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Opened 4 weeks ago
Last modified 4 weeks ago
#19302 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
Was trying to save a session.
From the Log:
save "/Users/drornoy/Desktop/DdHydAB compare.cxs"
Traceback (most recent call last): File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1058, in save session.save(output, version=version, include_maps=include_maps) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 741, in save mgr.discovery(self._state_containers) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 284, in discovery if hasattr(sm, "include_state") and not sm.include_state(value): ^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 295, in include_state self._python_instances = [[inst for inst in inst_func(self.session) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 295, in <listcomp> self._python_instances = [[inst for inst in inst_func(self.session) ^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2683, in <lambda> register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls), ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class return [x for x in instances if filt(x)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61, in <listcomp> return [x for x in instances if filt(x)] ^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 50, in <lambda> filt = lambda x: (not x.structure) or open_structure(x.structure) ^^^^^^^^^^^ 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 cget(self._c_pointer_ref, 1, v_ref) TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate 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 cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62, in display run(session, cmd) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1058, in save session.save(output, version=version, include_maps=include_maps) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 741, in save mgr.discovery(self._state_containers) File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 284, in discovery if hasattr(sm, "include_state") and not sm.include_state(value): ^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 295, in include_state self._python_instances = [[inst for inst in inst_func(self.session) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py", line 295, in <listcomp> self._python_instances = [[inst for inst in inst_func(self.session) ^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2683, in <lambda> register_class(reg_class, lambda *args, cls=reg_class: python_instances_of_class(cls), ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class return [x for x in instances if filt(x)] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 61, in <listcomp> return [x for x in instances if filt(x)] ^^^^^^^ File "/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 50, in <lambda> filt = lambda x: (not x.structure) or open_structure(x.structure) ^^^^^^^^^^^ 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 cget(self._c_pointer_ref, 1, v_ref) TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate TypeError: Cannot instantiate Python class corresponding to C++ 30QGraphicsSimpleTextItemPrivate 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 cget(self._c_pointer_ref, 1, v_ref)
Log:
UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB
> PSI.cxs" format session
Log from Wed Nov 5 11:09:20 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures
> and designs/PSI_DdH2ase dock design with all single chains variants.cxs"
> format session
Log from Wed Oct 29 10:26:11 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking
> design.cxs" format session
Log from Wed Oct 22 19:01:49 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking
> design.cxs" format session
Log from Wed Oct 22 18:27:07 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/Dropbox/Design to Martin/PSI-DdHyd
> design.cxs"
Frozen name "Hbonding" not restored: Nothing is selected by specifier
Log from Wed Sep 17 15:57:48 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
> format session
Log from Mon Sep 15 21:24:55 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
Log from Mon Sep 15 20:51:36 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
> format session
Log from Mon Sep 15 19:12:58 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs"
> format session
Log from Sun Sep 14 07:49:27 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs"
> format session
Log from Sat Sep 13 22:23:04 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
> PSI-BFd PSI-DdHyd PSI-FdhF.cxs" format session
Log from Tue Oct 22 11:40:52 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
> PSI-BFd PSI-DdHyd PSI-FdhF.cxs" format session
Associated PSI_BFD_SF4_opt_chains.pdb chain F to PSI_BFd_SF4_opt.pdb, chain F
with 0 mismatches
Log from Tue Oct 22 11:39:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
> PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs" format session
Associated PSI_BFD_SF4_opt_chains.pdb chain F to PSI_BFd_SF4_opt.pdb, chain F
with 0 mismatches
Log from Tue Oct 22 09:43:01 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd
> PSI-BFd AMBER opt.cxs"
Log from Mon Oct 21 23:18:11 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"
> format session
Log from Mon Oct 14 21:44:01 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"
> format session
Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M,
PSI_BFd_SF4_opt.pdb #4/F
Log from Mon Oct 14 18:11:28 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"
> format session
Log from Mon Oct 14 17:57:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/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" format session
Log from Fri Oct 11 10:32:45 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/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" format session
Log from Thu Oct 10 08:30:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/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" format session
Log from Wed Oct 9 21:29:02 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/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" format
> session
Frozen name "minAB" not restored: nothing is selected by specifier
Log from Tue Oct 8 17:54:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs" format session
Log from Sun Oct 6 13:38:31 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs" format session
Log from Fri Oct 4 15:14:28 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs" format session
Log from Fri Oct 4 10:09:32 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs" format session
Log from Fri Oct 4 09:37:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs" format session
Log from Thu Oct 3 21:28:49 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on
> PSI.cxs" format session
Log from Thu Oct 3 09:47:21 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/PSI Fdx best MPNN .cxs" format session
Log from Mon Sep 30 14:03:27 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs"
Log from Thu Sep 19 17:01:48 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/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" format
> session
Log from Tue Jun 4 19:01:21 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/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" format
> session
Log from Tue Jun 4 18:24:08 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/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" format
> session
Log from Sat Jun 1 14:26:44 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
> fdn small target.cxs" format session
Log from Sun May 19 17:29:55 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
> v2.cxs"
Log from Sat May 18 22:45:24 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/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" format session
Log from Sat May 18 17:13:54 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/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" format session
Log from Sat May 18 14:49:43 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI Fdx Fld combined.cxs" format session
Log from Fri May 17 15:09:06 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI_PetF/PSI base for design.cxs" format session
Log from Fri May 17 13:23:40 2024UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI stromal ridge PetF truncated for docking.cxs"
Log from Sun Sep 3 21:12:02 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI
> stromal ridge PetF coulombic interactions.cxs" format session
Log from Sun Sep 3 20:48:37 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI
> stromal ridge PetF PshB PscB.cxs" format session
Log from Sun Sep 3 20:15:18 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs"
Log from Tue Dec 20 17:39:04 2022UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/drornoy/Downloads/ChimeraX/AlphaFold/AF-A1Z1D6-F1-model_v4.cif
> format mmcif
Chain information for AF-A1Z1D6-F1-model_v4.cif #1
---
Chain | Description | UniProt
A | PshB | A1Z1D6_9FIRM
> select :Cys
54 atoms, 46 bonds, 9 residues, 1 model selected
> show sel atoms
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for AF-A1Z1D6-F1-model_v4.cif_A SES surface #1.1: minimum,
-13.99, mean -2.80, maximum 7.54
To also show corresponding color key, enter the above coulombic command and
add key true
> close #1.1
> select clear
> coulombic
Coulombic values for AF-A1Z1D6-F1-model_v4.cif_A SES surface #1.1: minimum,
-13.99, mean -2.80, maximum 7.54
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #1.1 models
> open 6yez
6yez title:
Plant PSI-ferredoxin-plastocyanin supercomplex [more info...]
Chain information for 6yez #2
---
Chain | Description | UniProt
1 | Lhca1 |
2 | Chlorophyll a-b binding protein, chloroplastic | Q41038_PEA
3 | Chlorophyll a-b binding protein 3, chloroplastic | CB23_PEA
4 | Chlorophyll a-b binding protein P4, chloroplastic | CB24_PEA
A | Photosystem I P700 chlorophyll a apoprotein A1 | A0A0F6NFW5_PEA
B | Photosystem I P700 chlorophyll a apoprotein A2 | A0A0F6NGI2_PEA
C | Photosystem I iron-sulfur center | PSAC_PEA
D | PsaD |
E | PsaE |
F | PsaF |
G | PsaG |
H | PsaH |
I | Photosystem I reaction center subunit VIII | PSAI_PEA
J | PsaJ |
K | Photosystem I reaction center subunit X psaK | E1C9L3_PEA
L | PsaL |
N | Ferredoxin-1, chloroplastic | FER1_PEA
P | Plastocyanin |
Non-standard residues in 6yez #2
---
3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)
BCR — β-carotene
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
CA — calcium ion
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
CU — copper (II) ion
DGD — digalactosyl diacyl glycerol (DGDG)
FES — FE2/S2 (inorganic) cluster
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
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 (violaxanthin)
> view
> select #2
39226 atoms, 40742 bonds, 678 pseudobonds, 3684 residues, 2 models selected
> hide sel atoms
> select #2/A-E/N
21037 atoms, 21881 bonds, 372 pseudobonds, 1981 residues, 2 models selected
> show sel cartoons
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> select #2/N &protein
724 atoms, 736 bonds, 97 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6yez_N SES surface #2.2: minimum, -22.35, mean -7.76,
maximum 6.07
To also show corresponding color key, enter the above coulombic command and
add key true
> view
> ui mousemode right "translate selected models"
> select #1
369 atoms, 372 bonds, 54 residues, 1 model selected
> view matrix models #1,1,0,0,38.794,0,1,0,146.26,0,0,1,93.086
> view matrix models #1,1,0,0,80.971,0,1,0,155.21,0,0,1,92.043
> view matrix models #1,1,0,0,118.66,0,1,0,188.05,0,0,1,73.54
> save "/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs"
> show #1.1 models
> hide #1.1 models
> hide #2.2 models
> select #2/N:Cys
30 atoms, 25 bonds, 5 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 30 atom styles
> color sel byhetero
> select #2/N:18
6 atoms, 5 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/N:39,44,47,77
24 atoms, 20 bonds, 4 residues, 1 model selected
> select #1
369 atoms, 372 bonds, 54 residues, 1 model selected
> view matrix models #1,1,0,0,125.11,0,1,0,180.57,0,0,1,83.231
> view matrix models #1,1,0,0,124.62,0,1,0,176.17,0,0,1,84.747
> show #1.1 models
> ui mousemode right "rotate selected models"
> 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
> transparency (#!1 & sel) 50
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> show #2.2 models
> transparency (#!2 & sel) 50
> select #1
369 atoms, 372 bonds, 54 residues, 1 model selected
> hide #1.1 models
> hide #2.2 models
> ui mousemode right "move picked models"
> view matrix models #2,1,0,0,-0.12823,0,1,0,-1.3842,0,0,1,0.015386
> select #1
369 atoms, 372 bonds, 54 residues, 1 model selected
> 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,-0.7201,114.24,0.84237,0.51416,0.16142,146.41,0.28594,-0.68032,0.67483,87.683
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> hide sel cartoons
> select #1
369 atoms, 372 bonds, 54 residues, 1 model selected
> 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,-0.65234,0,1,0,1.2309,0,0,1,0.14732
> save "/Users/drornoy/Documents/Protein Designs/PSI with PshB.cxs"
——— End of log from Tue Dec 20 17:39:04 2022 ———
opened ChimeraX session
> show #1.1 models
> show #2.2 models
> hide #2.2 models
> hide #2.1 models
> show #2.1 models
> hide #1.1 models
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> show sel cartoons
> select #2:FeS
4 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 4 atom styles
> select #2:FS4
Nothing selected
> select #2:SF4
24 atoms, 36 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 24 atom styles
> surface #2 enclose /C-D
> select add #2.3
1768 atoms, 36 bonds, 226 residues, 1 model selected
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
6yez #2/D LEU 211 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6yez_C SES surface #2.3: minimum, -12.54, mean -0.30,
maximum 9.66
Coulombic values for 6yez_D SES surface #2.4: minimum, -11.93, mean 1.16,
maximum 13.86
To also show corresponding color key, enter the above coulombic command and
add key true
> surface #2 enclose /E
> select add #2.5
2296 atoms, 36 bonds, 292 residues, 3 models selected
> select subtract #2.4
1164 atoms, 36 bonds, 149 residues, 4 models selected
> select subtract #2.3
552 atoms, 36 bonds, 69 residues, 3 models selected
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
6yez #2/E LYS 129 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for Surface /E #2.5: minimum, -13.31, mean 0.69, maximum 9.65
To also show corresponding color key, enter the above coulombic command and
add key true
> show #2.2 models
> hide #!1 models
> select add #2.4
1684 atoms, 36 bonds, 212 residues, 2 models selected
> select subtract #2.5
1156 atoms, 36 bonds, 146 residues, 3 models selected
> transparency (#!2 & sel) 60
> transparency (#!2 & sel) 0
> select subtract #2.4
24 atoms, 36 bonds, 3 residues, 2 models selected
> select add #2.3
636 atoms, 36 bonds, 83 residues, 1 model selected
> transparency (#!2 & sel) 60
> ui tool show AlphaFold
> alphafold match Q8KCZ6
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
1 AlphaFold model found using UniProt identifier: Q8KCZ6 (UniProt Q8KCZ6)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
Q8KCZ6 | Q8KCZ6 | 100.0 | 100.0
Opened 1 AlphaFold model
> rename #3 "AlphaFold Q8KCZ6 CbFdx"Fetching A1Z1D6 UniProt info from
> https://www.uniprot.org/uniprot/A1Z1D6.xml
> alphafold match A1Z1D6Fetching compressed AlphaFold A1Z1D6 from
> https://alphafold.ebi.ac.uk/files/AF-A1Z1D6-F1-model_v4.cif
1 AlphaFold model found using UniProt identifier: A1Z1D6 (UniProt A1Z1D6)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
A1Z1D6 | A1Z1D6 | 100.0 | 100.0
Opened 1 AlphaFold model
> rename #1 "AlphaFold A1Z1D6 PshB"> close #4> ui tool show Matchmaker> matchmaker #3 to #1 | Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AlphaFold A1Z1D6 PshB, chain A (#1) with AlphaFold Q8KCZ6 CbFdx,
chain A (#3), sequence alignment score = 92.4
RMSD between 42 pruned atom pairs is 0.750 angstroms; (across all 54 pairs:
3.659)
> hide #2.2 models
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> hide sel cartoons
> show #!1 models
> select #3:cys
54 atoms, 45 bonds, 9 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide #!2 models
> show #!2 models
> save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI
> stromal ridge PetF PshB PscB.cxs"
——— End of log from Sun Sep 3 20:15:18 2023 ———
opened ChimeraX session
> select #2/A:562-593
238 atoms, 243 bonds, 32 residues, 1 model selected
> select #2/A:417-442,562-593
466 atoms, 475 bonds, 58 residues, 1 model selected
> select #2/A:417-442,562-595
485 atoms, 496 bonds, 60 residues, 1 model selected
> select #2/A:16-73,417-442,562-595
959 atoms, 986 bonds, 118 residues, 1 model selected
> select #2/A:16-73,417-442,562-595,695-729
1238 atoms, 1272 bonds, 153 residues, 1 model selected
> select #2/A:16-73,320-354,417-442,562-595,695-729
1512 atoms, 1555 bonds, 188 residues, 1 model selected
> surface #2 enclose #2/A:16-73,320-354,417-442,562-595,695-729
> close #2.6
> surface #2 enclose #2/A:16-73,191-200,320-354,417-442,562-595,695-729
> select subtract #2.6
1 model selected
> close #2.6
> surface #2 enclose #2/A:16-73,191-200,315-354,417-442,562-595,695-729
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> select #2/B:2-41
327 atoms, 336 bonds, 40 residues, 1 model selected
> select #2/B:2-41,172-176,291-331
693 atoms, 710 bonds, 86 residues, 1 model selected
> select #2/B:2-41,172-176,291-331,392-421
945 atoms, 967 bonds, 116 residues, 1 model selected
> select #2/B:2-41,172-176,291-331,392-423
959 atoms, 981 bonds, 118 residues, 1 model selected
> select #2/B:2-41,172-176,291-331,392-419
929 atoms, 950 bonds, 114 residues, 1 model selected
> select #2/B:2-41,172-176,291-331,392-420
935 atoms, 956 bonds, 115 residues, 1 model selected
> select #2/B:2-41,172-176,291-331,392-420,535-573
1221 atoms, 1249 bonds, 154 residues, 1 model selected
> select #2/B:2-41,172-176,291-331,392-420,535-575
1234 atoms, 1262 bonds, 156 residues, 1 model selected
> select #2/B:2-44,172-176,291-331,392-420,535-575
1263 atoms, 1292 bonds, 159 residues, 1 model selected
> select #2/B:2-44,162-176,291-331,392-420,535-575
1345 atoms, 1378 bonds, 169 residues, 1 model selected
> select #2/B:2-44,162-176,291-331,392-420,535-575,666-705
1684 atoms, 1728 bonds, 209 residues, 1 model selected
> select #2/B:2-44,162-176,291-331,392-420,535-575,665-707
1711 atoms, 1755 bonds, 212 residues, 1 model selected
> surface #2 enclose #2/B:2-44,162-176,291-331,392-420,535-575,665-707
> show #2.5 models
> show #2.4 models
> show #2.3 models
> show #2.2 models
> hide #2.2 models
> select subtract #2.7
1 model selected
> select add #2.7
1711 atoms, 212 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6yez_B SES surface #2.7: minimum, -15.22, mean -0.70,
maximum 13.28
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #2.7
1 model selected
> select add #2.6
1649 atoms, 203 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6yez_A SES surface #2.6: minimum, -15.63, mean -1.25,
maximum 12.20
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #2.6
1 model selected
> hide #!1 models
> hide #3 models
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> show sel cartoons
> show #2.2 models
> select subtract #2.2
4 atoms, 4 bonds, 1 residue, 2 models selected
> select add #2.2
728 atoms, 4 bonds, 98 residues, 1 model selected
> coulombic sel
Coulombic values for 6yez_N SES surface #2.2: minimum, -22.35, mean -7.76,
maximum 6.07
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #2.2
4 atoms, 4 bonds, 1 residue, 2 models selected
> select add #2.2
728 atoms, 4 bonds, 98 residues, 1 model selected
> transparency (#!2 & sel) 30
> hide #2.2 models
> hide #2.3 models
> select #2/N:FES@FE1/C:3003@FE1
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance style radius 0.3
[Repeated 2 time(s)]
> distance style dashes 8
[Repeated 2 time(s)]
> distance style dashes 7
[Repeated 2 time(s)]
> distance style dashes 6
[Repeated 2 time(s)]
> distance style color #00f900
[Repeated 2 time(s)]
> distance #2/C:3003@FE1 #2/N:101@FE1
Distance between 6yez #2/C SF4 3003 FE1 and /N FES 101 FE1: 9.664Å
> show #2.2 models
> show #2.3 models
> select clear
> hide #2.5 models
> show #2.5 models
> save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI
> stromal ridge PetF coulombic interactions.cxs"
> select #2:CL1,CLA
8357 atoms, 8921 bonds, 564 pseudobonds, 141 residues, 2 models selected
> select #2:CL1
Nothing selected
> select #2:CHL
802 atoms, 862 bonds, 60 pseudobonds, 15 residues, 2 models selected
> select #2:CHL
802 atoms, 862 bonds, 60 pseudobonds, 15 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select #2/A-B:CHL
Nothing selected
> select #2/A-B:CL0
65 atoms, 69 bonds, 4 pseudobonds, 1 residue, 2 models selected
> show sel atoms
> select #2/A-B:CL0,CLA
5318 atoms, 5662 bonds, 344 pseudobonds, 86 residues, 2 models selected
> show sel atoms
> color (#!2 & sel) forest green
> color sel byhetero
> select clear
> save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI
> stromal ridge PetF coulombic interactions.cxs"
——— End of log from Sun Sep 3 20:48:37 2023 ———
opened ChimeraX session
> select #2/A &~:16-73,191-200,315-354,417-442,562-595,695-729
7373 atoms, 7698 bonds, 180 pseudobonds, 597 residues, 2 models selected
> select #2/A &~:16-73,191-200,315-354,417-442,562-595,695-729,SF4
7365 atoms, 7686 bonds, 180 pseudobonds, 596 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/B &~:2-44,162-176,291-331,392-420,535-575,665-707
7288 atoms, 7617 bonds, 177 pseudobonds, 580 residues, 2 models selected
> select #2/B &~:2-44,162-176,291-331,392-420,535-575,665-707,SF4
7288 atoms, 7617 bonds, 177 pseudobonds, 580 residues, 2 models selected
> select #2/B &~:2-44,162-176,291-331,392-420,535-575,665-707
7288 atoms, 7617 bonds, 177 pseudobonds, 580 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2 &~/A-E/N
18189 atoms, 18861 bonds, 305 pseudobonds, 1703 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> hide #2.6 models
> hide #2.7 models
> show #2.3 models
> show #2.4 models
> show #2.5 models
> show #2.6 models
> select add #2.6
1649 atoms, 203 residues, 1 model selected
> coulombic sel
Coulombic values for 6yez_A SES surface #2.6: minimum, -23.39, mean -1.01,
maximum 11.65
To also show corresponding color key, enter the above coulombic command and
add key true
> select subtract #2.6
1 model selected
> show #2.7 models
> select add #2.7
1711 atoms, 212 residues, 1 model selected
> coulombic sel
Coulombic values for 6yez_B SES surface #2.7: minimum, -15.05, mean 0.76,
maximum 12.84
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI
> PetF truncated.pdb" models #2
> save "/Users/drornoy/Documents/Grants/NSF-BSF MCB/Nanda Noy 2023/Models/PSI
> stromal ridge PetF truncated for docking.cxs"
——— End of log from Sun Sep 3 21:12:02 2023 ———
opened ChimeraX session
> hide #2.8 models
> show #2.8 models
> hide #2.7 models
> hide #2.6 models
> hide #2.5 models
> hide #2.4 models
> hide #2.3 models
> hide #2.2 models
> open 2fdn
2fdn title:
2[4FE-4S] ferredoxin from clostridium acidi-urici [more info...]
