 residues, 1 model selected<br>
11265<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8:390-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8:390-402">select #8:390-402</a></div></div>440 atoms, 442 bonds, 26 residues, 1 model selected<br>
11266<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime target cspf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime target cspf">color sel lime target cspf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:392 #9/A:392 #10/A:392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:392 #9/A:392 #10/A:392">select #3/A:392 #9/A:392 #10/A:392</a></div></div>21 atoms, 18 bonds, 3 residues, 3 models selected<br>
11267<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #3/A:392-393 #9/A:392-393 #10/A:392-393 #8/A:395-396</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #3/A:392-393 #9/A:392-393 #10/A:392-393 #8/A:395-396">select #3/A:392-393 #9/A:392-393 #10/A:392-393 #8/A:395-396</a></div></div>78 atoms, 74 bonds, 8 residues, 4 models selected<br>
11268MatchMaker Alignment [ID: 6] region chain A..chain A [395-396] RMSD: 30.689<br>
11269<br>
11270<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:392">select #8/A:392</a></div></div>22 atoms, 21 bonds, 1 residue, 1 model selected<br>
11271<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #8/A:392-396</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #8/A:392-396">select #8/A:392-396</a></div></div>88 atoms, 88 bonds, 5 residues, 1 model selected<br>
11272<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #10 id 11</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #10 id 11">rename #10 id 11</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
11273 <thead>
11274 <tr>
11275 <th colspan="2">Chain information for HydAB_PSI_Interface_model.cif #10</th>
11276 </tr>
11277 <tr>
11278 <th>Chain</th>
11279 <th>Description</th>
11280
11281 </tr>
11282 </thead>
11283 <tbody>
11284 <tr>
11285 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10/A:1-473">A</a></td>
11286 <td><a title="Show sequence" href="cxcmd:sequence chain #10/A">.</a></td>
11287
11288 </tr>
11289 </tbody>
11290</table><br/><p style="color:#ffb961">No chain in structure corresponds to chain ID given in local score info (chain &#x27;B&#x27;)<br>
11291</p>Associated HydAB_PSI_Interface_model.cif chain A to chain F with 0 mismatches<br>
11292[Repeated 1 time(s)]Computing secondary structure<br>
11293<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #10 HydAB_PSI_Interface_model_MSA.cif</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #10 HydAB_PSI_Interface_model_MSA.cif">rename #10 HydAB_PSI_Interface_model_MSA.cif</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
11294 <thead>
11295 <tr>
11296 <th colspan="2">Chain information for HydAB_PSI_Interface_model.cif #12</th>
11297 </tr>
11298 <tr>
11299 <th>Chain</th>
11300 <th>Description</th>
11301
11302 </tr>
11303 </thead>
11304 <tbody>
11305 <tr>
11306 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #12/A:1-473">A</a></td>
11307 <td><a title="Show sequence" href="cxcmd:sequence chain #12/A">.</a></td>
11308
11309 </tr>
11310 </tbody>
11311</table><br/><p style="color:#ffb961">No chain in structure corresponds to chain ID given in local score info (chain &#x27;B&#x27;)<br>
11312</p>Associated HydAB_PSI_Interface_model.cif chain A to chain F with 0 mismatches<br>
11313[Repeated 1 time(s)]Computing secondary structure<br>
11314<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!12 models">show #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;AlphaFold Error Plot&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;AlphaFold Error Plot&quot;">ui tool show &quot;AlphaFold Error Plot&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;">alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;</a></div></div><font color="crimson"><b>Structure HydAB_PSI_Interface_model_MSA.cif #10 does not match PAE matrix size 516.The structure has 461 polymer residues and 91 non-polymer atoms<br>
11315<br>
11316This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error.<br>
11317</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;">alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;</a></div></div><font color="crimson"><b>Structure HydAB_PSI_Interface_model_MSA.cif #10 does not match PAE matrix size 516.The structure has 461 polymer residues and 91 non-polymer atoms<br>
11318<br>
11319This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error.<br>
11320</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;">alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;</a></div></div><font color="crimson"><b>Structure HydAB_PSI_Interface_model_MSA.cif #10 does not match PAE matrix size 516.The structure has 461 polymer residues and 91 non-polymer atoms<br>
11321<br>
11322This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error.<br>
11323</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_summary_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_summary_confidences.json&quot;">alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_summary_confidences.json&quot;</a></div></div><font color="crimson"><b>JSON file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_summary_confidences.json&quot; is not AlphaFold predicted aligned error data, expected a top level list<br>
11324</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/seed-78674_sample-0/HydAB_PSI_Interface_seed-78674_sample-0_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/seed-78674_sample-0/HydAB_PSI_Interface_seed-78674_sample-0_confidences.json&quot;">alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/seed-78674_sample-0/HydAB_PSI_Interface_seed-78674_sample-0_confidences.json&quot;</a></div></div><font color="crimson"><b>Structure HydAB_PSI_Interface_model_MSA.cif #10 does not match PAE matrix size 516.The structure has 461 polymer residues and 91 non-polymer atoms<br>
11325<br>
11326This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error.<br>
11327</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #12 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #12 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;">alphafold pae #12 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json&quot;</a></div></div><font color="crimson"><b>Structure HydAB_PSI_Interface_model.cif #12 does not match PAE matrix size 516.The structure has 461 polymer residues and 91 non-polymer atoms<br>
11328<br>
11329This can happen if chains or atoms were deleted from the AlphaFold model or if the PAE data was applied to a structure that was not the one predicted by AlphaFold. Use the full-length AlphaFold model to show predicted aligned error.<br>
11330</b></font><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!10,12 to #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!10,12 to #9">matchmaker #!10,12 to #9</a></div></div>
11331 <table border=1 cellpadding=4 cellspacing=0>
11332 <tr>
11333 <th colspan="2">Parameters</th>
11334 </tr>
11335 <tr>
11336 <td>Chain pairing</td>
11337 <td>bb</td>
11338 </tr>
11339 <tr>
11340 <td>Alignment algorithm</td>
11341 <td>Needleman-Wunsch</td>
11342 </tr>
11343 <tr>
11344 <td>Similarity matrix</td>
11345 <td>BLOSUM-62</td>
11346 </tr>
11347
11348 <tr>
11349 <td>SS fraction</td>
11350 <td>0.3</td>
11351 </tr>
11352 <tr>
11353 <td>Gap open (HH/SS/other)</td>
11354 <td>18/18/6</td>
11355 </tr>
11356 <tr>
11357 <td>Gap extend</td>
11358 <td>1</td>
11359 </tr>
11360 <tr>
11361 <td>SS matrix</td>
11362 <td>
11363 <table>
11364 <tr>
11365 <th></th> <th>H</th> <th>S</th> <th>O</th>
11366 </tr>
11367 <tr>
11368 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
11369 </tr>
11370 <tr>
11371 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
11372 </tr>
11373 <tr>
11374 <th>O</th> <td></td> <td></td> <td align="right">4</td>
11375 </tr>
11376 </table>
11377 </td>
11378 </tr>
11379
11380 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
11381 </table>
11382 <br/>Matchmaker HydAB_TD_linker_model_MSA.cif, chain A (#9) with HydAB_PSI_Interface_model_MSA.cif, chain A (#10), sequence alignment score = 2279.9<br>
11383RMSD between 455 pruned atom pairs is 0.339 angstroms; (across all 470 pairs: 1.307)<br>
11384<br>
11385Matchmaker HydAB_TD_linker_model_MSA.cif, chain A (#9) with HydAB_PSI_Interface_model.cif, chain A (#12), sequence alignment score = 1931.8<br>
11386RMSD between 100 pruned atom pairs is 0.836 angstroms; (across all 470 pairs: 23.291)<br>
11387<br>
11388<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #3 models">show #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #3 models">hide #3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10:cys</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10:cys">select #10:cys</a></div></div>36 atoms, 30 bonds, 6 residues, 1 model selected<br>
11389<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10:cys,unk</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10:cys,unk">select #10:cys,unk</a></div></div>84 atoms, 67 bonds, 18 residues, 1 model selected<br>
11390<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10:unk</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10:unk">select #10:unk</a></div></div>48 atoms, 36 bonds, 12 residues, 1 model selected<br>
11391<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel orange</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel orange">color sel orange</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel yellow</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel yellow">color sel yellow</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot;</a></div></div><p>&mdash;&mdash;&mdash; End of log from Wed Nov 5 11:09:20 2025 &mdash;&mdash;&mdash;</p></details><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> session-start</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name session-start">view name session-start</a></div></div>opened ChimeraX session<br>
11392<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #12 id 16</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #12 id 16">rename #12 id 16</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #11 id 15</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #11 id 15">rename #11 id 15</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #10 id 14</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #10 id 14">rename #10 id 14</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #9 id 11</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #9 id 11">rename #9 id 11</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 8ryh</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 8ryh">open 8ryh</a></div></div>
11393<table border=1 cellpadding=4 cellspacing=0>
11394 <thead>
11395 <tr>
11396 <th colspan="2">Summary of feedback from opening 8ryh fetched from pdb</th>
11397 </tr>
11398 </thead>
11399 <tbody>
11400 <tr>
11401 <td><i>warning</i></td> <td style="background-color:#ffb961">Atom HS2 is not in the residue template for 402 /A:504</td> </tr>
11402 </tbody>
11403</table><br/><i>8ryh</i> title:<br><b>Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of Veillonella atypica</b> <a href="cxcmd:log metadata #9">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
11404 <thead>
11405 <tr>
11406 <th colspan="3">Chain information for 8ryh #9</th>
11407 </tr>
11408 <tr>
11409 <th>Chain</th>
11410 <th>Description</th>
11411 <th>UniProt</th>
11412 </tr>
11413 </thead>
11414 <tbody>
11415 <tr>
11416 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #9/A:3-478">A</a></td>
11417 <td><a title="Show sequence" href="cxcmd:sequence chain #9/A">Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit</a></td>
11418 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P07598 from uniprot associate #9/A">PHFL_DESVH</a> <a title="Select sequence" href="cxcmd:select #9/A:1-389">1-389</a>, <a title="Show annotations" href="cxcmd:open P07603 from uniprot associate #9/A">PHFS_DESVH</a> <a title="Select sequence" href="cxcmd:select #9/A:403-480">403-480</a></td>
11419 </tr>
11420 </tbody>
11421</table><br/><table border=1 cellpadding=4 cellspacing=0>
11422 <thead>
11423 <tr>
11424 <th>Non-standard residues in 8ryh #9</th>
11425 </tr>
11426 </thead>
11427 <tbody>
11428 <tr>
11429 <td><a title="select residue" href="cxcmd:sel ::name=&quot;402&quot;">402</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/402">dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)</a></td>
11430 </tr>
11431 <tr>
11432 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
11433 </tr>
11434 </tbody>
11435</table><br/>41 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/>Associated 8ryh chain A to chain L with 30 mismatches<br>
11436Associated 8ryh chain A to chain A with 7 mismatches<br>
11437<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #9 &quot;DdHydAB_L4 8ryh&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #9 &quot;DdHydAB_L4 8ryh&quot;">rename #9 &quot;DdHydAB_L4 8ryh&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!9 to #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!9 to #8">matchmaker #!9 to #8</a></div></div>
11438 <table border=1 cellpadding=4 cellspacing=0>
11439 <tr>
11440 <th colspan="2">Parameters</th>
11441 </tr>
11442 <tr>
11443 <td>Chain pairing</td>
11444 <td>bb</td>
11445 </tr>
11446 <tr>
11447 <td>Alignment algorithm</td>
11448 <td>Needleman-Wunsch</td>
11449 </tr>
11450 <tr>
11451 <td>Similarity matrix</td>
11452 <td>BLOSUM-62</td>
11453 </tr>
11454
11455 <tr>
11456 <td>SS fraction</td>
11457 <td>0.3</td>
11458 </tr>
11459 <tr>
11460 <td>Gap open (HH/SS/other)</td>
11461 <td>18/18/6</td>
11462 </tr>
11463 <tr>
11464 <td>Gap extend</td>
11465 <td>1</td>
11466 </tr>
11467 <tr>
11468 <td>SS matrix</td>
11469 <td>
11470 <table>
11471 <tr>
11472 <th></th> <th>H</th> <th>S</th> <th>O</th>
11473 </tr>
11474 <tr>
11475 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
11476 </tr>
11477 <tr>
11478 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
11479 </tr>
11480 <tr>
11481 <th>O</th> <td></td> <td></td> <td align="right">4</td>
11482 </tr>
11483 </table>
11484 </td>
11485 </tr>
11486
11487 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
11488 </table>
11489 <br/>Matchmaker DdHydAB_L3 9gbu, chain A (#8) with DdHydAB_L4 8ryh, chain A (#9), sequence alignment score = 2520.8<br>
11490RMSD between 468 pruned atom pairs is 0.433 angstroms; (across all 469 pairs: 0.443)<br>
11491<br>
11492<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/hHydAB_L4_linker_PDB_8ryh/hHydAB_L4_linker_PDB_8ryh_model.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/hHydAB_L4_linker_PDB_8ryh/hHydAB_L4_linker_PDB_8ryh_model.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/hHydAB_L4_linker_PDB_8ryh/hHydAB_L4_linker_PDB_8ryh_model.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
11493 <thead>
11494 <tr>
11495 <th colspan="2">Chain information for hHydAB_L4_linker_PDB_8ryh_model.cif #10</th>
11496 </tr>
11497 <tr>
11498 <th>Chain</th>
11499 <th>Description</th>
11500
11501 </tr>
11502 </thead>
11503 <tbody>
11504 <tr>
11505 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #10/A:1-490">A</a></td>
11506 <td><a title="Show sequence" href="cxcmd:sequence chain #10/A">.</a></td>
11507
11508 </tr>
11509 </tbody>
11510</table><br/><p style="color:#ffb961">No chain in structure corresponds to chain ID given in local score info (chain &#x27;B&#x27;)<br>
11511</p>Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to chain L with 30 mismatches<br>
11512Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to chain A with 7 mismatches<br>
11513Computing secondary structure<br>
11514<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;AlphaFold Error Plot&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;AlphaFold Error Plot&quot;">ui tool show &quot;AlphaFold Error Plot&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 id 13</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 id 13">rename #3 id 13</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #11 id 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #11 id 3">rename #11 id 3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #3 id 11</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #3 id 11">rename #3 id 11</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #5 id #3</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #5 id #3">rename #5 id #3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!14 models">show #!14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2.7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2.7 models">hide #!2.7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #2.6.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #2.6.1 models">hide #2.6.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #2.6.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #2.6.1 models">show #2.6.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #2 DdHyd_PSI_interface_opt</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #2 DdHyd_PSI_interface_opt">rename #2 DdHyd_PSI_interface_opt</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #4 id #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #4 id #5">rename #4 id #5</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #11 id #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #11 id #4">rename #11 id #4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!14 models">hide #!14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:2152-2156</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:2152-2156">select #2:2152-2156</a></div></div>65 atoms, 65 bonds, 5 residues, 1 model selected<br>
11515<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime target cspf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime target cspf">color sel lime target cspf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!3 models">show #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #5</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #5">select add #5</a></div></div>7032 atoms, 6379 bonds, 14 pseudobonds, 1600 residues, 5 models selected<br>
11516<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light salmon</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light salmon">color sel light salmon</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel gainsboro</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel gainsboro">color sel gainsboro</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel plum</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel plum">color sel plum</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel &amp; #!5 byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel &amp; #!5 byhetero">color sel &amp; #!5 byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!3 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!3 models">hide #!3 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #5:391-392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #5:391-392">select #5:391-392</a></div></div>30 atoms, 28 bonds, 4 residues, 1 model selected<br>
11517<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime">color sel lime</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel plum target aspf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel plum target aspf">color sel plum target aspf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/hHydAB_L4_linker_PDB_8ryh/hHydAB_L4_linker_PDB_8ryh_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/hHydAB_L4_linker_PDB_8ryh/hHydAB_L4_linker_PDB_8ryh_confidences.json&quot;">alphafold pae #10 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/hHydAB_L4_linker_PDB_8ryh/hHydAB_L4_linker_PDB_8ryh_confidences.json&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#byattribute">color bfactor</a> #10 palette alphafold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color bfactor #10 palette alphafold">color bfactor #10 palette alphafold</a></div></div>3825 atoms, 494 residues, atom bfactor range 17.3 to 99<br>
11518<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #!10 to #9</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #!10 to #9">matchmaker #!10 to #9</a></div></div>
11519 <table border=1 cellpadding=4 cellspacing=0>
11520 <tr>
11521 <th colspan="2">Parameters</th>
11522 </tr>
11523 <tr>
11524 <td>Chain pairing</td>
11525 <td>bb</td>
11526 </tr>
11527 <tr>
11528 <td>Alignment algorithm</td>
11529 <td>Needleman-Wunsch</td>
11530 </tr>
11531 <tr>
11532 <td>Similarity matrix</td>
11533 <td>BLOSUM-62</td>
11534 </tr>
11535
11536 <tr>
11537 <td>SS fraction</td>
11538 <td>0.3</td>
11539 </tr>
11540 <tr>
11541 <td>Gap open (HH/SS/other)</td>
11542 <td>18/18/6</td>
11543 </tr>
11544 <tr>
11545 <td>Gap extend</td>
11546 <td>1</td>
11547 </tr>
11548 <tr>
11549 <td>SS matrix</td>
11550 <td>
11551 <table>
11552 <tr>
11553 <th></th> <th>H</th> <th>S</th> <th>O</th>
11554 </tr>
11555 <tr>
11556 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
11557 </tr>
11558 <tr>
11559 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
11560 </tr>
11561 <tr>
11562 <th>O</th> <td></td> <td></td> <td align="right">4</td>
11563 </tr>
11564 </table>
11565 </td>
11566 </tr>
11567
11568 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
11569 </table>
11570 <br/>Matchmaker DdHydAB_L4 8ryh, chain A (#9) with hHydAB_L4_linker_PDB_8ryh_model.cif, chain A (#10), sequence alignment score = 2532.7<br>
11571RMSD between 468 pruned atom pairs is 0.400 angstroms; (across all 469 pairs: 0.426)<br>
11572<br>
11573<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10">select add #10</a></div></div>3855 atoms, 3954 bonds, 11 pseudobonds, 498 residues, 3 models selected<br>
11574<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel &amp; #!10 byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel &amp; #!10 byhetero">color sel &amp; #!10 byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #10">select subtract #10</a></div></div>30 atoms, 28 bonds, 4 residues, 1 model selected<br>
11575<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #9/A #10/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #9/A #10/A">sequence chain #9/A #10/A</a></div></div>Alignment identifier is 1<br>
11576<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/A:402 #10/A:402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/A:402 #10/A:402">select #9/A:402 #10/A:402</a></div></div>15 atoms, 13 bonds, 2 residues, 2 models selected<br>
11577<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/A:386-402 #10/A:386-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/A:386-402 #10/A:386-402">select #9/A:386-402 #10/A:386-402</a></div></div>270 atoms, 270 bonds, 1 pseudobond, 27 residues, 3 models selected<br>
11578Periplasmic [Fe] Hydrogenase Large subunit,Periplasmic [Fe] Hydrogenase Small Subunit [ID: 1] region 2 chains [386-402] RMSD: 1.363<br>
11579<br>
11580<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/A:390 #10/A:390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/A:390 #10/A:390">select #9/A:390 #10/A:390</a></div></div>35 atoms, 33 bonds, 2 residues, 2 models selected<br>
11581<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #9/A:390-402 #10/A:390-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #9/A:390-402 #10/A:390-402">select #9/A:390-402 #10/A:390-402</a></div></div>201 atoms, 199 bonds, 1 pseudobond, 19 residues, 3 models selected<br>
11582Periplasmic [Fe] Hydrogenase Large subunit,Periplasmic [Fe] Hydrogenase Small Subunit [ID: 1] region 2 chains [390-402] RMSD: 1.756<br>
11583<br>
11584<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel lime target cspf</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel lime target cspf">color sel lime target cspf</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #10:390-402</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #10:390-402">select #10:390-402</a></div></div>102 atoms, 102 bonds, 13 residues, 1 model selected<br>
11585<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!16 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!16 models">show #!16 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!16 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!16 models">hide #!16 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!14 models">show #!14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!14 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!14 models">hide #!14 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/toolshed.html#show">toolshed show</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:toolshed show">toolshed show</a></div></div>Alignment identifier is 1.1/A<br>
11586Alignment identifier is 1.1/B<br>
11587Alignment identifier is 1.1/C<br>
11588Alignment identifier is 1.1/D<br>
11589Alignment identifier is 1.1/E<br>
11590Alignment identifier is 2.6/F<br>
11591Alignment identifier is 6/B<br>
11592Alignment identifier is 7/A<br>
11593Alignment identifier is 3<br>
11594Alignment identifier is 5<br>
11595Alignment identifier is 7<br>
11596Alignment identifier is 8<br>
11597Alignment identifier is 9<br>
11598Alignment identifier is 10<br>
11599Alignment identifier is 11<br>