Chain information for 2fdn #5
---
Chain | Description | UniProt
A | FERREDOXIN | FER_CLOAC 1-55
Non-standard residues in 2fdn #5
---
SF4 — iron/sulfur cluster
> Align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2
Unknown command: Align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2
> help help:user
> align #5:61@FE2,FE3,S4,S1 toAtoms #2/N:FES@FE1,FE2,S1,S2
RMSD between 4 atom pairs is 0.181 angstroms
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> sequence chain #2/B
Alignment identifier is 2/B
> select #sel #2/A
Expected an objects specifier or a keyword
> select #2/A
1657 atoms, 1709 bonds, 7 pseudobonds, 204 residues, 3 models selected
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI_PetF/PSI base for design.cxs"
——— End of log from Fri May 17 13:23:40 2024 ———
opened ChimeraX session
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI_PetF/PSI_IsiB_noFld.pdb"
Chain information for PSI_IsiB_noFld.pdb #6
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #!6 to #2 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6yez, chain D (#2) with PSI_IsiB_noFld.pdb, chain A (#6), sequence
alignment score = 488.5
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6yez #2/D, PSI_IsiB_noFld.pdb
#6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 126 pruned atom pairs is 0.707 angstroms; (across all 142 pairs:
5.251)
> hide #!6 models
> show #!1 models
> select #2/A:16-73,191-200,315-354,417-442,562-595,695-729
1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected
> select #2/B
1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected
> select #2/B:2-44,162-176,291-331,392-420,535-575,665-707
1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected
> select #2/A:16-73,191-200,315-354,417-442,562-595,695-729
1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_0.pdb"
Chain information for PSI_6yez_A_B_for_docking_0.pdb #7
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #7 to #2 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6yez, chain B (#2) with PSI_6yez_A_B_for_docking_0.pdb, chain A
(#7), sequence alignment score = 572.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6yez #2/B,
PSI_6yez_A_B_for_docking_0.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 211 pruned atom pairs is 0.247 angstroms; (across all 211 pairs:
0.247)
> matchmaker #7 to #2 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6yez, chain B (#2) with PSI_6yez_A_B_for_docking_0.pdb, chain A
(#7), sequence alignment score = 572.4
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 6yez #2/B,
PSI_6yez_A_B_for_docking_0.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 211 pruned atom pairs is 0.247 angstroms; (across all 211 pairs:
0.247)
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2/A:73,191,200,315,354,417,442,562,595,695,729
108 atoms, 105 bonds, 5 pseudobonds, 11 residues, 2 models selected
> color (#!2 & sel) yellow
> select #2/B:44,162,176,291,331,392,420,535,575,665,707
90 atoms, 81 bonds, 5 pseudobonds, 11 residues, 2 models selected
> color (#!2 & sel) yellow
> hide #7 models
> select #2/B:707
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!2 & sel) hot pink
> select #2/B:2
5 atoms, 4 bonds, 1 residue, 1 model selected
> color (#!2 & sel) blue
> select #2/A:729/B:2
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #2/A:729
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!2 & sel) magenta
> close #7
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/outputs/PSI_6yez_A_B_for_docking_hike6_0.pdb"
Chain information for PSI_6yez_A_B_for_docking_hike6_0.pdb #7
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #7 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6yez, chain B (#2) with PSI_6yez_A_B_for_docking_hike6_0.pdb, chain
A (#7), sequence alignment score = 551.5
RMSD between 211 pruned atom pairs is 0.251 angstroms; (across all 212 pairs:
0.314)
> select #2/A-B:CYS
24 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> color sel byhetero
> select #7/A-B:CYS
16 atoms, 12 bonds, 4 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> select #7/A-B:CYS
16 atoms, 12 bonds, 4 residues, 1 model selected
> hide #!2 models
> show sel atoms
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI Fdx Fld combined.cxs"
——— End of log from Fri May 17 15:09:06 2024 ———
opened ChimeraX session
> hide #!1 models
> show #!2 models
> hide #!4 models
> hide #!5 models
> combine #2#7
Remapping chain ID 'A' in PSI_6yez_A_B_for_docking_hike6_0.pdb #7 to 'F'
> combine #2#7
Remapping chain ID 'A' in PSI_6yez_A_B_for_docking_hike6_0.pdb #7 to 'F'
> select #8/F
1916 atoms, 1915 bonds, 479 residues, 1 model selected
> select #8/F:GLY
392 atoms, 350 bonds, 98 residues, 1 model selected
> help help:user
> select sequence GGG
768 atoms, 735 bonds, 192 residues, 3 models selected
> select sequence GGG|sequence GGGGG
Expected a keyword
> select sequence GGG | GGGGG
Expected a keyword
> select sequence GGGGG
480 atoms, 471 bonds, 120 residues, 3 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/F
Alignment identifier is 8/F
> select #8/F:181-185,221-250,432-436
160 atoms, 157 bonds, 40 residues, 1 model selected
> select sequence GGG
768 atoms, 735 bonds, 192 residues, 3 models selected
> close #8-9
> close #7
> show #!5 models
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> show sel cartoons
> select #2/N:FES
4 atoms, 4 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 4 atom styles
> style sel ball
Changed 4 atom styles
> select #2/N:FES :<2 &/N:CYS
Nothing selected
> select #2/N:FES :<2.5 &/N:CYS
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #2/N:FES :<2.8 &/N:CYS
24 atoms, 20 bonds, 4 residues, 1 model selected
> show sel atoms
> select #2/N :<4.5 /A-E
106 atoms, 95 bonds, 12 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 106 atom styles
> color sel byhetero
> select #2/A-E :<4.5 /N
141 atoms, 134 bonds, 18 residues, 1 model selected
> style sel stick
Changed 141 atom styles
> show sel atoms
> color sel byhetero
> ui tool show H-Bonds
> hbonds sel dashes 6 intraMol false intraRes false reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 AlphaFold A1Z1D6 PshB
2 6yez
3 AlphaFold Q8KCZ6 CbFdx
5 2fdn
6 PSI_IsiB_noFld.pdb
61 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
AlphaFold A1Z1D6 PshB #1/A TYR 3 OH 6yez #2/N ASP 26 OD2 no hydrogen 3.274 N/A
AlphaFold A1Z1D6 PshB #1/A THR 6 OG1 6yez #2/N GLN 58 OE1 no hydrogen 2.570 N/A
AlphaFold A1Z1D6 PshB #1/A CYS 12 SG 6yez #2/N GLY 61 O no hydrogen 3.429 N/A
AlphaFold A1Z1D6 PshB #1/A CYS 20 SG 6yez #2/N SER 38 O no hydrogen 2.641 N/A
AlphaFold A1Z1D6 PshB #1/A THR 33 N 6yez #2/N SER 45 O no hydrogen 2.919 N/A
AlphaFold A1Z1D6 PshB #1/A THR 33 OG1 6yez #2/N SER 45 O no hydrogen 2.129 N/A
AlphaFold A1Z1D6 PshB #1/A LYS 45 NZ 6yez #2/N ALA 41 O no hydrogen 3.560 N/A
6yez #2/A ARG 42 NH1 6yez #2/N GLN 58 O no hydrogen 3.483 N/A
6yez #2/A LYS 46 NZ 6yez #2/N GLY 61 O no hydrogen 3.235 N/A
6yez #2/C LYS 35 NZ 6yez #2/N TYR 37 OH no hydrogen 2.696 N/A
6yez #2/E ARG 106 NH2 6yez #2/N ASP 26 OD1 no hydrogen 3.124 N/A
6yez #2/E THR 117 OG1 6yez #2/N ARG 40 O no hydrogen 3.442 N/A
6yez #2/N ASP 26 N AlphaFold A1Z1D6 PshB #1/A TYR 3 OH no hydrogen 3.023 N/A
6yez #2/N TYR 37 OH 2fdn #5/A HOH 179 O no hydrogen 1.912 N/A
6yez #2/N CYS 39 SG AlphaFold Q8KCZ6 CbFdx #3/A GLU 16 O no hydrogen 3.985 N/A
6yez #2/N ARG 40 NE 2fdn #5/A GLU 15 OE1 no hydrogen 1.468 N/A
6yez #2/N ARG 40 NH1 AlphaFold Q8KCZ6 CbFdx #3/A ASN 39 O no hydrogen 3.073 N/A
6yez #2/N ARG 40 NH2 AlphaFold Q8KCZ6 CbFdx #3/A ALA 45 O no hydrogen 3.441 N/A
6yez #2/N SER 43 OG AlphaFold A1Z1D6 PshB #1/A CYS 19 O no hydrogen 3.491 N/A
6yez #2/N CYS 44 SG AlphaFold A1Z1D6 PshB #1/A CYS 19 O no hydrogen 3.519 N/A
6yez #2/N CYS 44 SG AlphaFold Q8KCZ6 CbFdx #3/A CYS 19 O no hydrogen 3.157 N/A
6yez #2/N SER 45 OG 2fdn #5/A HOH 131 O no hydrogen 3.265 N/A
6yez #2/N GLN 58 N 2fdn #5/A HOH 143 O no hydrogen 2.715 N/A
6yez #2/N GLN 58 N 2fdn #5/A HOH 157 O no hydrogen 3.070 N/A
6yez #2/N SER 59 N 2fdn #5/A HOH 169 O no hydrogen 2.977 N/A
6yez #2/N THR 96 OG1 2fdn #5/A HOH 131 O no hydrogen 2.408 N/A
6yez #2/N THR 96 OG1 2fdn #5/A HOH 147 O no hydrogen 3.427 N/A
AlphaFold Q8KCZ6 CbFdx #3/A THR 6 OG1 6yez #2/N GLN 58 OE1 no hydrogen 2.737 N/A
AlphaFold Q8KCZ6 CbFdx #3/A CYS 12 SG 6yez #2/N GLY 61 O no hydrogen 3.245 N/A
AlphaFold Q8KCZ6 CbFdx #3/A ASP 34 N 6yez #2/N SER 45 O no hydrogen 2.864 N/A
AlphaFold Q8KCZ6 CbFdx #3/A CYS 41 SG 6yez #2/N ARG 40 O no hydrogen 2.641 N/A
2fdn #5/A SER 10 OG (alt loc A) 6yez #2/N TYR 37 O no hydrogen 0.740 N/A
2fdn #5/A CYS 11 SG 6yez #2/N SER 43 OG no hydrogen 3.518 N/A
2fdn #5/A GLU 15 N 6yez #2/N ARG 40 O 2fdn #5/A GLU 15 H 2.748 2.059
2fdn #5/A SER 25 OG (alt loc B) 6yez #2/N TYR 37 OH no hydrogen 2.248 N/A
2fdn #5/A TYR 30 OH 6yez #2/N SER 38 O 2fdn #5/A TYR 30 HH 3.238 2.616
2fdn #5/A CYS 47 SG 6yez #2/N CYS 44 O no hydrogen 1.073 N/A
2fdn #5/A HOH 114 O 6yez #2/N ILE 69 O no hydrogen 2.944 N/A
2fdn #5/A HOH 115 O 6yez #2/N ALA 41 O no hydrogen 2.833 N/A
2fdn #5/A HOH 118 O 6yez #2/N PHE 63 O no hydrogen 2.570 N/A
2fdn #5/A HOH 119 O 6yez #2/N GLN 58 O no hydrogen 2.512 N/A
2fdn #5/A HOH 131 O 6yez #2/N SER 45 OG no hydrogen 3.265 N/A
2fdn #5/A HOH 131 O 6yez #2/N THR 96 OG1 no hydrogen 2.408 N/A
2fdn #5/A HOH 138 O 6yez #2/N TYR 37 O no hydrogen 3.553 N/A
2fdn #5/A HOH 139 O 6yez #2/N GLY 61 O no hydrogen 1.926 N/A
2fdn #5/A HOH 141 O 6yez #2/N ARG 40 O no hydrogen 2.648 N/A
2fdn #5/A HOH 147 O 6yez #2/N THR 96 OG1 no hydrogen 3.427 N/A
2fdn #5/A HOH 148 O 6yez #2/N GLN 58 OE1 no hydrogen 2.593 N/A
2fdn #5/A HOH 153 O 6yez #2/N GLN 58 O no hydrogen 1.710 N/A
2fdn #5/A HOH 154 O 6yez #2/N SER 59 O no hydrogen 2.738 N/A
2fdn #5/A HOH 155 O 6yez #2/N GLN 58 O no hydrogen 3.210 N/A
2fdn #5/A HOH 159 O 6yez #2/N ASP 26 O no hydrogen 3.660 N/A
2fdn #5/A HOH 161 O 6yez #2/N TYR 37 O no hydrogen 2.800 N/A
2fdn #5/A HOH 171 O 6yez #2/N SER 38 O no hydrogen 2.044 N/A
2fdn #5/A HOH 179 O 6yez #2/N TYR 37 OH no hydrogen 1.912 N/A
2fdn #5/A HOH 186 O 6yez #2/N TYR 23 OH no hydrogen 2.883 N/A
2fdn #5/A HOH 190 O 6yez #2/N GLN 58 OE1 no hydrogen 2.133 N/A
2fdn #5/A HOH 190 O 6yez #2/N ILE 69 O no hydrogen 2.801 N/A
2fdn #5/A HOH 194 O 6yez #2/N ILE 69 O no hydrogen 3.081 N/A
PSI_IsiB_noFld.pdb #6/A LYS 28 NZ 6yez #2/N SER 59 O no hydrogen 2.762 N/A
PSI_IsiB_noFld.pdb #6/A LYS 28 NZ 6yez #2/N GLY 61 O no hydrogen 3.493 N/A
61 hydrogen bonds found
> hbonds sel interModel false intraMol false intraRes false reveal true log
> true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 6yez
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6yez #2/A ARG 42 NH1 6yez #2/N GLN 58 O no hydrogen 3.483 N/A
6yez #2/A LYS 46 NZ 6yez #2/N GLY 61 O no hydrogen 3.235 N/A
6yez #2/C LYS 35 NZ 6yez #2/N TYR 37 OH no hydrogen 2.696 N/A
6yez #2/E ARG 106 NH2 6yez #2/N ASP 26 OD1 no hydrogen 3.124 N/A
6yez #2/E THR 117 OG1 6yez #2/N ARG 40 O no hydrogen 3.442 N/A
5 hydrogen bonds found
> select #2/A-E :<4.5 /N
141 atoms, 134 bonds, 18 residues, 1 model selected
> hbonds sel interModel false intraModel false intraMol false intraRes false
> reveal true log true
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 6yez
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> close #7
> hbonds sel interModel false intraMol false intraRes false reveal true log
> true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 6yez
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6yez #2/A ARG 42 NH1 6yez #2/N GLN 58 O no hydrogen 3.483 N/A
6yez #2/A LYS 46 NZ 6yez #2/N GLY 61 O no hydrogen 3.235 N/A
6yez #2/C LYS 35 NZ 6yez #2/N TYR 37 OH no hydrogen 2.696 N/A
6yez #2/E ARG 106 NH2 6yez #2/N ASP 26 OD1 no hydrogen 3.124 N/A