11600<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">16,4,5,6,7,8,9</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">#16/A,#4-9/A</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> /A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align /A">sequence align /A</a></div></div>Alignment identifier is 1<br>
11601Associated DdHyd_PSI.opt.chains no DdHyd (1.1) chain A to #1.1/A with 0 mismatches<br>
11602Associated DdHyd_PSI.opt.chains (2.6) chain F to #16/A with 12 mismatches<br>
11603Associated DdHydAB_L2 9gnk chain A to #7/A with 0 mismatches<br>
11604Associated DdHydAB_L3 9gbu chain A to #8/A with 0 mismatches<br>
11605Associated DdHydAB_L3 9gbu chain B to #8/A with 0 mismatches<br>
11606Associated HydAB_PSI_Interface_model.cif chain A to #16/A with 0 mismatches<br>
11607Associated HydAB_TD_linker_model_noMSA.cif chain A to #15/A with 0 mismatches<br>
11608Associated HydAB_PSI_Interface_model_MSA.cif chain A to #16/A with 0 mismatches<br>
11609Associated DdHydAB_L4 8ryh chain A to #10/A with 0 mismatches<br>
11610Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to #10/A with 0 mismatches<br>
11611Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to #15/A with 0 mismatches<br>
11612Associated DdHydAHydB 1hfe chain L to #4/A with 25 mismatches<br>
11613Associated DdHydAHydB 1hfe chain M to #4/A with 25 mismatches<br>
11614Associated CrHydA1 3lx4 chain A to #5/A with 0 mismatches<br>
11615Associated CrHydA1 3lx4 chain B to #5/A with 0 mismatches<br>
11616Associated HydAB_TD_linker_model_MSA.cif chain A to #4/A with 0 mismatches<br>
11617Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
11618Webservices job id: NZ6M9RRWIFCG5ZGZ<br>
11619Webservices job finished: NZ6M9RRWIFCG5ZGZ<br>
11620<p style="color:#ffb961">Populating font family aliases took 225 ms. Replace uses of missing font family &quot;Times&quot; with one that exists to avoid this cost. <br>
11621</p><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/help.html">help</a> help:user</div><div class="cxcmd_as_cmd"><a href="cxcmd:help help:user">help help:user</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #4">select add #4</a></div></div>3720 atoms, 3816 bonds, 11 pseudobonds, 481 residues, 2 models selected<br>
11622<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #6</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #6">select add #6</a></div></div>11777 atoms, 11489 bonds, 36 pseudobonds, 1453 residues, 4 models selected<br>
11623<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #7</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #7">select add #7</a></div></div>19934 atoms, 19195 bonds, 60 pseudobonds, 2493 residues, 6 models selected<br>
11624<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #8</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #8">select add #8</a></div></div>35077 atoms, 34307 bonds, 108 pseudobonds, 3686 residues, 8 models selected<br>
11625<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #10</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #10">select add #10</a></div></div>38902 atoms, 38233 bonds, 119 pseudobonds, 4180 residues, 10 models selected<br>
11626Alignment identifier is 6/B<br>
11627Alignment identifier is 7/A<br>
11628Alignment identifier is 1<br>
11629Alignment identifier is 10/A<br>
11630Alignment identifier is 4/A<br>
11631<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #4/A">sequence chain #4/A</a></div></div>Alignment identifier is 4/A<br>
11632<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #4/D:1@FE3</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #4/D:1@FE3">select #4/D:1@FE3</a></div></div>1 atom, 1 residue, 1 model selected<br>
11633<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/cofr.html">cofr</a> sel</div><div class="cxcmd_as_cmd"><a href="cxcmd:cofr sel">cofr sel</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #4/A </div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #4/A ">sequence chain #4/A </a></div></div>Destroying pre-existing alignment with identifier 4/A<br>
11634Alignment identifier is 4/A<br>
11635<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #4-5/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #4-5/A">sequence chain #4-5/A</a></div></div><font color="crimson"><b>Chains must have same sequence</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #4/A#5/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #4/A#5/A">sequence chain #4/A#5/A</a></div></div><font color="crimson"><b>Chains must have same sequence</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #4/A #5/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #4/A #5/A">sequence chain #4/A #5/A</a></div></div><font color="crimson"><b>Chains must have same sequence</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #4/A">sequence chain #4/A</a></div></div>Alignment identifier is 4/A<br>
11636<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #6/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #6/A">sequence chain #6/A</a></div></div><font color="crimson"><b>Chains must have same sequence</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #6/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #6/B">sequence chain #6/B</a></div></div>Alignment identifier is 6/B<br>
11637<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #7/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #7/A">sequence chain #7/A</a></div></div>Alignment identifier is 7/A<br>
11638<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #8/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #8/A">sequence chain #8/A</a></div></div>Alignment identifier is 8/A<br>
11639<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #10/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #10/A">sequence chain #10/A</a></div></div>Alignment identifier is 10/A<br>
11640<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #16/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #16/A">sequence chain #16/A</a></div></div>Alignment identifier is 16/A<br>
11641<div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">id:4/A,id:6/b,id:7/A,id:8/A,id:10/A,id:16/A</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">id:4/A id:6/b id:7/A id:8/A id:10/A id:16/A</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">ID:4/A ID:6/B ID:7/A ID:8/A ID:10/A ID:16/A</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">ID:4</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 4</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 4">sequence align 4</a></div></div><font color="crimson"><b>Must specify 2 or more protein sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">4,6</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> 4 <span style="background-color:crimson;">6</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">4,6</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">ID:4,ID:6</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">[ID:4],[ID:6]</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">[ID:4/A],[ID:6/B]</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">[ID: 4/A],[ID: 6/B]</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">ID: 4/A,ID: 6/B</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">ID: 4, ID: 6</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">ID:4, ID:6</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> /Users/drornoy/Downloads/rcsb_pdb_8RYH.fasta</div><div class="cxcmd_as_cmd"><a href="cxcmd:open /Users/drornoy/Downloads/rcsb_pdb_8RYH.fasta">open /Users/drornoy/Downloads/rcsb_pdb_8RYH.fasta</a></div></div>
11642<table border=1 cellpadding=4 cellspacing=0>
11643 <thead>
11644 <tr>
11645 <th colspan="2">Summary of feedback from opening /Users/drornoy/Downloads/rcsb_pdb_8RYH.fasta</th>
11646 </tr>
11647 </thead>
11648 <tbody>
11649 <tr>
11650 <td><i>notes</i></td> <td style="background-color:Canvas">Alignment identifier is rcsb_pdb_8RYH.fasta<br>Associated DdHydAB_L3 9gbu chain A to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 7 mismatches<br>Associated DdHydAB_L3 9gbu chain B to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 7 mismatches<br>Associated DdHydAB_L4 8ryh chain A to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 0 mismatches<br>Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 0 mismatches<br>Associated DdHydAHydB 1hfe chain L to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 30 mismatches<br>Associated DdHydAHydB 1hfe chain M to 8RYH_1|Chain A|Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit|Desulfovibrio desulfuricans (876) with 30 mismatches</td> </tr>
11651 </tbody>
11652</table><br/>Opened 1 sequence from rcsb_pdb_8RYH.fasta<br>
11653<div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">4/A,6/B</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">4,6</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> 4/A <span style="background-color:crimson;">, 6/A</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> 4/A <span style="background-color:crimson;">6/A</span></div><font color="crimson"><b>Expected a keyword</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 4/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 4/A">sequence align 4/A</a></div></div><font color="crimson"><b>Must specify 2 or more protein sequences</b></font><br/><div class="cxcmd"><a href="help:user/commands/sequence.html#align">sequence align</a> <span style="background-color:crimson;">4/A,6/B</span></div><font color="crimson"><b>Missing or invalid &quot;seqSource&quot; argument: Expected alignment-id or sequences</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 4/A:1,6/B:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 4/A:1,6/B:1">sequence align 4/A:1,6/B:1</a></div></div>Alignment identifier is 1<br>
11654Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches<br>
11655Associated HydAB_TD_linker_model_noMSA.cif chain A to chain A with 0 mismatches<br>
11656Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to chain A with 0 mismatches<br>
11657Associated DdHydAHydB 1hfe chain L to chain A with 25 mismatches<br>
11658Associated DdHydAHydB 1hfe chain M to chain A with 25 mismatches<br>
11659Associated HydAB_TD_linker_model_MSA.cif chain A to chain A with 0 mismatches<br>
11660Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
11661Webservices job id: EQFV5H4VRVP51OI6<br>
11662Webservices job finished: EQFV5H4VRVP51OI6<br>
11663<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1">sequence align 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1</a></div></div>Traceback (most recent call last):<br>
11664&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
11665&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
11666&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
11667&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
11668&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11669&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 500, in seqalign_align<br>
11670&nbsp;&nbsp;&nbsp;&nbsp;input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)<br>
11671&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11672&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 476, in ensure_unique_seq_names<br>
11673&nbsp;&nbsp;&nbsp;&nbsp;renamed_seq.name = f&quot;{struct} {seq.name}&quot; if include_struct_name else f&quot;{seq.atomspec}&quot;<br>
11674&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^<br>
11675AttributeError: &#x27;StructureSeq&#x27; object has no attribute &#x27;atomspec&#x27;<br>
11676<br/>AttributeError: 'StructureSeq' object has no attribute 'atomspec'<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names<br> renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"<br> ^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 16/A:1,4/A:1,6/B:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 16/A:1,4/A:1,6/B:1">sequence align 16/A:1,4/A:1,6/B:1</a></div></div>Traceback (most recent call last):<br>
11677&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
11678&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
11679&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
11680&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
11681&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11682&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 500, in seqalign_align<br>
11683&nbsp;&nbsp;&nbsp;&nbsp;input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)<br>
11684&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11685&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 476, in ensure_unique_seq_names<br>