6yez #2/E THR 117 OG1 6yez #2/N ARG 40 O no hydrogen 3.442 N/A
5 hydrogen bonds found
> hide #!5 models
> ui tool show Contacts
> select #2/A-E
5656 atoms, 5816 bonds, 21 pseudobonds, 707 residues, 3 models selected
> contacts sel restrict #2/N distanceOnly 4.5 resSeparation 5 interModel false
> intraMol false select true color #fffb00 reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: False
85 distances
atom1 atom2 distance
6yez #2/C LYS 35 NZ 6yez #2/N TYR 37 OH 2.696
6yez #2/E ARG 106 NH2 6yez #2/N ASP 26 OD1 3.124
6yez #2/C GLN 16 NE2 6yez #2/N CYS 44 CB 3.133
6yez #2/A LYS 46 NZ 6yez #2/N GLY 61 O 3.235
6yez #2/C ILE 12 CD1 6yez #2/N CYS 39 CA 3.319
6yez #2/C GLN 16 NE2 6yez #2/N CYS 44 CA 3.355
6yez #2/E ARG 106 NH1 6yez #2/N TYR 23 CE2 3.379
6yez #2/E THR 117 OG1 6yez #2/N ARG 40 O 3.442
6yez #2/C LYS 35 CG 6yez #2/N TYR 37 OH 3.473
6yez #2/A ARG 42 NH1 6yez #2/N GLN 58 O 3.483
6yez #2/A ARG 42 NH1 6yez #2/N ILE 69 CG1 3.526
6yez #2/C LYS 35 CD 6yez #2/N TYR 37 OH 3.585
6yez #2/C LYS 35 CE 6yez #2/N TYR 37 OH 3.650
6yez #2/A LYS 46 CE 6yez #2/N SER 59 O 3.708
6yez #2/C ILE 12 CD1 6yez #2/N CYS 39 N 3.715
6yez #2/C ILE 12 CD1 6yez #2/N SER 38 O 3.754
6yez #2/C CYS 14 CA 6yez #2/N SER 38 OG 3.781
6yez #2/A LYS 46 CD 6yez #2/N SER 59 O 3.788
6yez #2/C ILE 12 CD1 6yez #2/N CYS 39 CB 3.788
6yez #2/C GLN 16 NE2 6yez #2/N SER 45 N 3.796
6yez #2/E ARG 70 CZ 6yez #2/N GLU 30 OE2 3.802
6yez #2/A ARG 42 NH1 6yez #2/N ILE 69 CD1 3.805
6yez #2/E THR 117 OG1 6yez #2/N ALA 41 CB 3.818
6yez #2/A ARG 42 CZ 6yez #2/N ILE 69 CG1 3.820
6yez #2/E ARG 70 NH1 6yez #2/N GLU 30 OE2 3.841
6yez #2/C ILE 12 CD1 6yez #2/N SER 38 C 3.847
6yez #2/C CYS 14 CB 6yez #2/N SER 38 OG 3.922
6yez #2/C GLN 16 NE2 6yez #2/N SER 43 O 3.930
6yez #2/A LYS 46 CG 6yez #2/N SER 59 OG 3.975
6yez #2/A LYS 46 CB 6yez #2/N SER 59 OG 3.987
6yez #2/A ARG 42 NE 6yez #2/N ILE 69 CG1 3.994
6yez #2/E ARG 70 NE 6yez #2/N GLU 30 OE2 4.021
6yez #2/E THR 117 OG1 6yez #2/N ALA 41 CA 4.021
6yez #2/C LYS 35 NZ 6yez #2/N TYR 37 CZ 4.039
6yez #2/C GLN 16 NE2 6yez #2/N CYS 44 C 4.040
6yez #2/A LYS 46 CG 6yez #2/N SER 59 O 4.085
6yez #2/C GLN 16 CD 6yez #2/N CYS 44 CB 4.085
6yez #2/A ARG 42 CD 6yez #2/N GLU 70 OE1 4.097
6yez #2/E THR 117 OG1 6yez #2/N ARG 40 C 4.100
6yez #2/C GLN 16 OE1 6yez #2/N PHE 63 CE2 4.103
6yez #2/C GLN 16 OE1 6yez #2/N PHE 63 CZ 4.120
6yez #2/E ARG 106 CZ 6yez #2/N TYR 23 CE2 4.121
6yez #2/C ARG 19 NH1 6yez #2/N THR 96 CG2 4.133
6yez #2/C GLN 16 CG 6yez #2/N CYS 44 CB 4.147
6yez #2/C PRO 59 CG 6yez #2/N CYS 39 CB 4.148
6yez #2/C PRO 59 CB 6yez #2/N SER 43 OG 4.171
6yez #2/E ARG 106 NH1 6yez #2/N TYR 23 CD2 4.173
6yez #2/C LYS 35 CG 6yez #2/N TYR 37 CZ 4.175
6yez #2/A LYS 46 NZ 6yez #2/N SER 59 O 4.182
6yez #2/A ARG 42 NE 6yez #2/N ILE 69 CG2 4.190
6yez #2/C LYS 35 CB 6yez #2/N TYR 37 OH 4.190
6yez #2/C GLN 16 CD 6yez #2/N SER 43 O 4.191
6yez #2/E ARG 106 CZ 6yez #2/N ASP 26 OD1 4.192
6yez #2/C GLN 16 NE2 6yez #2/N PHE 63 CE2 4.196
6yez #2/A ARG 42 NH1 6yez #2/N GLN 58 CB 4.208
6yez #2/E ARG 70 NH2 6yez #2/N GLU 30 OE2 4.209
6yez #2/C ILE 12 O 6yez #2/N SER 38 CB 4.235
6yez #2/E ARG 106 NH1 6yez #2/N TYR 23 OH 4.249
6yez #2/A LYS 46 CG 6yez #2/N SER 59 CA 4.265
6yez #2/A LYS 46 CE 6yez #2/N GLY 61 O 4.269
6yez #2/A LYS 46 CE 6yez #2/N GLN 58 O 4.274
6yez #2/E ARG 106 NH1 6yez #2/N TYR 23 CZ 4.275
6yez #2/C CYS 14 CA 6yez #2/N SER 38 CB 4.277
6yez #2/E ARG 106 NH2 6yez #2/N TYR 23 CE2 4.281
6yez #2/E ARG 106 NH2 6yez #2/N ASP 26 CG 4.311
6yez #2/C GLN 16 CG 6yez #2/N SER 43 O 4.316
6yez #2/C GLN 16 CD 6yez #2/N PHE 63 CE2 4.327
6yez #2/C PRO 59 CB 6yez #2/N CYS 39 CB 4.328
6yez #2/C GLN 16 CD 6yez #2/N CYS 44 CA 4.366
6yez #2/A LYS 46 NZ 6yez #2/N GLY 61 C 4.370
6yez #2/C ILE 12 CB 6yez #2/N SER 38 O 4.393
6yez #2/A ARG 42 NE 6yez #2/N ILE 69 CB 4.406
6yez #2/E THR 117 OG1 6yez #2/N ALA 41 N 4.411
6yez #2/E ARG 70 NH2 6yez #2/N ASP 26 O 4.425
6yez #2/C LYS 35 CB 6yez #2/N TYR 37 CZ 4.438
6yez #2/E ARG 106 NH1 6yez #2/N ASP 26 OD1 4.440
6yez #2/A ARG 42 NE 6yez #2/N GLU 70 OE1 4.443
6yez #2/C LYS 35 CD 6yez #2/N TYR 37 CZ 4.447
6yez #2/E THR 117 CB 6yez #2/N ARG 40 O 4.448
6yez #2/C ILE 12 CD1 6yez #2/N CYS 39 C 4.449
6yez #2/A ARG 42 NH1 6yez #2/N GLN 58 C 4.456
6yez #2/C ILE 12 CG1 6yez #2/N SER 38 O 4.458
6yez #2/E VAL 115 CG2 6yez #2/N ALA 41 CB 4.473
6yez #2/A LYS 46 CE 6yez #2/N SER 59 CA 4.493
6yez #2/A LYS 46 CE 6yez #2/N SER 59 C 4.500
85 distances
> show #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/N
Alignment identifier is 2/N
> select #2/N:23,26,30,37-45,58-63,96
142 atoms, 139 bonds, 19 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 142 atom styles
> color sel byhetero
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 19 items
> help help:user
> split #2 atoms /N
Split 6yez (#2) into 2 models
Chain information for 6yez 1 #2.1
---
Chain | Description
N | No description available
Chain information for 6yez 2 #2.2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
> hide #!2.1 models
> split #5:1-14
Did not split 2fdn, has only one piece
> select #5:1-14
168 atoms, 168 bonds, 14 residues, 1 model selected
> select #5:1-14,17-23,37-43
334 atoms, 333 bonds, 28 residues, 1 model selected
> select #5:1-14,17-23,31-43
409 atoms, 408 bonds, 34 residues, 1 model selected
> select #5:1-14,17-23,31-55
558 atoms, 559 bonds, 46 residues, 1 model selected
> color sel medium blue
> color sel byhetero
> hide #!2 models
> select #2/A-E :<4.5 
178 atoms, 150 bonds, 39 residues, 1 model selected
> select #2/A-E :<5 
213 atoms, 181 bonds, 45 residues, 1 model selected
> select #2/A-E :<3 
98 atoms, 86 bonds, 16 residues, 1 model selected
> select #2/A-E :<4 
164 atoms, 140 bonds, 33 residues, 1 model selected
> select #2/A-E :<4 &~:HOH
144 atoms, 140 bonds, 13 residues, 1 model selected
> select #2/A-E :<3 &~:HOH
88 atoms, 86 bonds, 6 residues, 1 model selected
> select #2/A-E :<2 &~:HOH
35 atoms, 33 bonds, 2 residues, 1 model selected
> select #2/A-E :<4 &~:HOH
144 atoms, 140 bonds, 13 residues, 1 model selected
> ui tool show Clashes
> show #!2 models
> clashes sel intraModel false ignoreHiddenModels true select true color
> #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
10 clashes
atom1 atom2 overlap distance
2fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 O 1.079 2.041
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C GLN 16 NE2 1.030 2.310
2fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 O 1.019 1.401
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C GLN 16 CG 0.900 2.680
2fdn #5/A ILE 9 HD12 6yez 2 #2.2/C GLN 16 NE2 0.839 1.801
2fdn #5/A CYS 11 HA 6yez 2 #2.2/C ILE 12 CD1 0.775 2.105
2fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 0.738 2.382
2fdn #5/A GLU 15 OE2 6yez 2 #2.2/E VAL 91 CG1 0.706 2.654
2fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 0.661 1.979
2fdn #5/A ILE 9 HD13 6yez 2 #2.2/C GLN 16 CG 0.632 2.248
10 clashes
> select #5
762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 151 items
> color sel byhetero
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"
> select #5:12,14,16,91
31 atoms, 29 bonds, 3 residues, 1 model selected
> select #5:9,11,15,49
60 atoms, 56 bonds, 4 residues, 1 model selected
> hide sel atoms
> show sel atoms
> color sel orange
> color sel byhetero
> show #!2.1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!2.2 models
> select #2/N:FES@FE1,FE2,S1,S2:44@SG
5 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #2/N:FES@FE1,FE2,S1,S2:44@SG:39@SG:47@SG:77@SG
8 atoms, 4 bonds, 4 pseudobonds, 5 residues, 2 models selected
> style sel ball
Changed 8 atom styles
> align #5:61@FE2,FE3,S4,S1,S3,S2:11@SG:14@SG toAtomsl
> #2/N:FES@FE1,FE2,S1,S2:44@SG:47@SG:39@SG:77@SG
Expected a keyword
> 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
RMSD between 8 atom pairs is 0.719 angstroms
> close #7
> select #2/A-E :<4 &~:HOH
120 atoms, 118 bonds, 10 residues, 1 model selected
> hide #!2 models
> show #!2 models
> select #5:1-55 :<4/A-E
86 atoms, 80 bonds, 11 residues, 1 model selected
> clashes sel intraModel false ignoreHiddenModels true select true color
> #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
31 clashes
atom1 atom2 overlap distance
6yez 2 #2.2/E ARG 106 CZ 2fdn #5/A HOH 183 O 2.185 0.885
6yez 2 #2.2/C ARG 19 CZ 2fdn #5/A HOH 149 O 1.833 1.237
6yez 2 #2.2/E ARG 106 NE 2fdn #5/A HOH 183 O 1.591 1.109
6yez 2 #2.2/E VAL 91 O 2fdn #5/A HOH 182 O 1.380 1.100
6yez 2 #2.2/E VAL 91 C 2fdn #5/A HOH 182 O 1.295 1.775
6yez 2 #2.2/C GLN 16 NE2 2fdn #5/A VAL 49 HG11 1.244 1.396
6yez 2 #2.2/C ARG 19 NH1 2fdn #5/A HOH 149 O 1.149 1.551
6yez 2 #2.2/C CYS 14 O 2fdn #5/A ILE 9 HG22 1.100 1.320
6yez 2 #2.2/C CYS 14 CB 2fdn #5/A ILE 9 HD11 1.095 1.785
6yez 2 #2.2/C CYS 14 O 2fdn #5/A ILE 9 CG2 1.094 2.026
6yez 2 #2.2/C CYS 14 CB 2fdn #5/A ILE 9 CD1 1.091 2.489
6yez 2 #2.2/E ARG 106 CD 2fdn #5/A HOH 183 O 1.078 2.262
6yez 2 #2.2/C ARG 19 NE 2fdn #5/A HOH 117 O 1.078 1.622
6yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 HB 1.036 1.844
6yez 2 #2.2/C GLN 16 NE2 2fdn #5/A VAL 49 CG1 1.032 2.308
6yez 2 #2.2/E ARG 106 NH2 2fdn #5/A HOH 183 O 1.015 1.685
6yez 2 #2.2/C ARG 19 NE 2fdn #5/A HOH 149 O 0.963 1.737
6yez 2 #2.2/E VAL 91 CG1 2fdn #5/A HOH 182 O 0.944 2.396
6yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 CB 0.919 2.661
6yez 2 #2.2/E VAL 91 CA 2fdn #5/A HOH 182 O 0.915 2.425
6yez 2 #2.2/C ILE 12 CD1 2fdn #5/A CYS 11 HA 0.873 2.007
6yez 2 #2.2/C ARG 19 CD 2fdn #5/A HOH 149 O 0.871 2.469
6yez 2 #2.2/E ARG 106 NH1 2fdn #5/A HOH 183 O 0.810 1.890
6yez 2 #2.2/C ARG 19 CZ 2fdn #5/A HOH 117 O 0.807 2.263
6yez 2 #2.2/C CYS 14 CB 2fdn #5/A ILE 9 CG1 0.774 2.806
6yez 2 #2.2/C CYS 14 O 2fdn #5/A ILE 9 CB 0.742 2.378
6yez 2 #2.2/C CYS 14 O 2fdn #5/A ILE 9 CD1 0.695 2.425
6yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 CG1 0.683 2.897
6yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 HD11 0.668 2.212
6yez 2 #2.2/C CYS 14 CA 2fdn #5/A ILE 9 CD1 0.667 2.913
6yez 2 #2.2/C GLN 16 NE2 2fdn #5/A PRO 48 CG 0.613 2.727
31 clashes
> close #7
> select #5:1-55
652 atoms, 657 bonds, 55 residues, 1 model selected
> clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select
> true color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
16 clashes
atom1 atom2 overlap distance
2fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 1.244 1.396
2fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 O 1.100 1.320
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CB 1.095 1.785
2fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 1.094 2.026
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CB 1.091 2.489
2fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CA 1.036 1.844
2fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 NE2 1.032 2.308
2fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CA 0.919 2.661
2fdn #5/A CYS 11 HA 6yez 2 #2.2/C ILE 12 CD1 0.873 2.007
2fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CB 0.774 2.806
2fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 O 0.742 2.378
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 O 0.695 2.425
2fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CA 0.683 2.897
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CA 0.668 2.212
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CA 0.667 2.913
2fdn #5/A PRO 48 CG 6yez 2 #2.2/C GLN 16 NE2 0.613 2.727
16 clashes
> select #5:9,11,48-49
59 atoms, 57 bonds, 4 residues, 1 model selected
> 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
RMSD between 10 atom pairs is 0.673 angstroms
> select #5:1-55
652 atoms, 657 bonds, 55 residues, 1 model selected
> clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select
> true color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
15 clashes
atom1 atom2 overlap distance
2fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 1.558 1.082
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CB 1.548 1.332
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CB 1.462 2.118
2fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 O 1.448 0.972
2fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 NE2 1.337 2.003
2fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 1.287 1.833
2fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CA 1.254 1.626
2fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CA 1.171 2.409
2fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CB 1.000 2.580
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CA 0.871 2.709
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CA 0.845 2.035
2fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CA 0.807 2.773
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 SG 0.730 2.040
2fdn #5/A CYS 11 HA 6yez 2 #2.2/C ILE 12 CD1 0.693 2.187
2fdn #5/A PRO 48 HB2 6yez 2 #2.2/C GLN 16 CD 0.623 1.987
15 clashes
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 98 items
> hide #!2.2 models
> 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
RMSD between 11 atom pairs is 0.654 angstroms
> select #5:1-55
652 atoms, 657 bonds, 55 residues, 1 model selected
> clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select
> true color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
0 clashes
atom1 atom2 overlap distance
No clashes
> show #!2.2 models
> clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select
> true color #fffb00 reveal true log true
No atoms match given atom specifier
> select #5:1-55
652 atoms, 657 bonds, 55 residues, 1 model selected
> clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select
> true color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
14 clashes
atom1 atom2 overlap distance
2fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 1.670 0.970
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CB 1.590 1.290
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CB 1.488 2.092
2fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 O 1.470 0.950
2fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 NE2 1.451 1.889
2fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 1.311 1.809
2fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CA 1.236 1.644
2fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CA 1.157 2.423
2fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CB 0.994 2.586
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CA 0.873 2.707
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CA 0.853 2.027
2fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CA 0.794 2.786
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 SG 0.743 2.027
2fdn #5/A CYS 11 HA 6yez 2 #2.2/C ILE 12 CD1 0.649 2.231
14 clashes
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> align #5:11@CB,CA,C:14 toAtoms #2/N:39@CB,CA,C
Unequal number of atoms to pair, 13 and 3
> align #5:11@CB,CA,C toAtoms #2/N:39@CB,CA,C
RMSD between 3 atom pairs is 0.032 angstroms
> hide #!2.1 models
> select #5:1-55
652 atoms, 657 bonds, 55 residues, 1 model selected
> clashes sel restrict #2/A-E intraModel false ignoreHiddenModels true select
> true color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Detect intra-residue clashes: False
Detect intra-molecule clashes: True
40 clashes
atom1 atom2 overlap distance
2fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 NE2 2.426 0.914
2fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 O 2.354 0.766
2fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 NE2 2.183 0.457
2fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CA 2.131 0.749
2fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CA 1.896 1.684
2fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 CD 1.861 1.449
2fdn #5/A ILE 9 HG23 6yez 2 #2.2/C CYS 14 O 1.757 0.663
2fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 CD 1.639 0.971
2fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 C 1.597 1.713
2fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CB 1.539 2.041
2fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 CB 1.513 2.067
2fdn #5/A VAL 49 CB 6yez 2 #2.2/C GLN 16 NE2 1.500 1.840
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 CB 1.492 2.088
2fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 O 1.464 0.956
2fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 CB 1.369 1.511
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 SG 1.353 1.417
2fdn #5/A ILE 9 HD11 6yez 2 #2.2/C CYS 14 CB 1.336 1.544
2fdn #5/A VAL 49 HG12 6yez 2 #2.2/C GLN 16 NE2 1.275 1.365
2fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 OE1 1.226 1.894
2fdn #5/A ILE 9 CG2 6yez 2 #2.2/C CYS 14 CA 1.180 2.400
2fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 C 1.152 2.158
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C CYS 14 SG 1.135 2.335
2fdn #5/A VAL 49 HG13 6yez 2 #2.2/C GLN 16 OE1 1.118 1.302
2fdn #5/A ILE 9 CB 6yez 2 #2.2/C CYS 14 O 1.081 2.039
2fdn #5/A ILE 9 HG23 6yez 2 #2.2/C CYS 14 C 1.052 1.558
2fdn #5/A ILE 9 HG22 6yez 2 #2.2/C CYS 14 C 1.047 1.563
2fdn #5/A VAL 49 HG13 6yez 2 #2.2/C GLN 16 CD 1.029 1.581
2fdn #5/A ILE 9 CD1 6yez 2 #2.2/C GLN 16 CG 1.005 2.575
2fdn #5/A ILE 9 HD12 6yez 2 #2.2/C GLN 16 CG 0.986 1.894
2fdn #5/A VAL 49 CG2 6yez 2 #2.2/C GLN 16 NE2 0.921 2.419
2fdn #5/A VAL 49 HG13 6yez 2 #2.2/C GLN 16 NE2 0.893 1.747
2fdn #5/A ILE 9 HG21 6yez 2 #2.2/C CYS 14 O 0.882 1.538
2fdn #5/A ILE 9 CG1 6yez 2 #2.2/C CYS 14 CA 0.881 2.699
2fdn #5/A ILE 9 CA 6yez 2 #2.2/C CYS 14 CA 0.878 2.702
2fdn #5/A ILE 9 HG13 6yez 2 #2.2/C CYS 14 CB 0.821 2.059
2fdn #5/A VAL 49 HG12 6yez 2 #2.2/C GLN 16 CD 0.810 1.800
2fdn #5/A ILE 9 HB 6yez 2 #2.2/C CYS 14 C 0.800 1.810
2fdn #5/A VAL 49 CG1 6yez 2 #2.2/C GLN 16 CG 0.772 2.808
2fdn #5/A VAL 49 CA 6yez 2 #2.2/C GLN 16 NE2 0.683 2.657
2fdn #5/A VAL 49 HG11 6yez 2 #2.2/C GLN 16 CG 0.683 2.197
40 clashes
> select #5:9,49
35 atoms, 33 bonds, 2 residues, 1 model selected
> hide sel atoms
> show #!2.1 models
> select #2/C:16
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> select #2/C:16|#5:1-55
661 atoms, 665 bonds, 17 pseudobonds, 56 residues, 3 models selected
> select #2/C:16/N
737 atoms, 748 bonds, 4 pseudobonds, 99 residues, 3 models selected
> hbonds sel restrict both interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2.1 6yez 1
2.2 6yez 2
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> ui tool show Contacts
> contacts sel restrict both resSeparation 5 interModel false intraMol false
> select true color #fffb00 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
19 contacts
atom1 atom2 overlap distance
6yez 1 #2.1/N GLY 42 CA 6yez 1 #2.1/N FES 101 S2 0.389 3.261
6yez 1 #2.1/N CYS 44 SG 6yez 1 #2.1/N FES 101 FE1 0.123 2.277
6yez 1 #2.1/N FES 101 FE1 6yez 1 #2.1/N CYS 39 SG 0.081 2.319
6yez 1 #2.1/N FES 101 FE2 6yez 1 #2.1/N CYS 47 SG 0.040 2.360
6yez 1 #2.1/N CYS 44 O 6yez 1 #2.1/N FES 101 S2 -0.022 3.212
6yez 1 #2.1/N LEU 75 CD1 6yez 1 #2.1/N FES 101 S2 -0.065 3.715
6yez 1 #2.1/N CYS 44 N 6yez 1 #2.1/N FES 101 S2 -0.080 3.090
6yez 1 #2.1/N GLY 42 C 6yez 1 #2.1/N FES 101 S2 -0.102 3.482
6yez 1 #2.1/N CYS 44 CA 6yez 1 #2.1/N FES 101 S2 -0.180 3.830
6yez 1 #2.1/N CYS 77 SG 6yez 1 #2.1/N FES 101 FE2 -0.190 2.590
6yez 1 #2.1/N CYS 47 CB 6yez 1 #2.1/N FES 101 S1 -0.219 3.869
6yez 1 #2.1/N SER 43 N 6yez 1 #2.1/N FES 101 S2 -0.245 3.255
6yez 1 #2.1/N ARG 40 N 6yez 1 #2.1/N FES 101 S1 -0.246 3.256
6yez 1 #2.1/N LEU 75 CD2 6yez 1 #2.1/N FES 101 S2 -0.266 3.916
6yez 1 #2.1/N SER 38 N 6yez 1 #2.1/N FES 101 S1 -0.279 3.289
6yez 1 #2.1/N TYR 37 CB 6yez 1 #2.1/N FES 101 S1 -0.280 3.930
6yez 1 #2.1/N ARG 40 CA 6yez 1 #2.1/N FES 101 S1 -0.346 3.996
6yez 1 #2.1/N FES 101 S1 6yez 1 #2.1/N TYR 37 CA -0.381 4.031
6yez 1 #2.1/N FES 101 S2 6yez 1 #2.1/N CYS 39 SG -0.394 3.534
19 contacts
> select #2/C:16/N
737 atoms, 748 bonds, 23 pseudobonds, 99 residues, 4 models selected
> select #2/C:16
9 atoms, 8 bonds, 1 residue, 1 model selected
> contacts sel restrict #2/N resSeparation 5 interModel false intraMol false
> select true color #fffb00 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> select #2/C:14
6 atoms, 5 bonds, 1 residue, 1 model selected
> contacts sel restrict #2/N resSeparation 5 interModel false intraMol false
> select true color #fffb00 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> close #8
> select #5:9,49
35 atoms, 33 bonds, 2 residues, 1 model selected
> show sel atoms
> hide #!2.1 models
> show #!2.1 models
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> style sel stick
Changed 728 atom styles
> color sel byhetero
> ui tool show Contacts
> contacts sel restrict #2/A-E resSeparation 5 interModel false intraMol false
> select true color #00f900 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict #2/A-E resSeparation 5 intraMol false select true
> color #00f900 reveal true log true
No atoms match given atom specifier
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> contacts sel restrict #2/A-E resSeparation 5 intraMol false select true
> color #00f900 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> select #2/N :<4.5 /A-E
106 atoms, 95 bonds, 12 residues, 1 model selected
> contacts sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false
> select true color #00f900 reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: False
44 distances
atom1 atom2 distance
6yez 2 #2.2/C CYS 14 SG 6yez 2 #2.2/C SF4 3003 FE1 2.513
6yez 2 #2.2/C LYS 35 NZ 6yez 2 #2.2/E ASP 94 OD1 2.817
6yez 2 #2.2/C LYS 35 CE 6yez 2 #2.2/E ASP 94 OD1 3.169
6yez 2 #2.2/C LYS 35 NZ 6yez 2 #2.2/E ASP 94 CB 3.301
6yez 2 #2.2/C CYS 14 SG 6yez 2 #2.2/C SF4 3003 S2 3.328
6yez 2 #2.2/C CYS 14 N 6yez 2 #2.2/C SF4 3003 S3 3.398
6yez 2 #2.2/C LYS 35 NZ 6yez 2 #2.2/E ASP 94 CG 3.427
6yez 2 #2.2/C CYS 14 CB 6yez 2 #2.2/C SF4 3003 FE1 3.477
6yez 2 #2.2/C PRO 59 CD 6yez 2 #2.2/C SF4 3003 S2 3.547
6yez 2 #2.2/C CYS 14 N 6yez 2 #2.2/C SF4 3003 FE1 3.558
6yez 2 #2.2/C ILE 12 N 6yez 2 #2.2/C SF4 3003 S4 3.574
6yez 2 #2.2/C ARG 19 CZ 6yez 2 #2.2/D GLU 176 CB 3.741
6yez 2 #2.2/C PRO 59 CD 6yez 2 #2.2/C SF4 3003 FE1 3.759
6yez 2 #2.2/C ARG 19 NH1 6yez 2 #2.2/D GLU 176 CG 3.791
6yez 2 #2.2/C LYS 35 CE 6yez 2 #2.2/E ASP 94 CB 3.834
6yez 2 #2.2/C PRO 59 O 6yez 2 #2.2/E VAL 115 CG1 3.837
6yez 2 #2.2/C CYS 14 SG 6yez 2 #2.2/C SF4 3003 S3 3.855
6yez 2 #2.2/C ARG 19 NH1 6yez 2 #2.2/D GLU 176 CB 3.861
6yez 2 #2.2/C LYS 35 CE 6yez 2 #2.2/E ASP 94 CG 3.942
6yez 2 #2.2/C ARG 19 CG 6yez 2 #2.2/D GLU 176 CB 3.953
6yez 2 #2.2/C ARG 19 NH2 6yez 2 #2.2/D GLU 176 O 3.953
6yez 2 #2.2/C PRO 59 O 6yez 2 #2.2/E VAL 115 CG2 3.956
6yez 2 #2.2/C ARG 19 NH2 6yez 2 #2.2/D GLU 176 CB 3.961
6yez 2 #2.2/C CYS 14 CA 6yez 2 #2.2/C SF4 3003 FE1 3.964
6yez 2 #2.2/C ILE 12 CG1 6yez 2 #2.2/C SF4 3003 S4 3.982
6yez 2 #2.2/C ARG 19 NE 6yez 2 #2.2/D GLU 176 CB 4.078
6yez 2 #2.2/C LYS 35 CE 6yez 2 #2.2/E THR 99 CG2 4.085
6yez 2 #2.2/C PRO 59 CD 6yez 2 #2.2/C SF4 3003 FE3 4.085
6yez 2 #2.2/C PRO 59 CD 6yez 2 #2.2/C SF4 3003 S4 4.089
6yez 2 #2.2/C ARG 19 CZ 6yez 2 #2.2/D GLU 176 CG 4.095
6yez 2 #2.2/C CYS 14 C 6yez 2 #2.2/C SF4 3003 S3 4.143
6yez 2 #2.2/C ILE 12 N 6yez 2 #2.2/C SF4 3003 FE2 4.195
6yez 2 #2.2/C CYS 14 CA 6yez 2 #2.2/C SF4 3003 S3 4.198
6yez 2 #2.2/C ARG 19 NH2 6yez 2 #2.2/D GLU 176 CG 4.263
6yez 2 #2.2/C LYS 35 CG 6yez 2 #2.2/E ASP 94 OD1 4.284
6yez 2 #2.2/C LYS 35 CD 6yez 2 #2.2/E ASP 94 OD1 4.295
6yez 2 #2.2/C PRO 59 O 6yez 2 #2.2/E VAL 115 CB 4.335
6yez 2 #2.2/C CYS 14 C 6yez 2 #2.2/C SF4 3003 FE1 4.384
6yez 2 #2.2/C PRO 59 N 6yez 2 #2.2/C SF4 3003 S2 4.384
6yez 2 #2.2/C CYS 14 SG 6yez 2 #2.2/C SF4 3003 FE4 4.408
6yez 2 #2.2/C GLN 16 N 6yez 2 #2.2/C SF4 3003 S2 4.411
6yez 2 #2.2/C ILE 12 CG1 6yez 2 #2.2/C SF4 3003 FE1 4.414