11686&nbsp;&nbsp;&nbsp;&nbsp;renamed_seq.name = f&quot;{struct} {seq.name}&quot; if include_struct_name else f&quot;{seq.atomspec}&quot;<br>
11687&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^<br>
11688AttributeError: &#x27;StructureSeq&#x27; object has no attribute &#x27;atomspec&#x27;<br>
11689<br/>AttributeError: 'StructureSeq' object has no attribute 'atomspec'<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names<br> renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"<br> ^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 16/A:1,4/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 16/A:1,4/A:1">sequence align 16/A:1,4/A:1</a></div></div>Traceback (most recent call last):<br>
11690&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
11691&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
11692&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
11693&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
11694&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11695&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 500, in seqalign_align<br>
11696&nbsp;&nbsp;&nbsp;&nbsp;input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)<br>
11697&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11698&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 476, in ensure_unique_seq_names<br>
11699&nbsp;&nbsp;&nbsp;&nbsp;renamed_seq.name = f&quot;{struct} {seq.name}&quot; if include_struct_name else f&quot;{seq.atomspec}&quot;<br>
11700&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^<br>
11701AttributeError: &#x27;StructureSeq&#x27; object has no attribute &#x27;atomspec&#x27;<br>
11702<br/>AttributeError: 'StructureSeq' object has no attribute 'atomspec'<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names<br> renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"<br> ^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 4/A:1,6/B:1,7/A:1,8/A:1,10/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 4/A:1,6/B:1,7/A:1,8/A:1,10/A:1">sequence align 4/A:1,6/B:1,7/A:1,8/A:1,10/A:1</a></div></div>Traceback (most recent call last):<br>
11703&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
11704&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
11705&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
11706&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
11707&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11708&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 500, in seqalign_align<br>
11709&nbsp;&nbsp;&nbsp;&nbsp;input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)<br>
11710&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11711&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 476, in ensure_unique_seq_names<br>
11712&nbsp;&nbsp;&nbsp;&nbsp;renamed_seq.name = f&quot;{struct} {seq.name}&quot; if include_struct_name else f&quot;{seq.atomspec}&quot;<br>
11713&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^<br>
11714AttributeError: &#x27;StructureSeq&#x27; object has no attribute &#x27;atomspec&#x27;<br>
11715<br/>AttributeError: 'StructureSeq' object has no attribute 'atomspec'<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names<br> renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"<br> ^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 4/A:1,6/B:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 4/A:1,6/B:1">sequence align 4/A:1,6/B:1</a></div></div>Alignment identifier is 1<br>
11716Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches<br>
11717Associated HydAB_TD_linker_model_noMSA.cif chain A to chain A with 0 mismatches<br>
11718Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to chain A with 0 mismatches<br>
11719Associated DdHydAHydB 1hfe chain L to chain A with 25 mismatches<br>
11720Associated DdHydAHydB 1hfe chain M to chain A with 25 mismatches<br>
11721Associated HydAB_TD_linker_model_MSA.cif chain A to chain A with 0 mismatches<br>
11722Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
11723Webservices job id: 2Z7P362WBNIJOMWR<br>
11724Webservices job finished: 2Z7P362WBNIJOMWR<br>
11725<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 7/A:1,8/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 7/A:1,8/A:1">sequence align 7/A:1,8/A:1</a></div></div>Traceback (most recent call last):<br>
11726&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
11727&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
11728&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
11729&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
11730&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11731&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 500, in seqalign_align<br>
11732&nbsp;&nbsp;&nbsp;&nbsp;input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)<br>
11733&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11734&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 476, in ensure_unique_seq_names<br>
11735&nbsp;&nbsp;&nbsp;&nbsp;renamed_seq.name = f&quot;{struct} {seq.name}&quot; if include_struct_name else f&quot;{seq.atomspec}&quot;<br>
11736&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^<br>
11737AttributeError: &#x27;StructureSeq&#x27; object has no attribute &#x27;atomspec&#x27;<br>
11738<br/>AttributeError: 'StructureSeq' object has no attribute 'atomspec'<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names<br> renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"<br> ^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><span style="background-color:crimson;">align4/A:1,8/A:1</span></div><font color="crimson"><b>Unknown command: sequence align4/A:1,8/A:1</b></font><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 4/A:1,8/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 4/A:1,8/A:1">sequence align 4/A:1,8/A:1</a></div></div>Traceback (most recent call last):<br>
11739&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
11740&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
11741&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
11742&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
11743&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11744&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 500, in seqalign_align<br>
11745&nbsp;&nbsp;&nbsp;&nbsp;input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)<br>
11746&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11747&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 476, in ensure_unique_seq_names<br>
11748&nbsp;&nbsp;&nbsp;&nbsp;renamed_seq.name = f&quot;{struct} {seq.name}&quot; if include_struct_name else f&quot;{seq.atomspec}&quot;<br>
11749&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^<br>
11750AttributeError: &#x27;StructureSeq&#x27; object has no attribute &#x27;atomspec&#x27;<br>
11751<br/>AttributeError: 'StructureSeq' object has no attribute 'atomspec'<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names<br> renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"<br> ^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 4/A:1,7/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 4/A:1,7/A:1">sequence align 4/A:1,7/A:1</a></div></div>Traceback (most recent call last):<br>
11752&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
11753&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
11754&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
11755&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
11756&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11757&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 500, in seqalign_align<br>
11758&nbsp;&nbsp;&nbsp;&nbsp;input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)<br>
11759&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11760&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 476, in ensure_unique_seq_names<br>
11761&nbsp;&nbsp;&nbsp;&nbsp;renamed_seq.name = f&quot;{struct} {seq.name}&quot; if include_struct_name else f&quot;{seq.atomspec}&quot;<br>
11762&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^<br>
11763AttributeError: &#x27;StructureSeq&#x27; object has no attribute &#x27;atomspec&#x27;<br>
11764<br/>AttributeError: 'StructureSeq' object has no attribute 'atomspec'<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names<br> renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"<br> ^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 4/A:1,7/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 4/A:1,7/A:1">sequence align 4/A:1,7/A:1</a></div></div>Traceback (most recent call last):<br>
11765&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
11766&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
11767&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
11768&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
11769&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11770&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 500, in seqalign_align<br>
11771&nbsp;&nbsp;&nbsp;&nbsp;input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)<br>
11772&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11773&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 476, in ensure_unique_seq_names<br>
11774&nbsp;&nbsp;&nbsp;&nbsp;renamed_seq.name = f&quot;{struct} {seq.name}&quot; if include_struct_name else f&quot;{seq.atomspec}&quot;<br>
11775&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^<br>
11776AttributeError: &#x27;StructureSeq&#x27; object has no attribute &#x27;atomspec&#x27;<br>
11777<br/>AttributeError: 'StructureSeq' object has no attribute 'atomspec'<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names<br> renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"<br> ^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 6/B:1,7/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 6/B:1,7/A:1">sequence align 6/B:1,7/A:1</a></div></div>Alignment identifier is 1<br>
11778Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches<br>
11779Associated DdHydAB_L2 9gnk chain A to chain A with 0 mismatches<br>
11780Associated DdHydAHydB 1hfe chain L to chain B with 25 mismatches<br>
11781Associated DdHydAHydB 1hfe chain M to chain B with 25 mismatches<br>
11782Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
11783Webservices job id: 8ZTRX39PHNG45CRR<br>
11784Webservices job finished: 8ZTRX39PHNG45CRR<br>
11785<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 6/B:1,8/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 6/B:1,8/A:1">sequence align 6/B:1,8/A:1</a></div></div>Alignment identifier is 3<br>
11786Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches<br>
11787Associated DdHydAB_L3 9gbu chain A to chain A with 0 mismatches<br>
11788Associated DdHydAB_L3 9gbu chain B to chain A with 0 mismatches<br>
11789Associated DdHydAB_L4 8ryh chain A to chain A with 7 mismatches<br>
11790Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to chain A with 7 mismatches<br>
11791Associated DdHydAHydB 1hfe chain L to chain B with 25 mismatches<br>
11792Associated DdHydAHydB 1hfe chain M to chain B with 25 mismatches<br>
11793Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 3<br>
11794Webservices job id: 8ICR98YVWHUEM7RR<br>
11795Webservices job finished: 8ICR98YVWHUEM7RR<br>
11796<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 7/A:1,8/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 7/A:1,8/A:1">sequence align 7/A:1,8/A:1</a></div></div>Traceback (most recent call last):<br>
11797&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py&quot;, line 319, in execute<br>
11798&nbsp;&nbsp;&nbsp;&nbsp;cmd.run(cmd_text)<br>
11799&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
11800&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
11801&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11802&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 500, in seqalign_align<br>
11803&nbsp;&nbsp;&nbsp;&nbsp;input_sequences = ensure_unique_seq_names(input_sequences, structure_name_limit=10)<br>
11804&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
11805&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py&quot;, line 476, in ensure_unique_seq_names<br>
11806&nbsp;&nbsp;&nbsp;&nbsp;renamed_seq.name = f&quot;{struct} {seq.name}&quot; if include_struct_name else f&quot;{seq.atomspec}&quot;<br>
11807&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^<br>
11808AttributeError: &#x27;StructureSeq&#x27; object has no attribute &#x27;atomspec&#x27;<br>