6yez 2 #2.2/C PRO 59 CG 6yez 2 #2.2/C SF4 3003 FE1 4.463
6yez 2 #2.2/C ILE 12 CG2 6yez 2 #2.2/E ASN 119 ND2 4.478
44 distances
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> contacts sel restrict #2/A-E distanceOnly 4.5 resSeparation 5 intraMol false
> select true color #00f900 reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: False
0 distances
atom1 atom2 distance
No distances
> close #8
> close #6
> close #3-4
> close #1
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"
> rename #2 id 1
> rename #1 id 2
> rename #5 id 1
> rename #7 id 3
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"
> combine #2.1#2.2
> hide #!2 models
> select #4/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> contacts sel restrict #4/A-E distanceOnly 4.5 resSeparation 5 intraMol false
> select true color #00f900 reveal true log true
Ignore distances between atoms separated by 4 bonds or less
Ignore distances between atoms in residues less than 5 apart in sequence
Detect intra-residue distances: False
Detect intra-molecule distances: False
85 distances
atom1 atom2 distance
combination #4/N TYR 37 OH combination #4/C LYS 35 NZ 2.696
combination #4/N ASP 26 OD1 combination #4/E ARG 106 NH2 3.124
combination #4/N CYS 44 CB combination #4/C GLN 16 NE2 3.133
combination #4/N GLY 61 O combination #4/A LYS 46 NZ 3.235
combination #4/N CYS 39 CA combination #4/C ILE 12 CD1 3.319
combination #4/N CYS 44 CA combination #4/C GLN 16 NE2 3.355
combination #4/N TYR 23 CE2 combination #4/E ARG 106 NH1 3.379
combination #4/N ARG 40 O combination #4/E THR 117 OG1 3.442
combination #4/N TYR 37 OH combination #4/C LYS 35 CG 3.473
combination #4/N GLN 58 O combination #4/A ARG 42 NH1 3.483
combination #4/N ILE 69 CG1 combination #4/A ARG 42 NH1 3.526
combination #4/N TYR 37 OH combination #4/C LYS 35 CD 3.585
combination #4/N TYR 37 OH combination #4/C LYS 35 CE 3.650
combination #4/N SER 59 O combination #4/A LYS 46 CE 3.708
combination #4/N CYS 39 N combination #4/C ILE 12 CD1 3.715
combination #4/N SER 38 O combination #4/C ILE 12 CD1 3.754
combination #4/N SER 38 OG combination #4/C CYS 14 CA 3.781
combination #4/N SER 59 O combination #4/A LYS 46 CD 3.788
combination #4/N CYS 39 CB combination #4/C ILE 12 CD1 3.788
combination #4/N SER 45 N combination #4/C GLN 16 NE2 3.796
combination #4/N GLU 30 OE2 combination #4/E ARG 70 CZ 3.802
combination #4/N ILE 69 CD1 combination #4/A ARG 42 NH1 3.805
combination #4/N ALA 41 CB combination #4/E THR 117 OG1 3.818
combination #4/N ILE 69 CG1 combination #4/A ARG 42 CZ 3.820
combination #4/N GLU 30 OE2 combination #4/E ARG 70 NH1 3.841
combination #4/N SER 38 C combination #4/C ILE 12 CD1 3.847
combination #4/N SER 38 OG combination #4/C CYS 14 CB 3.922
combination #4/N SER 43 O combination #4/C GLN 16 NE2 3.930
combination #4/N SER 59 OG combination #4/A LYS 46 CG 3.975
combination #4/N SER 59 OG combination #4/A LYS 46 CB 3.987
combination #4/N ILE 69 CG1 combination #4/A ARG 42 NE 3.994
combination #4/N GLU 30 OE2 combination #4/E ARG 70 NE 4.021
combination #4/N ALA 41 CA combination #4/E THR 117 OG1 4.021
combination #4/N TYR 37 CZ combination #4/C LYS 35 NZ 4.039
combination #4/N CYS 44 C combination #4/C GLN 16 NE2 4.040
combination #4/N SER 59 O combination #4/A LYS 46 CG 4.085
combination #4/N CYS 44 CB combination #4/C GLN 16 CD 4.085
combination #4/N GLU 70 OE1 combination #4/A ARG 42 CD 4.097
combination #4/N ARG 40 C combination #4/E THR 117 OG1 4.100
combination #4/N PHE 63 CE2 combination #4/C GLN 16 OE1 4.103
combination #4/N PHE 63 CZ combination #4/C GLN 16 OE1 4.120
combination #4/N TYR 23 CE2 combination #4/E ARG 106 CZ 4.121
combination #4/N THR 96 CG2 combination #4/C ARG 19 NH1 4.133
combination #4/N CYS 44 CB combination #4/C GLN 16 CG 4.147
combination #4/N CYS 39 CB combination #4/C PRO 59 CG 4.148
combination #4/N SER 43 OG combination #4/C PRO 59 CB 4.171
combination #4/N TYR 23 CD2 combination #4/E ARG 106 NH1 4.173
combination #4/N TYR 37 CZ combination #4/C LYS 35 CG 4.175
combination #4/N SER 59 O combination #4/A LYS 46 NZ 4.182
combination #4/N ILE 69 CG2 combination #4/A ARG 42 NE 4.190
combination #4/N TYR 37 OH combination #4/C LYS 35 CB 4.190
combination #4/N SER 43 O combination #4/C GLN 16 CD 4.191
combination #4/N ASP 26 OD1 combination #4/E ARG 106 CZ 4.192
combination #4/N PHE 63 CE2 combination #4/C GLN 16 NE2 4.196
combination #4/N GLN 58 CB combination #4/A ARG 42 NH1 4.208
combination #4/N GLU 30 OE2 combination #4/E ARG 70 NH2 4.209
combination #4/N SER 38 CB combination #4/C ILE 12 O 4.235
combination #4/N TYR 23 OH combination #4/E ARG 106 NH1 4.249
combination #4/N SER 59 CA combination #4/A LYS 46 CG 4.265
combination #4/N GLY 61 O combination #4/A LYS 46 CE 4.269
combination #4/N GLN 58 O combination #4/A LYS 46 CE 4.274
combination #4/N TYR 23 CZ combination #4/E ARG 106 NH1 4.275
combination #4/N SER 38 CB combination #4/C CYS 14 CA 4.277
combination #4/N TYR 23 CE2 combination #4/E ARG 106 NH2 4.281
combination #4/N ASP 26 CG combination #4/E ARG 106 NH2 4.311
combination #4/N SER 43 O combination #4/C GLN 16 CG 4.316
combination #4/N PHE 63 CE2 combination #4/C GLN 16 CD 4.327
combination #4/N CYS 39 CB combination #4/C PRO 59 CB 4.328
combination #4/N CYS 44 CA combination #4/C GLN 16 CD 4.366
combination #4/N GLY 61 C combination #4/A LYS 46 NZ 4.370
combination #4/N SER 38 O combination #4/C ILE 12 CB 4.393
combination #4/N ILE 69 CB combination #4/A ARG 42 NE 4.406
combination #4/N ALA 41 N combination #4/E THR 117 OG1 4.411
combination #4/N ASP 26 O combination #4/E ARG 70 NH2 4.425
combination #4/N TYR 37 CZ combination #4/C LYS 35 CB 4.438
combination #4/N ASP 26 OD1 combination #4/E ARG 106 NH1 4.440
combination #4/N GLU 70 OE1 combination #4/A ARG 42 NE 4.443
combination #4/N TYR 37 CZ combination #4/C LYS 35 CD 4.447
combination #4/N ARG 40 O combination #4/E THR 117 CB 4.448
combination #4/N CYS 39 C combination #4/C ILE 12 CD1 4.449
combination #4/N GLN 58 C combination #4/A ARG 42 NH1 4.456
combination #4/N SER 38 O combination #4/C ILE 12 CG1 4.458
combination #4/N ALA 41 CB combination #4/E VAL 115 CG2 4.473
combination #4/N SER 59 CA combination #4/A LYS 46 CE 4.493
combination #4/N SER 59 C combination #4/A LYS 46 CE 4.500
85 distances
> hide #!1 models
> contacts sel restrict #4/A-E resSeparation 5 intraMol false select true
> color #00f900 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
26 contacts
atom1 atom2 overlap distance
combination #4/C ILE 12 CD1 combination #4/N CYS 39 CA 0.441 3.319
combination #4/C GLN 16 NE2 combination #4/N CYS 44 CB 0.387 3.133
combination #4/C LYS 35 NZ combination #4/E ASP 94 CB 0.219 3.301
combination #4/N CYS 44 CA combination #4/C GLN 16 NE2 0.165 3.355
combination #4/C LYS 35 CE combination #4/E ASP 94 OD1 0.131 3.169
combination #4/C LYS 35 NZ combination #4/E ASP 94 CG 0.093 3.427
combination #4/N TYR 23 CE2 combination #4/E ARG 106 NH1 0.021 3.379
combination #4/N TYR 37 OH combination #4/C LYS 35 NZ 0.004 2.696
combination #4/N ILE 69 CG1 combination #4/A ARG 42 NH1 -0.006 3.526
combination #4/C ILE 12 CD1 combination #4/N CYS 39 CB -0.028 3.788
combination #4/C LYS 35 CE combination #4/E ASP 94 CB -0.074 3.834
combination #4/N TYR 37 OH combination #4/C LYS 35 CG -0.133 3.473
combination #4/C LYS 35 NZ combination #4/E ASP 94 OD1 -0.157 2.817
combination #4/C LYS 35 CE combination #4/E ASP 94 CG -0.182 3.942
combination #4/C ILE 12 CD1 combination #4/N CYS 39 N -0.195 3.715
combination #4/N TYR 37 OH combination #4/C LYS 35 CD -0.245 3.585
combination #4/C ARG 19 NH1 combination #4/D GLU 176 CG -0.271 3.791
combination #4/A ARG 42 NH1 combination #4/N ILE 69 CD1 -0.285 3.805
combination #4/N TYR 37 OH combination #4/C LYS 35 CE -0.310 3.650
combination #4/C LYS 35 CE combination #4/E THR 99 CG2 -0.325 4.085
combination #4/N ILE 69 CG1 combination #4/A ARG 42 CZ -0.330 3.820
combination #4/C ILE 12 CG1 combination #4/C SF4 3003 S4 -0.332 3.982
combination #4/C ARG 19 NH1 combination #4/D GLU 176 CB -0.341 3.861
combination #4/N SER 38 C combination #4/C ILE 12 CD1 -0.357 3.847
combination #4/N CYS 44 CB combination #4/C GLN 16 CG -0.387 4.147
combination #4/N CYS 39 CB combination #4/C PRO 59 CG -0.388 4.148
26 contacts
> ui tool show H-Bonds
> select #4/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> hbonds sel restrict #4/A-E interModel false intraMol false intraRes false
> reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
4 combination
5 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
combination #4/A ARG 42 NH1 combination #4/N GLN 58 O no hydrogen 3.483 N/A
combination #4/A LYS 46 NZ combination #4/N GLY 61 O no hydrogen 3.235 N/A
combination #4/C LYS 35 NZ combination #4/N TYR 37 OH no hydrogen 2.696 N/A
combination #4/E ARG 106 NH2 combination #4/N ASP 26 OD1 no hydrogen 3.124 N/A
combination #4/E THR 117 OG1 combination #4/N ARG 40 O no hydrogen 3.442 N/A
5 hydrogen bonds found
> select #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117
91 atoms, 82 bonds, 9 pseudobonds, 10 residues, 3 models selected
> show sel atoms
> select clear
> hide #3 models
> hide #4.3 models
> select #4#2b&protein
Expected an objects specifier or a keyword
> select #4#2 &protein
12712 atoms, 13032 bonds, 72 pseudobonds, 1602 residues, 8 models selected
> style sel & #!4 stick
Changed 6356 atom styles
> color sel & #!4 byhetero
> select clear
> select #4/N:58,61,37,26,40/A:42,46/C:35/E:106,117
91 atoms, 82 bonds, 9 pseudobonds, 10 residues, 3 models selected
> show #!1 models
> select #1:41-46
60 atoms, 59 bonds, 6 residues, 1 model selected
> color sel lime
> color sel byhetero
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> show #4.3 models
> hide #!4 models
> hide #!2.1 models
> select #1:HOH
94 atoms, 94 residues, 1 model selected
> hide sel atoms
> hide #2.2.4 models
> show #!4 models
> hide #!4 models
> select #1:48-51
52 atoms, 52 bonds, 4 residues, 1 model selected
> color sel lime
> color sel byhetero
> select #1:41-43
27 atoms, 26 bonds, 3 residues, 1 model selected
> color sel medium blue
> color sel byhetero
> select #1:9-10
26 atoms, 25 bonds, 2 residues, 1 model selected
> color sel lime
> color sel byhetero
> show #!4 models
> hide #!4 models
> select #1:15-17
39 atoms, 39 bonds, 3 residues, 1 model selected
> color sel lime
> color sel byhetero
> show #!4 models
> select #1:23-31
92 atoms, 92 bonds, 9 residues, 1 model selected
> color sel lime
> color sel byhetero
> hide #!4 models
> select #2/C:3003 @<12 :61
6 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/C:3003 @<10 :61
2 atoms, 1 bond, 1 residue, 1 model selected
> select #2/C:3003 @<9 :61
Nothing selected
> select #2/C:3003 @<9.5 :61
1 atom, 1 residue, 1 model selected
> select #1:61@S3
1 atom, 1 residue, 1 model selected
> select #1:61@S3 @<9.5 /C:3003
1 atom, 1 residue, 1 model selected
> select #1:61@S3|#2/C:3003@FE1
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance #2.2/C:3003@FE1 #1/A:61@S3
Distance between 6yez 2 #2.2/C SF4 3003 FE1 and 2fdn #1/A SF4 61 S3: 9.093Å
> help help:user
> select @@color="lime"
93 atoms, 72 bonds, 21 residues, 1 model selected
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"
> select #2
6384 atoms, 6556 bonds, 69 pseudobonds, 805 residues, 7 models selected
> select #2/E
528 atoms, 540 bonds, 66 residues, 1 model selected
> style sel stick
Changed 528 atom styles
> color sel byhetero
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> select @@color="lime"
93 atoms, 72 bonds, 21 residues, 1 model selected
> select #1:1-8,11-14,18-22,32-43,47,52-55
410 atoms, 407 bonds, 34 residues, 1 model selected
> hide #!2 models
> open 6yez
6yez title:
Plant PSI-ferredoxin-plastocyanin supercomplex [more info...]
Chain information for 6yez #6
---
Chain | Description | UniProt
1 | Lhca1 |
2 | Chlorophyll a-b binding protein, chloroplastic | Q41038_PEA 58-265
3 | Chlorophyll a-b binding protein 3, chloroplastic | CB23_PEA 55-275
4 | Chlorophyll a-b binding protein P4, chloroplastic | CB24_PEA 52-249
A | Photosystem I P700 chlorophyll a apoprotein A1 | A0A0F6NFW5_PEA 16-758
B | Photosystem I P700 chlorophyll a apoprotein A2 | A0A0F6NGI2_PEA 2-734
C | Photosystem I iron-sulfur center | PSAC_PEA 2-81
D | PsaD |
E | PsaE |
F | PsaF |
G | PsaG |
H | PsaH |
I | Photosystem I reaction center subunit VIII | PSAI_PEA 2-32
J | PsaJ |
K | Photosystem I reaction center subunit X psaK | E1C9L3_PEA 46-126
L | PsaL |
N | Ferredoxin-1, chloroplastic | FER1_PEA 1-97
P | Plastocyanin, chloroplastic | PLAS_PEA 1-99
Non-standard residues in 6yez #6
---
3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)
BCR — β-carotene
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
CA — calcium ion
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
CU — copper (II) ion
DGD — digalactosyl diacyl glycerol (DGDG)
FES — FE2/S2 (inorganic) cluster
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
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 (violaxanthin)
> select add #6
39627 atoms, 41140 bonds, 678 pseudobonds, 3718 residues, 3 models selected
> select add #1
39979 atoms, 41414 bonds, 686 pseudobonds, 3835 residues, 4 models selected
> select subtract #1
39217 atoms, 40733 bonds, 678 pseudobonds, 3684 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #6/F-Z
8235 atoms, 8462 bonds, 68 pseudobonds, 894 residues, 2 models selected
> hide sel cartoons
> select #6/F-Z/1-4
18908 atoms, 19592 bonds, 309 pseudobonds, 1801 residues, 2 models selected
> hide sel cartoons
> log metadata #6
Metadata for 6yez #6
---
Title | Plant PSI-ferredoxin-plastocyanin supercomplex
Citation | 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. Nat.Plants, 6, 1300-1305. PMID: 33020607. DOI: 10.1038/s41477-020-00779-9
Non-standard residues | 3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)
BCR — β-carotene
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
CA — calcium ion
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
CU — copper (II) ion
DGD — digalactosyl diacyl glycerol (DGDG)
FES — FE2/S2 (inorganic) cluster
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
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 (violaxanthin)
Sources (natural) | Pisum sativum (garden pea)
Pisum sativum (pea)
CryoEM Map | EMDB 10798 — open map
Experimental method | Electron microscopy
Resolution | 2.7Å
> select #6/F-Z/1-4
18908 atoms, 19592 bonds, 309 pseudobonds, 1801 residues, 2 models selected
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show sel atoms
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> combine #1#6
Remapping chain ID 'A' in 6yez #6 to 'F'
> hide #!6 models
> hide #!1 models
> hide #!7 models
> show #!7 models
> close #7
> show #!6 models
> show #!1 models
> select #6/N
Nothing selected
> ui tool show "Change Chain IDs"
> select #1
762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected
> ui tool show "Change Chain IDs"
> changechains sel M
Chain IDs of 151 residues changed
> combine #1#6
> hide #!6 models
> hide #!1 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
> interface/Bfdx_PSI_toDiffusion.pdb" models #7
> combine #7/A:700
> close #8
> select #7/A:700
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #7/A:740
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:759
Nothing selected
> select #7/A:758
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #7/A:758/B:2
10 atoms, 8 bonds, 2 residues, 1 model selected
> hide #!7 models
> show #!2 models
> select #2/A:758/B:724
Nothing selected
> select #2/A:758/B:707
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:696/C:2
15 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/B:696@C/C:2@N
2 atoms, 2 residues, 1 model selected
> select #2/B:696@C/C:2@N
2 atoms, 2 residues, 1 model selected
> distance #2.2/B:696@C #2.2/C:2@N
Distance between 6yez 2 #2.2/B LYS 696 C and /C SER 2 N: 16.567Å
> select #2/D:59@N/C:81@C
1 atom, 1 residue, 1 model selected
> select #2/D:69@N/C:81@C
2 atoms, 2 residues, 1 model selected
> distance #2.2/C:81@C #2.2/D:69@N
Distance between 6yez 2 #2.2/C TYR 81 C and /D GLY 69 N: 36.658Å
> select #2/E:64@N/D:211@C
2 atoms, 2 residues, 1 model selected
> distance #2.2/E:64@N #2.2/D:211@C
Distance between 6yez 2 #2.2/E PRO 64 N and /D LEU 211 C: 36.932Å
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/bacteriofdx PSI interface design.cxs"
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI stromal ridge single
> chain/PSI_stromal_ridge_0.pdb"
Chain information for PSI_stromal_ridge_0.pdb #8
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #8 to #2.2 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6yez 2, chain A (#2.2) with PSI_stromal_ridge_0.pdb, chain A (#8),
sequence alignment score = 924.3
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 6yez 2 #2.2/A,
PSI_stromal_ridge_0.pdb #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 203 pruned atom pairs is 0.259 angstroms; (across all 203 pairs:
0.259)
> sequence header consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
> select #8/A:59
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #8/A:59-62
16 atoms, 15 bonds, 4 residues, 1 model selected
> select #8:59-62
16 atoms, 15 bonds, 4 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select #8:58-63
24 atoms, 23 bonds, 6 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select #2/A:192
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> hide sel cartoons
> ui tool show "Build Structure"
> combine #8
Associated copy of PSI_stromal_ridge_0.pdb chain A to PSI_stromal_ridge_0.pdb,
chain A with 0 mismatches
Chains 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
> help help:user
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9 sequence GGGG
676 atoms, 663 bonds, 169 residues, 1 model selected
> 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
676 atoms, 663 bonds, 169 residues, 1 model selected
> color sel cyan
> hide #8 models
> hide #!2 models
> show #!2 models
> select add #2.2
6332 atoms, 6479 bonds, 68 pseudobonds, 876 residues, 6 models selected
> style sel stick
Changed 6332 atom styles
> select add #2
7060 atoms, 7219 bonds, 72 pseudobonds, 974 residues, 9 models selected
> select subtract #2
676 atoms, 663 bonds, 169 residues, 1 model selected
> hide #!2.2 models
> show #!2.1 models
> help help:user
> 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 copy of PSI_stromal_ridge_0.pdb (#9) into 14 models
Chain information for copy of PSI_stromal_ridge_0.pdb 1 #9.1
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 2 #9.2
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 3 #9.3
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 4 #9.4
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 5 #9.5
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 6 #9.6
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 7 #9.7
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 8 #9.8
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 9 #9.9
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 10 #9.10
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 11 #9.11
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 12 #9.12
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 13 #9.13
---
Chain | Description
A | No description available
Chain information for copy of PSI_stromal_ridge_0.pdb 14 #9.14
---
Chain | Description
A | No description available
Associated copy of PSI_stromal_ridge_0.pdb 6 (9.6) chain A to
PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated copy of PSI_stromal_ridge_0.pdb 11 (9.11) chain A to
PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated copy of PSI_stromal_ridge_0.pdb 12 (9.12) chain A to
PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated copy of PSI_stromal_ridge_0.pdb 13 (9.13) chain A to
PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Associated copy of PSI_stromal_ridge_0.pdb 14 (9.14) chain A to
PSI_stromal_ridge_0.pdb, chain A with 0 mismatches
Chains 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
> hide #9.14 models
> show #!2.2 models
> select add #9
3316 atoms, 3289 bonds, 829 residues, 15 models selected
> select subtract #9.14
676 atoms, 663 bonds, 169 residues, 14 models selected
> show sel atoms
> hide sel cartoons
> color sel byhetero
> select add #9
3316 atoms, 3289 bonds, 829 residues, 15 models selected
> select subtract #9
Nothing selected
> hide #9.13 models
> hide #9.12 models
> hide #9.11 models
> hide #9.10 models
> hide #9.9 models
> hide #9.8 models
> hide #9.7 models
> hide #9.6 models
> hide #9.5 models
> hide #9.4 models
> hide #9.3 models
> hide #9.2 models
> ui tool show "Add Hydrogens"
> ui tool show "Build Structure"
> save "/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"
——— End of log from Sat May 18 14:49:43 2024 ———
opened ChimeraX session
> select #9.1:58@C:59@N
1 atom, 1 residue, 1 model selected
> show #9.14 models
> ~bond sel
> select #2/A:73@C#9.1:59@N
2 atoms, 2 residues, 2 models selected
> hide sel cartoons
> show sel atoms
> build join peptide sel length 1.33 omega 180 phi -120 move small
No chain-terminal carbons in atoms
> ~bond sel
> select #2.2/A:73@C#9.1:59@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
No chain-terminal carbons in atoms
> hide #9.14 models
> show #9.14 models
> hide #9.14 models
> show #9.14 models
> hide #9.14 models
> show #9.14 models
> hide #9.14 models
> show #9.14 models
> hide #9.14 models
> split #2.2 atoms /A:1-73
Split 6yez 2 (#2.2) into 2 models
Chain information for 6yez 2 1 #2.2.1
---
Chain | Description
A | No description available
Chain information for 6yez 2 2 #2.2.2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
Associated 6yez 2 1 (2.2.1) chain A to 6yez 2, chain A with 0 mismatches
Associated 6yez 2 2 (2.2.2) chain A to PSI_stromal_ridge_0.pdb, chain A with 0
mismatches
Associated 6yez 2 2 (2.2.2) chain D to PSI_stromal_ridge_0.pdb, chain A with 0
mismatches
Associated 6yez 2 2 (2.2.2) chain C to PSI_stromal_ridge_0.pdb, chain A with 0
mismatches
Associated 6yez 2 2 (2.2.2) chain E to PSI_stromal_ridge_0.pdb, chain A with 0
mismatches
> hide #!2.2.2 models
> select #2.2.1/A:73
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select #2.2.1/A:73@C#9.1:59@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move small
> show #8 models
> help help:user
> align #2.2.1/A:132-135 toAtoms #8:59-63 matchAtomNames true move residues
Pairing dropped 0 atoms and 4 reference atoms
RMSD between 16 atom pairs is 0.000 angstroms
> save "/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"
> hide #2.2.1 models
> hide #8 models
> show #!2.2.2 models
> show #2.2.1 models
> align #2.2.2/A:191
Missing required "to_atoms" argument
> select #2.2.2/A:191
7 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> color sel byhetero
> select #2.2.2/A:191@N#2.2.1/A:135@C
2 atoms, 2 residues, 2 models selected
> ui tool show "Build Structure"
> build join peptide sel length 1.33 omega 180 phi -120 move N
> show #!4 models
> hide #!4 models
> select #2.2.1/A:191
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!4 models
> select #4/A:191-*
Expected an objects specifier or a keyword
> select #4/A:191-707/B-E
5003 atoms, 5138 bonds, 26 pseudobonds, 626 residues, 4 models selected
> select #2.2.1/A:191-707/B-E
5003 atoms, 5138 bonds, 60 pseudobonds, 626 residues, 4 models selected
> hide #!2.1 models
> show #!2.1 models
> select #2.2.1/A:191-707/B-E to #4/A:191-707/B-E matchA t matchN t move res
Expected a keyword
> align #2.2.1/A:191-707/B-E toAtoms #4/A:191-707/B-E matchAtomNames true
> matchNumbering true move residues
RMSD between 5003 atom pairs is 0.000 angstroms
> align #2.2.1/A:708-729,3001 toAtoms #4/A:708-729,3001 matchAtomNames true
> matchNumbering true move residues
RMSD between 179 atom pairs is 0.000 angstroms
> save "/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"
> hide #!2.2 models
> show #!2.2 models
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> 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
5004 atoms, 5140 bonds, 59 pseudobonds, 627 residues, 4 models selected
> 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 6yez 2 1 (#2.2.1) into 14 models
Chain information for 6yez 2 1 1 #2.2.1.1
---
Chain | Description
A | No description available
Chain information for 6yez 2 1 2 #2.2.1.2
---
Chain | Description
A | No description available
Chain information for 6yez 2 1 3 #2.2.1.3
---
Chain | Description
A | No description available
Chain information for 6yez 2 1 4 #2.2.1.4
---
Chain | Description
A | No description available
Chain information for 6yez 2 1 5 #2.2.1.5
---
Chain | Description
B | No description available
Chain information for 6yez 2 1 6 #2.2.1.6
---
Chain | Description
B | No description available
Chain information for 6yez 2 1 7 #2.2.1.7
---
Chain | Description
B | No description available
Chain information for 6yez 2 1 8 #2.2.1.8
---
Chain | Description
B | No description available
Chain information for 6yez 2 1 9 #2.2.1.9
---
Chain | Description
B | No description available
Chain information for 6yez 2 1 10 #2.2.1.10
---
Chain | Description
B | No description available
Chain information for 6yez 2 1 11 #2.2.1.11
---
Chain | Description
C | No description available
Chain information for 6yez 2 1 12 #2.2.1.12
---
Chain | Description
D | No description available
Chain information for 6yez 2 1 13 #2.2.1.13
---
Chain | Description
E | No description available
Chain information for 6yez 2 1 14 #2.2.1.14
---
Chain | Description
A | No description available
B | No description available
Associated 6yez 2 1 1 (2.2.1.1) chain A to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 2 (2.2.1.2) chain A to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 3 (2.2.1.3) chain A to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 4 (2.2.1.4) chain A to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 5 (2.2.1.5) chain B to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 6 (2.2.1.6) chain B to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 7 (2.2.1.7) chain B to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 8 (2.2.1.8) chain B to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 9 (2.2.1.9) chain B to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 11 (2.2.1.11) chain C to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 12 (2.2.1.12) chain D to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 13 (2.2.1.13) chain E to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 14 (2.2.1.14) chain A to PSI_stromal_ridge_0.pdb, chain A
with 0 mismatches
Associated 6yez 2 1 14 (2.2.1.14) chain B to 6yez 2, chain A with 1 mismatch
> hide #2.2.1.14 models
> show #2.2.1.14 models
> hide #2.2.1.14 models
> show #2.2.1.14 models
> hide #2.2.1.13 models
> show #2.2.1.13 models
> hide #2.2.1.1 models
> show #2.2.1.1 models
> hide #2.2.1.1 models
> show #2.2.1.1 models
> hide #!2.2.1 models
> show #!2.2.1 models
> hide #2.2.1.1 models
> show #2.2.1.1 models
> show #9.2 models
> select #2.2/A:200@C#9.2:73@N
2 atoms, 2 residues, 2 models selected
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:273-276 toAtoms #8:73-76 matchAtomNames true move residues
RMSD between 16 atom pairs is 0.000 angstroms
> show #8 models
> hide #8 models
> select #2.2/A:276@C:315@N
2 atoms, 2 residues, 2 models selected
> save "/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"
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:315-354 toAtoms #4/A:315-354 matchAtomNames true
> matchNumbering true move residues
RMSD between 322 atom pairs is 0.000 angstroms
> select #2.2/A:276-315
14 atoms, 14 bonds, 2 residues, 1 model selected
> show sel cartoons
> select #2.2/A:72-315
149 atoms, 153 bonds, 21 residues, 1 model selected
> show sel cartoons
> save "/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"
> show #9.3 models
> select #2.2/A:354@C#9.3:117@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> show #8 models
> align #2.2.1/A:117-120 toAtoms #8:117-120 matchAtomNames true move residues
RMSD between 16 atom pairs is 0.000 angstroms
> hide #8 models
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select #2.2/A:120@C#2.2:417@N
3 atoms, 3 residues, 3 models selected
> hide #2.2.1.8 models
> show #2.2.1.8 models
> hide #2.2.1.8 models
> show #2.2.1.8 models
> hide #2.2.1.2 models
> show #2.2.1.2 models
> select #2.2/A:120@C#2.2:417@N
3 atoms, 3 residues, 3 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:417-442 toAtoms #4/A:417-442 matchAtomNames true
> matchNumbering true move residues
RMSD between 228 atom pairs is 0.000 angstroms
> select #2.2.1/A:417-442
228 atoms, 232 bonds, 26 residues, 1 model selected
> show sel cartoons
[Repeated 1 time(s)]
> select #2.2.1/A:72-442
705 atoms, 725 bonds, 90 residues, 1 model selected
> show sel cartoons
> show #9.4 models
> select #2.2/A:442@C#9.4:147@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:147-150 toAtoms #8:147-150 matchAtomNames true move residues
RMSD between 16 atom pairs is 0.000 angstroms
> select #2.2/A:150@C#2.2:562@N
3 atoms, 3 residues, 3 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:562-595 toAtoms #4/A:562-595 matchAtomNames true
> matchNumbering true move residues
RMSD between 257 atom pairs is 0.000 angstroms
> save "/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"
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #9.5 models
> select #2.2/A:595@C#9.5:185@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:780-787 toAtoms #8:185-192 matchAtomNames true move residues
RMSD between 32 atom pairs is 0.000 angstroms
> select #2.2/A:787@C#2.2:695@N
3 atoms, 3 residues, 3 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:695-729 toAtoms #4/A:695-729 matchAtomNames true
> matchNumbering true move residues
RMSD between 279 atom pairs is 0.000 angstroms
> save "/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"
> show #8 models
> hide #2.2.1.14 models
> show #2.2.1.14 models
> hide #2.2.1.14 models
> show #2.2.1.14 models
> select #2.2/A
1753 atoms, 1810 bonds, 228 residues, 1 model selected
> show sel cartoons
> hide #8 models
> show #9.6 models
> select #2.2/A:729@C#9.6:228@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:228-257 toAtoms #8:228-257 matchAtomNames true move residues