11809<br/>AttributeError: 'StructureSeq' object has no attribute 'atomspec'<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/seqalign/cmd.py", line 476, in ensure_unique_seq_names<br> renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else f"{seq.atomspec}"<br> ^^^^^^^^^^^^<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#rename">sequence rename</a> &quot;6/B:chain B&quot; DdHydAB_L1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence rename &quot;6/B:chain B&quot; DdHydAB_L1">sequence rename &quot;6/B:chain B&quot; DdHydAB_L1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#rename">sequence rename</a> &quot;4/A:chain A&quot; DdHydAB_TD</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence rename &quot;4/A:chain A&quot; DdHydAB_TD">sequence rename &quot;4/A:chain A&quot; DdHydAB_TD</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#rename">sequence rename</a> &quot;7/A:chain A&quot; DdHydAB_L2</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence rename &quot;7/A:chain A&quot; DdHydAB_L2">sequence rename &quot;7/A:chain A&quot; DdHydAB_L2</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#rename">sequence rename</a> &quot;10/A:chain A&quot; DdHydAB_L3</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence rename &quot;10/A:chain A&quot; DdHydAB_L3">sequence rename &quot;10/A:chain A&quot; DdHydAB_L3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#rename">sequence rename</a> 10/A:DdHydAB_L3 DdHydAB_L4</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence rename 10/A:DdHydAB_L3 DdHydAB_L4">sequence rename 10/A:DdHydAB_L3 DdHydAB_L4</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#rename">sequence rename</a> &quot;8/A:chain A&quot; DdHydAB_L3</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence rename &quot;8/A:chain A&quot; DdHydAB_L3">sequence rename &quot;8/A:chain A&quot; DdHydAB_L3</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#rename">sequence rename</a> &quot;16/A:chain A&quot; DdHydAB_PSI_Interface</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence rename &quot;16/A:chain A&quot; DdHydAB_PSI_Interface">sequence rename &quot;16/A:chain A&quot; DdHydAB_PSI_Interface</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1">sequence align 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1</a></div></div>Alignment identifier is 1<br>
11810Associated DdHyd_PSI.opt.chains (2.6) chain F to DdHydAB_PSI_Interface with 12 mismatches<br>
11811Associated DdHydAB_L1 8ru6 chain B to DdHydAB_L1 with 0 mismatches<br>
11812Associated DdHydAB_L2 9gnk chain A to DdHydAB_L2 with 0 mismatches<br>
11813Associated DdHydAB_L3 9gbu chain A to DdHydAB_L3 with 0 mismatches<br>
11814Associated DdHydAB_L3 9gbu chain B to DdHydAB_L3 with 0 mismatches<br>
11815Associated HydAB_PSI_Interface_model.cif chain A to DdHydAB_PSI_Interface with 0 mismatches<br>
11816Associated HydAB_TD_linker_model_noMSA.cif chain A to DdHydAB_TD with 0 mismatches<br>
11817Associated HydAB_PSI_Interface_model_MSA.cif chain A to DdHydAB_PSI_Interface with 0 mismatches<br>
11818Associated DdHydAB_L4 8ryh chain A to DdHydAB_L4 with 0 mismatches<br>
11819Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to DdHydAB_L4 with 0 mismatches<br>
11820Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to DdHydAB_TD with 0 mismatches<br>
11821Associated DdHydAHydB 1hfe chain L to DdHydAB_TD with 25 mismatches<br>
11822Associated DdHydAHydB 1hfe chain M to DdHydAB_TD with 25 mismatches<br>
11823Associated HydAB_TD_linker_model_MSA.cif chain A to DdHydAB_TD with 0 mismatches<br>
11824Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 1<br>
11825Webservices job id: F9UBN2MFBD72KX6R<br>
11826Webservices job finished: F9UBN2MFBD72KX6R<br>
11827<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Model Panel&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Model Panel&quot;">ui tool show &quot;Model Panel&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> 4xdc</div><div class="cxcmd_as_cmd"><a href="cxcmd:open 4xdc">open 4xdc</a></div></div><i>4xdc</i> title:<br><b>Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe] cofactor</b> <a href="cxcmd:log metadata #11">[more&nbsp;info...]</a><br><br/><table border=1 cellpadding=4 cellspacing=0>
11828 <thead>
11829 <tr>
11830 <th colspan="3">Chain information for 4xdc #11</th>
11831 </tr>
11832 <tr>
11833 <th>Chain</th>
11834 <th>Description</th>
11835 <th>UniProt</th>
11836 </tr>
11837 </thead>
11838 <tbody>
11839 <tr>
11840 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #11/A:1-581">A</a> <a title="Select chain" href="cxcmd:select #11/B:2-579">B</a></td>
11841 <td><a title="Show sequence" href="cxcmd:sequence chain #11/A#11/B">Iron hydrogenase 1</a></td>
11842 <td style="text-align:center"><a title="Show annotations" href="cxcmd:open P29166 from uniprot associate #11/A,B">PHF1_CLOPA</a> <a title="Select sequence" href="cxcmd:select #11/A,B:1-574">1-574</a></td>
11843 </tr>
11844 </tbody>
11845</table><br/><table border=1 cellpadding=4 cellspacing=0>
11846 <thead>
11847 <tr>
11848 <th>Non-standard residues in 4xdc #11</th>
11849 </tr>
11850 </thead>
11851 <tbody>
11852 <tr>
11853 <td><a title="select residue" href="cxcmd:sel ::name=&quot;402&quot;">402</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/402">dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)</a></td>
11854 </tr>
11855 <tr>
11856 <td><a title="select residue" href="cxcmd:sel :FES">FES</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/FES">FE2/S2 (inorganic) cluster</a></td>
11857 </tr>
11858 <tr>
11859 <td><a title="select residue" href="cxcmd:sel :MG">MG</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/MG">magnesium ion</a></td>
11860 </tr>
11861 <tr>
11862 <td><a title="select residue" href="cxcmd:sel :SF4">SF4</a> &mdash; <a title="show residue info" href="http://www.rcsb.org/ligand/SF4">iron/sulfur cluster</a></td>
11863 </tr>
11864 </tbody>
11865</table><br/><table border=1 cellpadding=4 cellspacing=0>
11866<tr><th colspan=3>4xdc mmCIF Assemblies
11867<tr><td><a title="Generate assembly" href="cxcmd:sym #11 assembly 1 ; view">1</a><td>author_and_software_defined_assembly
11868<tr><td><a title="Generate assembly" href="cxcmd:sym #11 assembly 2 ; view">2</a><td>author_and_software_defined_assembly
11869</table><br/>63 atoms have alternate locations. Control/examine alternate locations with <b><a href="cxcmd:help help:user/tools/altlocexplorer.html">Altloc Explorer</a></b> [<a href="cxcmd:ui tool show 'Altloc Explorer'">start&nbsp;tool...</a>] or the <b><a href="cxcmd:help altlocs">altlocs</a></b> command.<br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #11 id 12</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #11 id 12">rename #11 id 12</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #10 id 11</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #10 id 11">rename #10 id 11</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #9 id 10</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #9 id 10">rename #9 id 10</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #8 id 9</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #8 id 9">rename #8 id 9</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #7 id 8</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #7 id 8">rename #7 id 8</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #6 id 7</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #6 id 7">rename #6 id 7</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/rename.html">rename</a> #12 id 6</div><div class="cxcmd_as_cmd"><a href="cxcmd:rename #12 id 6">rename #12 id 6</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #6/A to #5/A pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #6/A to #5/A pairing ss">matchmaker #6/A to #5/A pairing ss</a></div></div>
11870 <table border=1 cellpadding=4 cellspacing=0>
11871 <tr>
11872 <th colspan="2">Parameters</th>
11873 </tr>
11874 <tr>
11875 <td>Chain pairing</td>
11876 <td>ss</td>
11877 </tr>
11878 <tr>
11879 <td>Alignment algorithm</td>
11880 <td>Needleman-Wunsch</td>
11881 </tr>
11882 <tr>
11883 <td>Similarity matrix</td>
11884 <td>BLOSUM-62</td>
11885 </tr>
11886
11887 <tr>
11888 <td>SS fraction</td>
11889 <td>0.3</td>
11890 </tr>
11891 <tr>
11892 <td>Gap open (HH/SS/other)</td>
11893 <td>18/18/6</td>
11894 </tr>
11895 <tr>
11896 <td>Gap extend</td>
11897 <td>1</td>
11898 </tr>
11899 <tr>
11900 <td>SS matrix</td>
11901 <td>
11902 <table>
11903 <tr>
11904 <th></th> <th>H</th> <th>S</th> <th>O</th>
11905 </tr>
11906 <tr>
11907 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
11908 </tr>
11909 <tr>
11910 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
11911 </tr>
11912 <tr>
11913 <th>O</th> <td></td> <td></td> <td align="right">4</td>
11914 </tr>
11915 </table>
11916 </td>
11917 </tr>
11918
11919 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
11920 </table>
11921 <br/>Matchmaker CrHydA1 3lx4, chain A (#5) with 4xdc, chain A (#6), sequence alignment score = 892.2<br>
11922RMSD between 262 pruned atom pairs is 1.077 angstroms; (across all 362 pairs: 3.983)<br>
11923<br>
11924<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/B</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/B">select #6/B</a></div></div>9582 atoms, 9080 bonds, 40 pseudobonds, 1170 residues, 2 models selected<br>
11925<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel cartoons</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel cartoons">hide sel cartoons</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide sel atoms">hide sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/A:139-207</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/A:139-207">select #6/A:139-207</a></div></div>1016 atoms, 1019 bonds, 69 residues, 1 model selected<br>
11926<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!11 models">hide #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Color Actions&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Color Actions&quot;">ui tool show &quot;Color Actions&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light steel blue">color sel light steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel steel blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel steel blue">color sel steel blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel slate gray</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel slate gray">color sel slate gray</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light slate gray</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light slate gray">color sel light slate gray</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel sky blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel sky blue">color sel sky blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light sky blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light sky blue">color sel light sky blue</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel sky blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel sky blue">color sel sky blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light blue">color sel light blue</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/A:1-138</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/A:1-138">select #6/A:1-138</a></div></div>2183 atoms, 2194 bonds, 138 residues, 1 model selected<br>
11927<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel light gray</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel light gray">color sel light gray</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel silver</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel silver">color sel silver</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel powder blue</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel powder blue">color sel powder blue</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel silver</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel silver">color sel silver</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/A">select #6/A</a></div></div>9693 atoms, 9132 bonds, 49 pseudobonds, 1233 residues, 2 models selected<br>
11928<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.1.4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.1.4 models">hide #1.1.4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #1.1.5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #1.1.5 models">hide #1.1.5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2:SF4</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2:SF4">select #2:SF4</a></div></div>32 atoms, 12 bonds, 54 pseudobonds, 4 residues, 3 models selected<br>