RMSD between 120 atom pairs is 0.000 angstroms
> select #2.2/A:257@C#2.2/B:2@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true matchNumbering
> true move residues
Pairing dropped 356 atoms and 356 reference atoms
No atoms paired for alignment
> show #!4 models
> align #2.2.1/A:789-831 toAtoms #4/B:2-44 matchAtomNames true move residues
RMSD between 356 atom pairs is 0.000 angstroms
> save "/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"
> show #9.7 models
> hide #9.7 models
> show #9.7 models
> select #2.2/A:831@C#9.7:301@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:301-304 toAtoms #8:301-304 matchAtomNames true move residues
RMSD between 16 atom pairs is 0.000 angstroms
> hide #!4 models
> select #2.2/A:304@C#2.2/B:162@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:162-176 toAtoms #4/B:162-176 matchAtomNames true move
> residues
RMSD between 124 atom pairs is 0.000 angstroms
> show #9.8 models
> select #2.2/A:176@C#9.8:320@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:1151-1154 toAtoms #8:320-323 matchAtomNames true move
> residues
RMSD between 16 atom pairs is 0.000 angstroms
> save "/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"
> select #2.2/A:1154@C#2.2/B:291@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:1445-1485 toAtoms #4/B:291-331 matchAtomNames true move
> residues
RMSD between 324 atom pairs is 0.000 angstroms
> save "/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"
> show #9.9 models
> hide #9.9 models
> show #9.9 models
> select #2.2/A:1485@C#9.9:365@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:365-368 toAtoms #8:365-368 matchAtomNames true move residues
RMSD between 16 atom pairs is 0.000 angstroms
> select #2.2/A:368@C#2.2/B:392@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:1877-1905 toAtoms #4/B:392-420 matchAtomNames true move
> residues
RMSD between 242 atom pairs is 0.000 angstroms
> show #9.10 models
> select #2.2/A:1905@C#9.10:398@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:398-401 toAtoms #8:398-401 matchAtomNames true move residues
RMSD between 16 atom pairs is 0.000 angstroms
> select #2.2/A:401@C#2.2/B:535@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:2440-2480 toAtoms #4/B:535-575 matchAtomNames true move
> residues
RMSD between 299 atom pairs is 0.000 angstroms
> save "/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"
> show #9.11 models
> select #2.2/A:2480@C#9.11:443@N
2 atoms, 2 residues, 2 models selected
> select #2.2/A:2480@C#9.11:443@N
2 atoms, 2 residues, 2 models selected
> show #8 models
> select #2.2/A
3282 atoms, 3377 bonds, 443 residues, 1 model selected
> show sel cartoons
> hide #2.2.1.14 models
> show #2.2.1.14 models
> hide #2.2.1.14 models
> show #2.2.1.14 models
> hide #2.2.1.10 models
> show #2.2.1.10 models
> hide #2.2.1.14 models
> show #2.2.1.14 models
> select #2.2/A:2480@C#9.11:443@N
2 atoms, 2 residues, 2 models selected
> hide #8 models
> show #8 models
> hide #8 models
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:443-470 toAtoms #8:443-470 matchAtomNames true move residues
RMSD between 112 atom pairs is 0.000 angstroms
> show #9.12 models
> hide #9.12 models
> show #8 models
> hide #8 models
> select #2.2/A:470@C#2.2/C:2@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:2482-2561 toAtoms #4/C:2-81 matchAtomNames true move residues
RMSD between 612 atom pairs is 0.000 angstroms
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> align #2.2.1/A:3002-3003 toAtoms #4/C:3002-3003 matchAtomNames true move
> residues
RMSD between 16 atom pairs is 0.000 angstroms
> hide #!4 models
> save "/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"
> show #9.12 models
> select #2.2/A:2561@C#9.11:551@N
1 atom, 1 residue, 1 model selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
No nitrogens in specified atoms
> select #2.2/A:2561@C#9.12:551@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> show #8 models
> hide #8 models
> show #8 models
> align #2.2.1/A:3112-3147 toAtoms #8:551-586 matchAtomNames true move
> residues
RMSD between 144 atom pairs is 0.000 angstroms
> hide #8 models
> show #!4 models
> hide #2.2.1.10 models
> hide #2.2.1.12 models
> show #2.2.1.12 models
> hide #2.2.1.12 models
> show #2.2.1.12 models
> hide #2.2.1.12 models
> show #2.2.1.12 models
> hide #2.2.1.12 models
> hide #2.2.1.13 models
> hide #!2.2.1.14 models
> show #!2.2.1.14 models
> show #9.13 models
> hide #9.13 models
> show #9.13 models
> hide #9.13 models
> show #9.13 models
> hide #9.13 models
> hide #!4 models
> show #2.2.1.13 models
> hide #2.2.1.13 models
> show #2.2.1.12 models
> select #2/D:69
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> color sel byhetero
> select #2.2/A:3147@C#2.2/D:69@N
2 atoms, 2 residues, 2 models selected
> build join peptide sel length 1.33 omega 180 phi -120 move N
> align #2.2.1/A:3216-3358 toAtoms #4/D:69-211 matchAtomNames true move
> residues
RMSD between 1132 atom pairs is 0.000 angstroms
> show #!4 models
> hide #!4 models
> show #2.2.1.10 models
> hide #2.2.1.10 models
> show #2.2.1.10 models
> show #9.13 models
> show #!4 models
> save "/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"
——— End of log from Sat May 18 17:13:54 2024 ———
opened ChimeraX session
> close #2.2
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> close #6
> close #8#9
> close #7
> close #3
> close #5
> hide #!2.1 models
> show #!2.1 models
> close #2
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
> v2.cxs"
> open "/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" format pdb
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
---
warnings | Ignored bad PDB record found on line 34701
SEQRES *** A 830
Ignored bad PDB record found on line 34702
SEQRES *** A 830
Ignored bad PDB record found on line 34703
SEQRES *** A 830
Ignored bad PDB record found on line 34704
SEQRES *** A 830
Ignored bad PDB record found on line 34705
SEQRES *** A 830
92885266 messages similar to the above omitted
Chain information for SingleChainStromalRidge_PetF_Fdn.pdb #2
---
Chain | Description
A | No description available
M | No description available
N | No description available
> help help:user/tools/modelpanel.html
> save "/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" models #2
> hide #!4 models
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select #2
7455 atoms, 7544 bonds, 23 pseudobonds, 1082 residues, 3 models selected
> ui tool show "Color Actions"
> color sel bychain
> select #2:FES,SF4
44 atoms, 64 bonds, 6 residues, 1 model selected
> color sel byhetero
> select #2
7455 atoms, 7544 bonds, 23 pseudobonds, 1082 residues, 3 models selected
> color sel byhetero
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> select #2:FES,SF4,CYS
238 atoms, 231 bonds, 19 pseudobonds, 33 residues, 2 models selected
> show sel atoms
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
> v2.cxs"
——— End of log from Sat May 18 22:45:24 2024 ———
opened ChimeraX session
> hide #!2 models
> show #!4 models
> close #2
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
> v3.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/A:729
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/A:729
9 atoms, 8 bonds, 1 residue, 1 model selected
> rename #4 id 2
> select #2/A:16-73,191-200,315-354,417-442,562-595,695-729
1649 atoms, 1697 bonds, 5 pseudobonds, 203 residues, 2 models selected
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
> v3.cxs"
> select #2/A:16-73
474 atoms, 490 bonds, 58 residues, 1 model selected
> ui tool show "Renumber Residues"
> renumber #2/A:16-73 start 1
58 residues renumbered
> select #2/A:191
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:191
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:191-200
89 atoms, 92 bonds, 10 residues, 1 model selected
> renumber #2/A:191-200 start 63
10 residues renumbered
> select #2/A:315-354
322 atoms, 333 bonds, 40 residues, 1 model selected
> renumber #2/A:315-354 start 77
40 residues renumbered
> select #2/A:417-442
228 atoms, 232 bonds, 26 residues, 1 model selected
> renumber #2/A:417-442 start 121
26 residues renumbered
> select #2/A:562-595
257 atoms, 264 bonds, 34 residues, 1 model selected
> renumber #2/A:562-595 start 151
34 residues renumbered
> select #2/A:695-729
279 atoms, 286 bonds, 35 residues, 1 model selected
> renumber #2/A:695-729 start 193
35 residues renumbered
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI stromal ridge single chain/PSI single chain
> v3.cxs"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/B
Alignment identifier is 2/B
> select #2/B:2-44,162-176,291-331,392-420,535-575,665-696/A:227
1639 atoms, 1681 bonds, 5 pseudobonds, 202 residues, 2 models selected
> select #2/B:2-44/A:227
365 atoms, 374 bonds, 44 residues, 1 model selected
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/PSI stromal ridge single
> chain/PSI_stromal_ridge_0.pdb"
Chain information for PSI_stromal_ridge_0.pdb #3
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker combination, chain A (#2) with PSI_stromal_ridge_0.pdb, chain A
(#3), sequence alignment score = 924.3
RMSD between 203 pruned atom pairs is 0.259 angstroms; (across all 203 pairs:
0.259)
> select #2/B:2-44/A:227
365 atoms, 374 bonds, 44 residues, 1 model selected
> hide #3 models
> show #3 models
> select #2/B:2-44
356 atoms, 366 bonds, 43 residues, 1 model selected
> renumber #2/B:2-44 start 258
Proposed renumbering conflicts with existing residue combination #2/B TYR 291
> select #2/B:2-44,162-176,291-331,392-420,535-575,665-696
1630 atoms, 1673 bonds, 5 pseudobonds, 201 residues, 2 models selected
> select #2/B:2-44,162-176,291-331,392-420,535-575,665-696
1630 atoms, 1673 bonds, 5 pseudobonds, 201 residues, 2 models selected
> renumber #2/B:2-696 start 1002
201 residues renumbered
> select #2/B:697
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:697-707
81 atoms, 81 bonds, 11 residues, 1 model selected
> renumber #2/B:697-707 start 1697
11 residues renumbered
> select #3 sequence GGGG
676 atoms, 663 bonds, 169 residues, 1 model selected
> color sel cyan
> hide #3 models
> show #3 models
> hide #3 models
> select #2/B:1002-1044
356 atoms, 366 bonds, 43 residues, 1 model selected
> show #3 models
> renumber #2/B:1002-1044 start 258
43 residues renumbered
> select #2/B:1162-1176
124 atoms, 127 bonds, 15 residues, 1 model selected
> select #2/B:300
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:300-1162
18 atoms, 16 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #2/B:1162-1176
124 atoms, 127 bonds, 15 residues, 1 model selected
> renumber #2/B:1162-1176 start 305
15 residues renumbered
> select #2/B:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:319-1291
20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #2/B:1291-1331
324 atoms, 333 bonds, 41 residues, 1 model selected
> hide #3 models
> hide #!2 models
> show #!2 models
> select #2/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> show #!1 models
> open "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion
> round1/PSI_fdn_0.pdb" "/Users/drornoy/Library/CloudStorage/OneDrive-
> Migal/NSF-BSF grant 2024/Nanda Noy 2023/Models/BacetrioFdx PSI
> interface/RFdiffusion round1/PSI_fdn_1.pdb"
> "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant 2024/Nanda
> Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI_fdn_2.pdb"
Chain information for PSI_fdn_0.pdb #4
---
Chain | Description
A | No description available
Chain information for PSI_fdn_1.pdb #5
---
Chain | Description
A | No description available
Chain information for PSI_fdn_2.pdb #6
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #4-6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2fdn, chain M (#1) with PSI_fdn_0.pdb, chain A (#4), sequence
alignment score = 139.6
RMSD between 46 pruned atom pairs is 0.501 angstroms; (across all 53 pairs:
2.902)
Matchmaker 2fdn, chain M (#1) with PSI_fdn_1.pdb, chain A (#5), sequence
alignment score = 147.1
RMSD between 47 pruned atom pairs is 0.590 angstroms; (across all 53 pairs:
2.756)
Matchmaker 2fdn, chain M (#1) with PSI_fdn_2.pdb, chain A (#6), sequence
alignment score = 135.4
RMSD between 44 pruned atom pairs is 0.540 angstroms; (across all 48 pairs:
2.878)
> select #4-6/A
10668 atoms, 10665 bonds, 2667 residues, 3 models selected
> select #4-6:1-831
9972 atoms, 9969 bonds, 2493 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
> fdn large target.cxs"
> show #3 models
> hide #3 models
> close #4-6
> select #2/B:1291-1331
324 atoms, 333 bonds, 41 residues, 1 model selected
> show #3 models
> select #2/B:319
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:319-1291
20 atoms, 19 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #2/B:1291-1331
324 atoms, 333 bonds, 41 residues, 1 model selected
> renumber #2/B:1291-1331 start 305
Proposed renumbering conflicts with existing residue combination #2/B LYS 305
> select #2/B:305
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:2-44,162-176,291-331,392-420,535-575,665-696
208 atoms, 211 bonds, 1 pseudobond, 25 residues, 2 models selected
> hide #3 models
> select #2/B:1291-1331
324 atoms, 333 bonds, 41 residues, 1 model selected
> show #3 models
> renumber #2/B:1291-1331 start 324
41 residues renumbered
> select #2/B:1392-1420
242 atoms, 246 bonds, 29 residues, 1 model selected
> select #2/B:364
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:364-1392
18 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #2/B:1392-1420
242 atoms, 246 bonds, 29 residues, 1 model selected
> select #2/B:364
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:364-1392
18 atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #2/B:1392-1420
242 atoms, 246 bonds, 29 residues, 1 model selected
> renumber #2/B:1392-1420 start 369
29 residues renumbered
> select #2/B:397
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:397-1535
13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #2/B:1535-1575
299 atoms, 306 bonds, 41 residues, 1 model selected
> renumber #2/B:1535-1575 start 402
41 residues renumbered
> select #2/B:1665-1696
285 atoms, 295 bonds, 32 residues, 1 model selected
> select #2/B:442
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:442-1665
13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected
> select #2/B:1665-1696
285 atoms, 295 bonds, 32 residues, 1 model selected
> select #2/B:1665-170
Nothing selected
> show cartoons
> select #2/B:1665-1707
366 atoms, 377 bonds, 43 residues, 1 model selected
> show sel cartoons
> renumber #2/B:1665-1707 start 451
43 residues renumbered
> hide #3 models
> select #2/B
1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected
> select #2/B
1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected
> select #2/C
628 atoms, 649 bonds, 8 pseudobonds, 82 residues, 3 models selected
> select #2/C
628 atoms, 649 bonds, 8 pseudobonds, 82 residues, 3 models selected
> select #2/C:2-81
612 atoms, 625 bonds, 80 residues, 1 model selected
> show sel cartoons
> select #2/C:2
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #3 models
> renumber #2/C:2 start 471
1 residues renumbered
> ui tool show "Show Sequence Viewer"
> sequence chain #2/C
Alignment identifier is 2/C
> select #2/C:2-81
606 atoms, 619 bonds, 79 residues, 1 model selected
> renumber #2/C:3-81 start 472
79 residues renumbered
> select #2/D
1132 atoms, 1163 bonds, 143 residues, 1 model selected
> select #2/D
1132 atoms, 1163 bonds, 143 residues, 1 model selected
> renumber #2/D start 587
143 residues renumbered
> select #2/E
528 atoms, 540 bonds, 66 residues, 1 model selected
> renumber #2/E start 764
66 residues renumbered
> hide #3 models
> save "/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"
> ui tool show "Show Sequence Viewer"
> sequence chain #2/D
Alignment identifier is 2/D
> ui tool show "Show Sequence Viewer"
> sequence chain #2/E
Alignment identifier is 2/E
> select #2/D
1132 atoms, 1163 bonds, 143 residues, 1 model selected
> select #2/D:701-729
224 atoms, 228 bonds, 29 residues, 1 model selected
> hide sel cartoons
> select #2/B
1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> select #2/A:1-15
119 atoms, 120 bonds, 15 residues, 1 model selected
> hide sel cartoons
> select #2/A:1-15,63-115
516 atoms, 529 bonds, 1 pseudobond, 64 residues, 2 models selected
> select #2/A:1-15,63-146
758 atoms, 777 bonds, 2 pseudobonds, 91 residues, 2 models selected
> hide sel cartoons
> select #2/A:1-15,63-146/C/D:587-700/E
2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected
> ui tool show "Change Chain IDs"
> changechains sel A
Cannot reassign chain ID to only part of polymeric chain (combination #2/A)
> combine #2
> rename #4 "Stromal ridge small"
> select #2/A:1-15,63-146/C/D:587-700/E
2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide #!2 models
> select #4/A:1-15,63-146/C/D:587-700/E
2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
[Repeated 1 time(s)]
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> show #!2 models
> hide #!4 models
> select #2/A:1-15,63-146/C/D:587-700/E
2822 atoms, 2900 bonds, 19 pseudobonds, 353 residues, 4 models selected
> select #2/A:16-62,147/C/D:587-700/E
2419 atoms, 2492 bonds, 17 pseudobonds, 305 residues, 3 models selected
> select #2/A:16-62,147-227/C/D:587-700/E
2955 atoms, 3042 bonds, 18 pseudobonds, 374 residues, 4 models selected
> select #2/A:16-62,147-227,3001/C/D:587-700/E
2963 atoms, 3054 bonds, 20 pseudobonds, 375 residues, 4 models selected
> select #4/A:1-15,63-146/B/D:701-729
2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected
> select #4/A:1-15,63-146/B/D:701-729
2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected
> select #4/A:1-15,63-146/B/D:701-729
2693 atoms, 2760 bonds, 7 pseudobonds, 332 residues, 2 models selected
> show #!4 models
> hide #!2 models
> select #4/A:1-15,63-146/D:701-729
982 atoms, 1005 bonds, 2 pseudobonds, 120 residues, 2 models selected
> hide sel cartoons
> select #4/A:1-12,46-146/D:701-729
1065 atoms, 1090 bonds, 3 pseudobonds, 130 residues, 2 models selected
> select #4/A:1-12,55-146/D:701-729
994 atoms, 1016 bonds, 3 pseudobonds, 121 residues, 2 models selected
> hide sel cartoons
> select #4/B
1711 atoms, 1755 bonds, 5 pseudobonds, 212 residues, 2 models selected
> show sel cartoons
> select #4/B &~:425-436
1635 atoms, 1676 bonds, 5 pseudobonds, 200 residues, 2 models selected
> hide sel cartoons
> select #4/A:16-54,151-227,3001/C/D:587-700/E
2929 atoms, 3020 bonds, 20 pseudobonds, 371 residues, 4 models selected
> hide sel cartoons
> show sel cartoons