11929<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel &amp; #!2.6 stick</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel &amp; #!2.6 stick">style sel &amp; #!2.6 stick</a></div></div>Changed 24 atom styles<br>
11930<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel &amp; #!2.6 ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel &amp; #!2.6 ball">style sel &amp; #!2.6 ball</a></div></div>Changed 24 atom styles<br>
11931<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel &amp; #!2.6 sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel &amp; #!2.6 sphere">style sel &amp; #!2.6 sphere</a></div></div>Changed 24 atom styles<br>
11932<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel &amp; #!2.6 ball</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel &amp; #!2.6 ball">style sel &amp; #!2.6 ball</a></div></div>Changed 24 atom styles<br>
11933<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1.1 models">hide #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1.1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1.1 models">show #!1.1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!4 models">show #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!5 models">hide #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/A:19-26 :&lt;4.5 &amp; #6/A:513-520</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/A:19-26 :&lt;4.5 &amp; #6/A:513-520">select #6/A:19-26 :&lt;4.5 &amp; #6/A:513-520</a></div></div>51 atoms, 50 bonds, 3 residues, 1 model selected<br>
11934<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 51 atom styles<br>
11935<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #6/A:513-520 :&lt;4.5 &amp; #6/A:19-26</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #6/A:513-520 :&lt;4.5 &amp; #6/A:19-26">select #6/A:513-520 :&lt;4.5 &amp; #6/A:19-26</a></div></div>46 atoms, 44 bonds, 2 residues, 1 model selected<br>
11936<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> sel atoms</div><div class="cxcmd_as_cmd"><a href="cxcmd:show sel atoms">show sel atoms</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/style.html">style</a> sel sphere</div><div class="cxcmd_as_cmd"><a href="cxcmd:style sel sphere">style sel sphere</a></div></div>Changed 46 atom styles<br>
11937<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsal structures DdHAB PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsal structures DdHAB PSI.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsal structures DdHAB PSI.cxs&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_model.cif&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_model.cif&quot;">open &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_model.cif&quot;</a></div></div><table border=1 cellpadding=4 cellspacing=0>
11938 <thead>
11939 <tr>
11940 <th colspan="2">Chain information for hydab_psi_interface_model.cif #12</th>
11941 </tr>
11942 <tr>
11943 <th>Chain</th>
11944 <th>Description</th>
11945
11946 </tr>
11947 </thead>
11948 <tbody>
11949 <tr>
11950 <td style="text-align:center"><a title="Select chain" href="cxcmd:select #12/A:1-473">A</a></td>
11951 <td><a title="Show sequence" href="cxcmd:sequence chain #12/A">.</a></td>
11952
11953 </tr>
11954 </tbody>
11955</table><br/><p style="color:#ffb961">No chain in structure corresponds to chain ID given in local score info (chain &#x27;B&#x27;)<br>
11956</p>Associated hydab_psi_interface_model.cif chain A to chain F with 12 mismatches<br>
11957Associated hydab_psi_interface_model.cif chain A to DdHydAB_PSI_Interface with 12 mismatches<br>
11958Computing secondary structure<br>
11959<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!12 models">show #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!16 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!16 models">show #!16 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!16 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!16 models">hide #!16 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Log</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Log">ui tool show Log</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> Matchmaker</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show Matchmaker">ui tool show Matchmaker</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/matchmaker.html">matchmaker</a> #12/A to #2.6/F pairing ss</div><div class="cxcmd_as_cmd"><a href="cxcmd:matchmaker #12/A to #2.6/F pairing ss">matchmaker #12/A to #2.6/F pairing ss</a></div></div>
11960 <table border=1 cellpadding=4 cellspacing=0>
11961 <tr>
11962 <th colspan="2">Parameters</th>
11963 </tr>
11964 <tr>
11965 <td>Chain pairing</td>
11966 <td>ss</td>
11967 </tr>
11968 <tr>
11969 <td>Alignment algorithm</td>
11970 <td>Needleman-Wunsch</td>
11971 </tr>
11972 <tr>
11973 <td>Similarity matrix</td>
11974 <td>BLOSUM-62</td>
11975 </tr>
11976
11977 <tr>
11978 <td>SS fraction</td>
11979 <td>0.3</td>
11980 </tr>
11981 <tr>
11982 <td>Gap open (HH/SS/other)</td>
11983 <td>18/18/6</td>
11984 </tr>
11985 <tr>
11986 <td>Gap extend</td>
11987 <td>1</td>
11988 </tr>
11989 <tr>
11990 <td>SS matrix</td>
11991 <td>
11992 <table>
11993 <tr>
11994 <th></th> <th>H</th> <th>S</th> <th>O</th>
11995 </tr>
11996 <tr>
11997 <th>H</th> <td align="right">6</td> <td align="right">-9</td> <td align="right">-6</td>
11998 </tr>
11999 <tr>
12000 <th>S</th> <td></td> <td align="right">6</td> <td align="right">-6</td>
12001 </tr>
12002 <tr>
12003 <th>O</th> <td></td> <td></td> <td align="right">4</td>
12004 </tr>
12005 </table>
12006 </td>
12007 </tr>
12008
12009 <tr> <td>Iteration cutoff</td> <td>2</td></tr>
12010 </table>
12011 <br/>Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with hydab_psi_interface_model.cif, chain A (#12), sequence alignment score = 2357.4<br>
12012RMSD between 459 pruned atom pairs is 0.458 angstroms; (across all 473 pairs: 1.168)<br>
12013<br>
12014<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!6 models">hide #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!7 models">hide #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!8 models">hide #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!9 models">hide #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;AlphaFold Error Plot&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;AlphaFold Error Plot&quot;">ui tool show &quot;AlphaFold Error Plot&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/alphafold.html#pae">alphafold pae</a> #12 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_confidences.json&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:alphafold pae #12 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_confidences.json&quot;">alphafold pae #12 file &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_confidences.json&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html#byattribute">color bfactor</a> #12 palette alphafold</div><div class="cxcmd_as_cmd"><a href="cxcmd:color bfactor #12 palette alphafold">color bfactor #12 palette alphafold</a></div></div>3658 atoms, 477 residues, atom bfactor range 24.2 to 99<br>
12015<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #16</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #16">close #16</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#tool-show">ui tool show</a> &quot;Show Sequence Viewer&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui tool show &quot;Show Sequence Viewer&quot;">ui tool show &quot;Show Sequence Viewer&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#chain">sequence chain</a> #12/A</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence chain #12/A">sequence chain #12/A</a></div></div>Alignment identifier is 12/A<br>
12016<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#align">sequence align</a> 12/A:1,1:2,1:3,1:4,1:5,1:6</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence align 12/A:1,1:2,1:3,1:4,1:5,1:6">sequence align 12/A:1,1:2,1:3,1:4,1:5,1:6</a></div></div>Alignment identifier is 3<br>
12017Associated DdHyd_PSI.opt.chains (2.6) chain F to chain A with 12 mismatches<br>
12018Associated HydAB_TD_linker_model_noMSA.cif chain A to DdHydAB_TD with 0 mismatches<br>
12019Associated HydAB_PSI_Interface_model_MSA.cif chain A to chain A with 0 mismatches<br>
12020Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to DdHydAB_TD with 0 mismatches<br>
12021Associated DdHydAHydB 1hfe chain L to DdHydAB_TD with 25 mismatches<br>
12022Associated DdHydAHydB 1hfe chain M to DdHydAB_TD with 25 mismatches<br>
12023Associated HydAB_TD_linker_model_MSA.cif chain A to DdHydAB_TD with 0 mismatches<br>
12024Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to DdHydAB_L4 with 0 mismatches<br>
12025Associated DdHydAB_L4 8ryh chain A to DdHydAB_L4 with 0 mismatches<br>
12026Associated DdHydAB_L3 9gbu chain A to DdHydAB_L3 with 0 mismatches<br>
12027Associated DdHydAB_L3 9gbu chain B to DdHydAB_L3 with 0 mismatches<br>
12028Associated DdHydAB_L2 9gnk chain A to DdHydAB_L2 with 0 mismatches<br>
12029Associated DdHydAB_L1 8ru6 chain B to DdHydAB_L1 with 0 mismatches<br>
12030Associated hydab_psi_interface_model.cif chain A to chain A with 0 mismatches<br>
12031Showing conservation header (&quot;seq_conservation&quot; residue attribute) for alignment 3<br>
12032Webservices job id: 6XMP5FXUI3IT234Y<br>
12033Webservices job finished: 6XMP5FXUI3IT234Y<br>
12034<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.6/F:1796 #14/A:31 #12/A:31</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.6/F:1796 #14/A:31 #12/A:31">select #2.6/F:1796 #14/A:31 #12/A:31</a></div></div>20 atoms, 17 bonds, 3 residues, 3 models selected<br>
12035<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2.6/F:1796 #14/A:31 #12/A:31</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2.6/F:1796 #14/A:31 #12/A:31">select #2.6/F:1796 #14/A:31 #12/A:31</a></div></div>20 atoms, 17 bonds, 3 residues, 3 models selected<br>
12036Clustal Omega Alignment [ID: 3] region chain A [35] RMSD: 0.945<br>
12037<br>
12038<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#rename">sequence rename</a> &quot;3:chain A&quot; DdHydAB_PSI_interface</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence rename &quot;3:chain A&quot; DdHydAB_PSI_interface">sequence rename &quot;3:chain A&quot; DdHydAB_PSI_interface</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#disassociate">sequence disassociate</a> #3/L 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence disassociate #3/L 3">sequence disassociate #3/L 3</a></div></div>Disassociated DdHydAHydB 1hfe chain L from DdHydAB_TD<br>
12039<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#disassociate">sequence disassociate</a> #3/M 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence disassociate #3/M 3">sequence disassociate #3/M 3</a></div></div>Disassociated DdHydAHydB 1hfe chain M from DdHydAB_TD<br>
12040<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#disassociate">sequence disassociate</a> #2.6/F 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence disassociate #2.6/F 3">sequence disassociate #2.6/F 3</a></div></div>Disassociated DdHyd_PSI.opt.chains (2.6) chain F from DdHydAB_PSI_interface<br>
12041<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#associate">sequence associate</a> #2.6/F 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence associate #2.6/F 3">sequence associate #2.6/F 3</a></div></div>Associated DdHyd_PSI.opt.chains (2.6) chain F to DdHydAB_PSI_interface with 12 mismatches<br>
12042<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/sequence.html#disassociate">sequence disassociate</a> #2.6/F 3</div><div class="cxcmd_as_cmd"><a href="cxcmd:sequence disassociate #2.6/F 3">sequence disassociate #2.6/F 3</a></div></div>Disassociated DdHyd_PSI.opt.chains (2.6) chain F from DdHydAB_PSI_interface<br>
12043<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #14/A:31,34,37,41,65,68,71,75,178,233,377,381 #12/A:31,34,37,41,65,68,71,75,178,233,377,381</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #14/A:31,34,37,41,65,68,71,75,178,233,377,381 #12/A:31,34,37,41,65,68,71,75,178,233,377,381">select #14/A:31,34,37,41,65,68,71,75,178,233,377,381 #12/A:31,34,37,41,65,68,71,75,178,233,377,381</a></div></div>120 atoms, 96 bonds, 24 residues, 2 models selected<br>
12044<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #12</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #12">select #12</a></div></div>3658 atoms, 3754 bonds, 11 pseudobonds, 477 residues, 2 models selected<br>
12045<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/color.html">color</a> sel byhetero</div><div class="cxcmd_as_cmd"><a href="cxcmd:color sel byhetero">color sel byhetero</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!12 models">show #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!2 models">show #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #14/A:392 #12/A:392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #14/A:392 #12/A:392">select #14/A:392 #12/A:392</a></div></div>24 atoms, 24 bonds, 2 residues, 2 models selected<br>
12046<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #14/A:390-392 #12/A:390-392</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #14/A:390-392 #12/A:390-392">select #14/A:390-392 #12/A:390-392</a></div></div>66 atoms, 68 bonds, 6 residues, 2 models selected<br>
12047Clustal Omega Alignment [ID: 3] region DdHydAB_PSI_interface [402-404] RMSD: 0.896<br>
12048<br>
12049<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #14/A:390 #12/A:390</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #14/A:390 #12/A:390">select #14/A:390 #12/A:390</a></div></div>24 atoms, 24 bonds, 2 residues, 2 models selected<br>
12050<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #14/A:390-391 #12/A:390-391</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #14/A:390-391 #12/A:390-391">select #14/A:390-391 #12/A:390-391</a></div></div>42 atoms, 42 bonds, 4 residues, 2 models selected<br>
12051Clustal Omega Alignment [ID: 3] region DdHydAB_PSI_interface [402-403] RMSD: 1.024<br>
12052<br>
12053<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #14/A:387 #12/A:387</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #14/A:387 #12/A:387">select #14/A:387 #12/A:387</a></div></div>8 atoms, 6 bonds, 2 residues, 2 models selected<br>
12054<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #14/A:387-391 #12/A:387-391</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #14/A:387-391 #12/A:387-391">select #14/A:387-391 #12/A:387-391</a></div></div>76 atoms, 76 bonds, 10 residues, 2 models selected<br>
12055Clustal Omega Alignment [ID: 3] region DdHydAB_PSI_interface [391-403] RMSD: 2.113<br>
12056<br>
12057<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!4 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!4 models">hide #!4 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!12 models">show #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!2 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!2 models">hide #!2 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #14</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #14">close #14</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #15</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #15">close #15</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/close.html">close</a> #13</div><div class="cxcmd_as_cmd"><a href="cxcmd:close #13">close #13</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!12 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!12 models">hide #!12 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!5 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!5 models">show #!5 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!6 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!6 models">show #!6 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!7 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!7 models">show #!7 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!8 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!8 models">show #!8 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!9 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!9 models">show #!9 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!10 models">show #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#add">select add</a> #12</div><div class="cxcmd_as_cmd"><a href="cxcmd:select add #12">select add #12</a></div></div>3658 atoms, 3754 bonds, 11 pseudobonds, 477 residues, 2 models selected<br>
12058<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#subtract">select subtract</a> #12</div><div class="cxcmd_as_cmd"><a href="cxcmd:select subtract #12">select subtract #12</a></div></div>Nothing selected<br>
12059<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!10 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!10 models">hide #!10 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!11 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!11 models">show #!11 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html#name">view name</a> linkers_zoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view name linkers_zoom">view name linkers_zoom</a></div></div>[Repeated 1 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/view.html">view</a> linkers_zoom</div><div class="cxcmd_as_cmd"><a href="cxcmd:view linkers_zoom">view linkers_zoom</a></div></div>[Repeated 2 time(s)]<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsal structures DdHAB PSI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsal structures DdHAB PSI.cxs&quot;">save &quot;/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsal structures DdHAB PSI.cxs&quot;</a></div></div>Traceback (most recent call last):<br>
12060&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 1058, in save<br>
12061&nbsp;&nbsp;&nbsp;&nbsp;session.save(output, version=version, include_maps=include_maps)<br>
12062&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 741, in save<br>
12063&nbsp;&nbsp;&nbsp;&nbsp;mgr.discovery(self._state_containers)<br>
12064&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 284, in discovery<br>
12065&nbsp;&nbsp;&nbsp;&nbsp;if hasattr(sm, &quot;include_state&quot;) and not sm.include_state(value):<br>
12066&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12067&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in include_state<br>
12068&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12069&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12070&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in &lt;listcomp&gt;<br>
12071&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12072&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12073&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py&quot;, line 2683, in &lt;lambda&gt;<br>
12074&nbsp;&nbsp;&nbsp;&nbsp;register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls),<br>
12075&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12076&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in python_instances_of_class<br>
12077&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12078&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12079&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in &lt;listcomp&gt;<br>
12080&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12081&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^<br>
12082&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 50, in &lt;lambda&gt;<br>
12083&nbsp;&nbsp;&nbsp;&nbsp;filt = lambda x: (not x.structure) or open_structure(x.structure)<br>
12084&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^<br>
12085&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 96, in get_prop<br>
12086&nbsp;&nbsp;&nbsp;&nbsp;cget(self._c_pointer_ref, 1, v_ref)<br>
12087TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br>
12088<br/>TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 96, in get_prop<br> cget(self._c_pointer_ref, 1, v_ref)<br><br><i>See log for complete Python traceback.</i><br><br/>Traceback (most recent call last):<br>
12089&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py&quot;, line 127, in &lt;lambda&gt;<br>
12090&nbsp;&nbsp;&nbsp;&nbsp;lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=&quot;Save output file&quot;,<br>
12091&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12092&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py&quot;, line 138, in show_save_file_dialog<br>
12093&nbsp;&nbsp;&nbsp;&nbsp;_dlg.display(session, **kw)<br>
12094&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py&quot;, line 62, in display<br>
12095&nbsp;&nbsp;&nbsp;&nbsp;run(session, cmd)<br>
12096&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py&quot;, line 49, in run<br>
12097&nbsp;&nbsp;&nbsp;&nbsp;results = command.run(text, log=log, return_json=return_json)<br>
12098&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12099&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
12100&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
12101&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12102&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py&quot;, line 86, in cmd_save<br>
12103&nbsp;&nbsp;&nbsp;&nbsp;Command(session, registry=registry).run(provider_cmd_text, log=log)<br>
12104&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
12105&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
12106&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12107&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py&quot;, line 101, in provider_save<br>
12108&nbsp;&nbsp;&nbsp;&nbsp;saver_info.save(session, path, **provider_kw)<br>
12109&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py&quot;, line 95, in save<br>
12110&nbsp;&nbsp;&nbsp;&nbsp;return cxs_save(session, path, **kw)<br>
12111&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12112&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 1058, in save<br>
12113&nbsp;&nbsp;&nbsp;&nbsp;session.save(output, version=version, include_maps=include_maps)<br>
12114&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 741, in save<br>
12115&nbsp;&nbsp;&nbsp;&nbsp;mgr.discovery(self._state_containers)<br>
12116&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 284, in discovery<br>
12117&nbsp;&nbsp;&nbsp;&nbsp;if hasattr(sm, &quot;include_state&quot;) and not sm.include_state(value):<br>
12118&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12119&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in include_state<br>
12120&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12121&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12122&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in &lt;listcomp&gt;<br>
12123&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12124&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12125&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py&quot;, line 2683, in &lt;lambda&gt;<br>
12126&nbsp;&nbsp;&nbsp;&nbsp;register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls),<br>
12127&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12128&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in python_instances_of_class<br>
12129&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12130&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12131&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in &lt;listcomp&gt;<br>
12132&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12133&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^<br>
12134&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 50, in &lt;lambda&gt;<br>
12135&nbsp;&nbsp;&nbsp;&nbsp;filt = lambda x: (not x.structure) or open_structure(x.structure)<br>
12136&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^<br>
12137&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 96, in get_prop<br>
12138&nbsp;&nbsp;&nbsp;&nbsp;cget(self._c_pointer_ref, 1, v_ref)<br>
12139TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br>
12140<br/>TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 96, in get_prop<br> cget(self._c_pointer_ref, 1, v_ref)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/Compare DdHydAB variants CrHydA1 CpI.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/Compare DdHydAB variants CrHydA1 CpI.cxs&quot;">save &quot;/Users/drornoy/Google Drive/ISF_DFG_project/Structures/Compare DdHydAB variants CrHydA1 CpI.cxs&quot;</a></div></div>Traceback (most recent call last):<br>
12141&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 1058, in save<br>
12142&nbsp;&nbsp;&nbsp;&nbsp;session.save(output, version=version, include_maps=include_maps)<br>
12143&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 741, in save<br>
12144&nbsp;&nbsp;&nbsp;&nbsp;mgr.discovery(self._state_containers)<br>
12145&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 284, in discovery<br>
12146&nbsp;&nbsp;&nbsp;&nbsp;if hasattr(sm, &quot;include_state&quot;) and not sm.include_state(value):<br>
12147&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12148&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in include_state<br>
12149&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12150&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12151&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in &lt;listcomp&gt;<br>
12152&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12153&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12154&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py&quot;, line 2683, in &lt;lambda&gt;<br>
12155&nbsp;&nbsp;&nbsp;&nbsp;register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls),<br>
12156&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12157&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in python_instances_of_class<br>
12158&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12159&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12160&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in &lt;listcomp&gt;<br>
12161&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12162&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^<br>
12163&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 50, in &lt;lambda&gt;<br>
12164&nbsp;&nbsp;&nbsp;&nbsp;filt = lambda x: (not x.structure) or open_structure(x.structure)<br>
12165&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^<br>
12166&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 96, in get_prop<br>
12167&nbsp;&nbsp;&nbsp;&nbsp;cget(self._c_pointer_ref, 1, v_ref)<br>
12168TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br>
12169<br/>TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 96, in get_prop<br> cget(self._c_pointer_ref, 1, v_ref)<br><br><i>See log for complete Python traceback.</i><br><br/>Traceback (most recent call last):<br>
12170&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py&quot;, line 127, in &lt;lambda&gt;<br>
12171&nbsp;&nbsp;&nbsp;&nbsp;lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=&quot;Save output file&quot;,<br>
12172&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12173&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py&quot;, line 138, in show_save_file_dialog<br>
12174&nbsp;&nbsp;&nbsp;&nbsp;_dlg.display(session, **kw)<br>
12175&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py&quot;, line 62, in display<br>
12176&nbsp;&nbsp;&nbsp;&nbsp;run(session, cmd)<br>
12177&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py&quot;, line 49, in run<br>
12178&nbsp;&nbsp;&nbsp;&nbsp;results = command.run(text, log=log, return_json=return_json)<br>
12179&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12180&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
12181&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
12182&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12183&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py&quot;, line 86, in cmd_save<br>
12184&nbsp;&nbsp;&nbsp;&nbsp;Command(session, registry=registry).run(provider_cmd_text, log=log)<br>
12185&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
12186&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
12187&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12188&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py&quot;, line 101, in provider_save<br>
12189&nbsp;&nbsp;&nbsp;&nbsp;saver_info.save(session, path, **provider_kw)<br>
12190&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py&quot;, line 95, in save<br>
12191&nbsp;&nbsp;&nbsp;&nbsp;return cxs_save(session, path, **kw)<br>
12192&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12193&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 1058, in save<br>
12194&nbsp;&nbsp;&nbsp;&nbsp;session.save(output, version=version, include_maps=include_maps)<br>
12195&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 741, in save<br>
12196&nbsp;&nbsp;&nbsp;&nbsp;mgr.discovery(self._state_containers)<br>
12197&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 284, in discovery<br>
12198&nbsp;&nbsp;&nbsp;&nbsp;if hasattr(sm, &quot;include_state&quot;) and not sm.include_state(value):<br>
12199&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12200&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in include_state<br>
12201&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12202&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12203&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in &lt;listcomp&gt;<br>
12204&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12205&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12206&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py&quot;, line 2683, in &lt;lambda&gt;<br>
12207&nbsp;&nbsp;&nbsp;&nbsp;register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls),<br>
12208&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12209&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in python_instances_of_class<br>
12210&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12211&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12212&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in &lt;listcomp&gt;<br>
12213&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12214&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^<br>
12215&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 50, in &lt;lambda&gt;<br>
12216&nbsp;&nbsp;&nbsp;&nbsp;filt = lambda x: (not x.structure) or open_structure(x.structure)<br>
12217&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^<br>
12218&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 96, in get_prop<br>
12219&nbsp;&nbsp;&nbsp;&nbsp;cget(self._c_pointer_ref, 1, v_ref)<br>
12220TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br>
12221<br/>TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 96, in get_prop<br> cget(self._c_pointer_ref, 1, v_ref)<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;/Users/drornoy/Desktop/DdHydAB compare.cxs&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;/Users/drornoy/Desktop/DdHydAB compare.cxs&quot;">save &quot;/Users/drornoy/Desktop/DdHydAB compare.cxs&quot;</a></div></div>Traceback (most recent call last):<br>
12222&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 1058, in save<br>
12223&nbsp;&nbsp;&nbsp;&nbsp;session.save(output, version=version, include_maps=include_maps)<br>
12224&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 741, in save<br>
12225&nbsp;&nbsp;&nbsp;&nbsp;mgr.discovery(self._state_containers)<br>
12226&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 284, in discovery<br>
12227&nbsp;&nbsp;&nbsp;&nbsp;if hasattr(sm, &quot;include_state&quot;) and not sm.include_state(value):<br>
12228&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12229&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in include_state<br>
12230&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12231&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12232&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in &lt;listcomp&gt;<br>
12233&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12234&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12235&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py&quot;, line 2683, in &lt;lambda&gt;<br>
12236&nbsp;&nbsp;&nbsp;&nbsp;register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls),<br>
12237&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12238&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in python_instances_of_class<br>
12239&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12240&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12241&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in &lt;listcomp&gt;<br>
12242&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12243&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^<br>
12244&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 50, in &lt;lambda&gt;<br>
12245&nbsp;&nbsp;&nbsp;&nbsp;filt = lambda x: (not x.structure) or open_structure(x.structure)<br>
12246&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^<br>
12247&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 96, in get_prop<br>
12248&nbsp;&nbsp;&nbsp;&nbsp;cget(self._c_pointer_ref, 1, v_ref)<br>
12249TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br>
12250<br/>TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 96, in get_prop<br> cget(self._c_pointer_ref, 1, v_ref)<br><br><i>See log for complete Python traceback.</i><br><br/>Traceback (most recent call last):<br>
12251&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py&quot;, line 127, in &lt;lambda&gt;<br>
12252&nbsp;&nbsp;&nbsp;&nbsp;lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=&quot;Save output file&quot;,<br>
12253&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12254&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py&quot;, line 138, in show_save_file_dialog<br>
12255&nbsp;&nbsp;&nbsp;&nbsp;_dlg.display(session, **kw)<br>
12256&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py&quot;, line 62, in display<br>
12257&nbsp;&nbsp;&nbsp;&nbsp;run(session, cmd)<br>
12258&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py&quot;, line 49, in run<br>
12259&nbsp;&nbsp;&nbsp;&nbsp;results = command.run(text, log=log, return_json=return_json)<br>
12260&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12261&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
12262&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
12263&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12264&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py&quot;, line 86, in cmd_save<br>
12265&nbsp;&nbsp;&nbsp;&nbsp;Command(session, registry=registry).run(provider_cmd_text, log=log)<br>
12266&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py&quot;, line 3221, in run<br>
12267&nbsp;&nbsp;&nbsp;&nbsp;result = ci.function(session, **kw_args)<br>
12268&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12269&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py&quot;, line 101, in provider_save<br>
12270&nbsp;&nbsp;&nbsp;&nbsp;saver_info.save(session, path, **provider_kw)<br>
12271&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py&quot;, line 95, in save<br>
12272&nbsp;&nbsp;&nbsp;&nbsp;return cxs_save(session, path, **kw)<br>
12273&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12274&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 1058, in save<br>
12275&nbsp;&nbsp;&nbsp;&nbsp;session.save(output, version=version, include_maps=include_maps)<br>
12276&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 741, in save<br>
12277&nbsp;&nbsp;&nbsp;&nbsp;mgr.discovery(self._state_containers)<br>
12278&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py&quot;, line 284, in discovery<br>
12279&nbsp;&nbsp;&nbsp;&nbsp;if hasattr(sm, &quot;include_state&quot;) and not sm.include_state(value):<br>
12280&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12281&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in include_state<br>
12282&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12283&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12284&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py&quot;, line 295, in &lt;listcomp&gt;<br>
12285&nbsp;&nbsp;&nbsp;&nbsp;self._python_instances = [[inst for inst in inst_func(self.session)<br>
12286&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^<br>
12287&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py&quot;, line 2683, in &lt;lambda&gt;<br>
12288&nbsp;&nbsp;&nbsp;&nbsp;register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls),<br>
12289&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12290&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in python_instances_of_class<br>
12291&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12292&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
12293&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 61, in &lt;listcomp&gt;<br>
12294&nbsp;&nbsp;&nbsp;&nbsp;return [x for x in instances if filt(x)]<br>
12295&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^<br>
12296&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py&quot;, line 50, in &lt;lambda&gt;<br>
12297&nbsp;&nbsp;&nbsp;&nbsp;filt = lambda x: (not x.structure) or open_structure(x.structure)<br>
12298&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;^^^^^^^^^^^<br>
12299&nbsp;&nbsp;File &quot;/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py&quot;, line 96, in get_prop<br>
12300&nbsp;&nbsp;&nbsp;&nbsp;cget(self._c_pointer_ref, 1, v_ref)<br>
12301TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br>
12302<br/>TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate<br><br> File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 96, in get_prop<br> cget(self._c_pointer_ref, 1, v_ref)<br><br><i>See log for complete Python traceback.</i><br><br/></body>
12303</html>