> select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
3005 atoms, 3097 bonds, 22 pseudobonds, 383 residues, 4 models selected
> hide sel cartoons
> show sel cartoons
> surface #4 enclose #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for Stromal ridge small_A SES surface #4.5: minimum, -23.39,
mean -1.01, maximum 11.65
Coulombic values for Stromal ridge small_B SES surface #4.6: minimum, -18.54,
mean 0.17, maximum 12.46
Coulombic values for Stromal ridge small_C SES surface #4.7: minimum, -12.54,
mean -0.30, maximum 9.66
Coulombic values for Stromal ridge small_D SES surface #4.8: minimum, -11.89,
mean 1.48, maximum 14.01
Coulombic values for Stromal ridge small_E SES surface #4.9: minimum, -13.21,
mean 1.18, maximum 10.80
To also show corresponding color key, enter the above coulombic command and
add key true
> close #4.5-9
> select add #4.4
3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected
> select subtract #4.4
3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected
> select add #4.4
3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected
> select subtract #4.4
3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected
> select add #4.4
3005 atoms, 3097 bonds, 31 pseudobonds, 383 residues, 4 models selected
> close #4.4
> select #4/M
Nothing selected
> select #4/N
728 atoms, 740 bonds, 4 pseudobonds, 98 residues, 2 models selected
> hide #!1 models
> hide sel cartoons
> hide sel atoms
> select #4 &@@display
184 atoms, 176 bonds, 15 pseudobonds, 24 residues, 3 models selected
> select #4 &@@~display
184 atoms, 176 bonds, 15 pseudobonds, 24 residues, 3 models selected
> show sel atoms
> select #4 &~@@display
6200 atoms, 6338 bonds, 4 pseudobonds, 784 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> show sel atoms
> select #4
6384 atoms, 6556 bonds, 46 pseudobonds, 805 residues, 4 models selected
> ui tool show "Change Chain IDs"
> changechains sel A
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (A/477/)
> select #4/B
1711 atoms, 1755 bonds, 212 residues, 1 model selected
> show sel cartoons
> show #3 models
> hide sel cartoons
> select #4/B:402-442
299 atoms, 306 bonds, 41 residues, 1 model selected
> show sel cartoons
> hide #3 models
> select #4/A:402-442
Nothing selected
> select #4/C:402-442
Nothing selected
> select #4/D:402-442
Nothing selected
> select #4/E:402-442
Nothing selected
> select #4/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected
> select #4&~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
3379 atoms, 3454 bonds, 4 pseudobonds, 422 residues, 2 models selected
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
> fdn small target.cxs"
> select #4&~/A:16-54,151-227,3001/B:425-436/C/D:587-700/E
3379 atoms, 3454 bonds, 4 pseudobonds, 422 residues, 2 models selected
> delete atoms (#!4 & sel)
> delete bonds (#!4 & sel)
> select #4
3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected
> ui tool show "Change Chain IDs"
> changechains sel A
Chain IDs of 274 residues changed
> changechains sel A
Chain IDs of 0 residues changed
> select #4/A
3005 atoms, 3097 bonds, 21 pseudobonds, 383 residues, 3 models selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> combine #4#5
> rename #5 "Stromal ridge and 2fdn"
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
> fdn small target.cxs"
> select #5/A &protein
2981 atoms, 3061 bonds, 9 pseudobonds, 380 residues, 2 models selected
> hide sel atoms
> hide #!4 models
> select #5/A:27, 31, 504, 807,818, 481, 485, 528
72 atoms, 66 bonds, 8 residues, 1 model selected
> show sel atoms
> show #!2 models
> hide sel atoms
> select #2/A:27, 31, 504, 807,818, 481, 485, 528
20 atoms, 18 bonds, 2 residues, 1 model selected
> hide #!2 models
> show #!1 models
> hide #!1 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Nanda Noy 2023/Models/BacetrioFdx PSI interface/RFdiffusion round1/PSI
> fdn small target.cxs"
——— End of log from Sun May 19 17:29:55 2024 ———
opened ChimeraX session
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!5 models
> show #3 models
> hide #3 models
> close #3
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> rename #2 "PSI chains"
> select #5/M
Nothing selected
> split #2
Split PSI chains (#2) into 6 models
Chain information for PSI chains A #2.1
---
Chain | Description
A | No description available
Chain information for PSI chains B #2.2
---
Chain | Description
B | No description available
Chain information for PSI chains C #2.3
---
Chain | Description
C | No description available
Chain information for PSI chains D #2.4
---
Chain | Description
D | No description available
Chain information for PSI chains E #2.5
---
Chain | Description
E | No description available
Chain information for PSI chains N #2.6
---
Chain | Description
N | No description available
> hide #!2.1 models
> hide #!2.2 models
> hide #!2.3 models
> hide #2.4 models
> hide #2.5 models
> rename #2 "PSI 6yez chains"
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> hide #!2 models
> split #5/B
> select #5/B
Nothing selected
> show #!2 models
> show #!1 models
> show #!4 models
> hide #!4 models
> close #4
> rename #5 id 3
> open "/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"
> "/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"
> "/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"
> "/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"
> "/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"
> "/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"
> "/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"
> "/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"
> "/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"
Chain information for best.pdb #4
---
Chain | Description
A | No description available
B | No description available
Chain information for best_design7.pdb #5
---
Chain | Description
A | No description available
B | No description available
Chain information for best_design6.pdb #6
---
Chain | Description
A | No description available
B | No description available
Chain information for best_design5.pdb #7
---
Chain | Description
A | No description available
B | No description available
Chain information for best_design4.pdb #8
---
Chain | Description
A | No description available
B | No description available
Chain information for best_design3.pdb #9
---
Chain | Description
A | No description available
B | No description available
Chain information for best_design2.pdb #10
---
Chain | Description
A | No description available
B | No description available
Chain information for best_design1.pdb #11
---
Chain | Description
A | No description available
B | No description available
Chain information for best_design0.pdb #12
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> rename #3 "Stromal ridge target"
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #!4-12 to #3
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Stromal ridge target, chain A (#3) with best.pdb, chain A (#4),
sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs:
0.365)
Matchmaker Stromal ridge target, chain A (#3) with best_design7.pdb, chain A
(#5), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.362 angstroms; (across all 114 pairs:
0.362)
Matchmaker Stromal ridge target, chain A (#3) with best_design6.pdb, chain A
(#6), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs:
0.365)
Matchmaker Stromal ridge target, chain A (#3) with best_design5.pdb, chain A
(#7), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs:
0.366)
Matchmaker Stromal ridge target, chain A (#3) with best_design4.pdb, chain A
(#8), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.367 angstroms; (across all 114 pairs:
0.367)
Matchmaker Stromal ridge target, chain A (#3) with best_design3.pdb, chain A
(#9), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs:
0.366)
Matchmaker Stromal ridge target, chain A (#3) with best_design2.pdb, chain A
(#10), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.364 angstroms; (across all 114 pairs:
0.364)
Matchmaker Stromal ridge target, chain A (#3) with best_design1.pdb, chain A
(#11), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.365 angstroms; (across all 114 pairs:
0.365)
Matchmaker Stromal ridge target, chain A (#3) with best_design0.pdb, chain A
(#12), sequence alignment score = 561.8
RMSD between 114 pruned atom pairs is 0.366 angstroms; (across all 114 pairs:
0.366)
> hide #!2 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> select #4/B:8-11,14-18,38-41,44-48
112 atoms, 108 bonds, 18 residues, 1 model selected
> show sel atoms
> save "/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"
> open "/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"
Chain information for
Fdx_mod_MPNN_620be_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000.pdb #13
---
Chain | Description
A | No description available
> ui tool show Matchmaker
> matchmaker #13 to #4 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
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
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains 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
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 36 pruned atom pairs is 0.894 angstroms; (across all 54 pairs:
2.833)
> sequence header consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
> rename #13 Best_alphafold2_rank5.pdb
> open "/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"
> "/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"
> "/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"
> "/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"
Chain information for
Fdx_mod_MPNN_620be_unrelaxed_rank_003_alphafold2_ptm_model_2_seed_000.pdb #14
---
Chain | Description
A | No description available
Chain information for
Fdx_mod_MPNN_620be_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #15
---
Chain | Description
A | No description available
Chain information for
Fdx_mod_MPNN_620be_unrelaxed_rank_002_alphafold2_ptm_model_4_seed_000.pdb #16
---
Chain | Description
A | No description available
Chain information for
Fdx_mod_MPNN_620be_unrelaxed_rank_004_alphafold2_ptm_model_5_seed_000.pdb #17
---
Chain | Description
A | No description available
> rename #14 Best_alphafold2_rank3.pdb
> rename #15 Best_alphafold2_rank1.pdb
> rename #16 Best_alphafold2_rank2.pdb
> rename #17 Best_alphafold2_rank4.pdb
> rename #13 id 18
> rename #15 id 13
> rename #14 id 15
> rename #16 id 14
> rename #18 id 17
> rename #17.1 id 18
> rename #17 id 16
> rename #18 id 17
> save "/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"
> ui tool show Matchmaker
> matchmaker #13-17 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank1.pdb, chain A
(#13), sequence alignment score = 235.1
RMSD between 34 pruned atom pairs is 0.831 angstroms; (across all 54 pairs:
3.025)
Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank2.pdb, chain A
(#14), sequence alignment score = 228.2
RMSD between 32 pruned atom pairs is 0.678 angstroms; (across all 54 pairs:
3.041)
Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank3.pdb, chain A
(#15), sequence alignment score = 235.1
RMSD between 32 pruned atom pairs is 0.771 angstroms; (across all 54 pairs:
3.139)
Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank4.pdb, chain A
(#16), sequence alignment score = 235.1
RMSD between 34 pruned atom pairs is 0.832 angstroms; (across all 54 pairs:
3.177)
Matchmaker best.pdb, chain B (#4) with Best_alphafold2_rank5.pdb, chain A
(#17), sequence alignment score = 242.6
RMSD between 36 pruned atom pairs is 0.894 angstroms; (across all 54 pairs:
2.833)
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #!3 models
> hide #!4 models
> select #13/B:8-11,14-18,38-41,44-48
Nothing selected
> select #13/A:8-11,14-18,38-41,44-48
112 atoms, 108 bonds, 18 residues, 1 model selected
> show #14 models
> show #15 models
> show #16 models
> show #17 models
> show sel atoms
> hide #17 models
> hide #16 models
> hide #15 models
> hide #14 models
> save "/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"
——— End of log from Sat Jun 1 14:26:44 2024 ———
opened ChimeraX session
> hide #!1 models
> show #!4 models
> hide #13 models
> show #!3 models
> hide #!4 models
> help help:user
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> info #3/A:16 rescolor
Expected a keyword
> help help:user
> info rescolor #3/A:16
#3/A:16 color #b89a8c
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!2.6 models
> show #!2.2 models
> show #!3 models
> hide #!2.2 models
> select #3/A &@@color=#b89a8c
Expected a keyword
bad color: b89a8c: Invalid color name or specifier
> select #3/A &@@color#b89a8c
Expected a keyword
> select #3/A &@@color='#b89a8c'
518 atoms, 413 bonds, 104 residues, 1 model selected
> select #3/A &@@color='plum'
Nothing selected
> info rescolor #3/A:430
#3/A:430 color #d9b3f5
> info rescolor #3/A:804
#3/A:804 color #ebe6fb
> info rescolor #3/A:498
#3/A:498 color #b88eb1
> info rescolor #3/A:685
#3/A:685 color #c8e69e
> select #3/A &@@color='#b89a8c'
518 atoms, 413 bonds, 104 residues, 1 model selected
> info residues sel attribute num
> info residues #3/A &@@color='#b89a8c' attribute num
> info residues #3/A &@@color='#b89a8c' attribute number
residue id #3/A:16 number 16 index 15
residue id #3/A:17 number 17 index 16
residue id #3/A:18 number 18 index 17
residue id #3/A:152 number 152 index 135
residue id #3/A:153 number 153 index 136
residue id #3/A:154 number 154 index 137
residue id #3/A:155 number 155 index 138
residue id #3/A:156 number 156 index 139
residue id #3/A:157 number 157 index 140
residue id #3/A:158 number 158 index 141
residue id #3/A:159 number 159 index 142
residue id #3/A:160 number 160 index 143
residue id #3/A:161 number 161 index 144
residue id #3/A:162 number 162 index 145
residue id #3/A:163 number 163 index 146
residue id #3/A:164 number 164 index 147
residue id #3/A:165 number 165 index 148
residue id #3/A:166 number 166 index 149
residue id #3/A:52 number 52 index 51
residue id #3/A:53 number 53 index 52
residue id #3/A:54 number 54 index 53
residue id #3/A:19 number 19 index 18
residue id #3/A:20 number 20 index 19
residue id #3/A:21 number 21 index 20
residue id #3/A:22 number 22 index 21
residue id #3/A:23 number 23 index 22
residue id #3/A:24 number 24 index 23
residue id #3/A:25 number 25 index 24
residue id #3/A:26 number 26 index 25
residue id #3/A:27 number 27 index 26
residue id #3/A:28 number 28 index 27
residue id #3/A:29 number 29 index 28
residue id #3/A:30 number 30 index 29
residue id #3/A:31 number 31 index 30
residue id #3/A:32 number 32 index 31
residue id #3/A:33 number 33 index 32
residue id #3/A:34 number 34 index 33
residue id #3/A:35 number 35 index 34
residue id #3/A:36 number 36 index 35
residue id #3/A:37 number 37 index 36
residue id #3/A:38 number 38 index 37
residue id #3/A:39 number 39 index 38
residue id #3/A:40 number 40 index 39
residue id #3/A:41 number 41 index 40
residue id #3/A:42 number 42 index 41
residue id #3/A:43 number 43 index 42
residue id #3/A:44 number 44 index 43
residue id #3/A:45 number 45 index 44
residue id #3/A:46 number 46 index 45
residue id #3/A:47 number 47 index 46
residue id #3/A:48 number 48 index 47
residue id #3/A:49 number 49 index 48
residue id #3/A:50 number 50 index 49
residue id #3/A:51 number 51 index 50
residue id #3/A:209 number 209 index 184
residue id #3/A:210 number 210 index 185
residue id #3/A:211 number 211 index 186
residue id #3/A:212 number 212 index 187
residue id #3/A:213 number 213 index 188
residue id #3/A:214 number 214 index 189
residue id #3/A:215 number 215 index 190
residue id #3/A:216 number 216 index 191
residue id #3/A:217 number 217 index 192
residue id #3/A:218 number 218 index 193
residue id #3/A:219 number 219 index 194
residue id #3/A:220 number 220 index 195
residue id #3/A:221 number 221 index 196
residue id #3/A:222 number 222 index 197
residue id #3/A:223 number 223 index 198
residue id #3/A:224 number 224 index 199
residue id #3/A:225 number 225 index 200
residue id #3/A:226 number 226 index 201
residue id #3/A:167 number 167 index 150
residue id #3/A:168 number 168 index 151
residue id #3/A:169 number 169 index 152
residue id #3/A:170 number 170 index 153
residue id #3/A:171 number 171 index 154
residue id #3/A:172 number 172 index 155
residue id #3/A:173 number 173 index 156
residue id #3/A:174 number 174 index 157
residue id #3/A:175 number 175 index 158
residue id #3/A:176 number 176 index 159
residue id #3/A:177 number 177 index 160
residue id #3/A:178 number 178 index 161
residue id #3/A:179 number 179 index 162
residue id #3/A:180 number 180 index 163
residue id #3/A:181 number 181 index 164
residue id #3/A:182 number 182 index 165
residue id #3/A:183 number 183 index 166
residue id #3/A:194 number 194 index 169
residue id #3/A:195 number 195 index 170
residue id #3/A:196 number 196 index 171
residue id #3/A:197 number 197 index 172
residue id #3/A:198 number 198 index 173
residue id #3/A:199 number 199 index 174
residue id #3/A:200 number 200 index 175
residue id #3/A:201 number 201 index 176
residue id #3/A:202 number 202 index 177
residue id #3/A:203 number 203 index 178
residue id #3/A:204 number 204 index 179
residue id #3/A:205 number 205 index 180
residue id #3/A:206 number 206 index 181
residue id #3/A:207 number 207 index 182
residue id #3/A:208 number 208 index 183
> info residues sel attribute number
residue id #3/A:16 number 16 index 15
residue id #3/A:17 number 17 index 16
residue id #3/A:18 number 18 index 17
residue id #3/A:152 number 152 index 135
residue id #3/A:153 number 153 index 136
residue id #3/A:154 number 154 index 137
residue id #3/A:155 number 155 index 138
residue id #3/A:156 number 156 index 139
residue id #3/A:157 number 157 index 140
residue id #3/A:158 number 158 index 141
residue id #3/A:159 number 159 index 142
residue id #3/A:160 number 160 index 143
residue id #3/A:161 number 161 index 144
residue id #3/A:162 number 162 index 145
residue id #3/A:163 number 163 index 146
residue id #3/A:164 number 164 index 147
residue id #3/A:165 number 165 index 148
residue id #3/A:166 number 166 index 149
residue id #3/A:52 number 52 index 51
residue id #3/A:53 number 53 index 52
residue id #3/A:54 number 54 index 53
residue id #3/A:19 number 19 index 18
residue id #3/A:20 number 20 index 19
residue id #3/A:21 number 21 index 20
residue id #3/A:22 number 22 index 21
residue id #3/A:23 number 23 index 22
residue id #3/A:24 number 24 index 23
residue id #3/A:25 number 25 index 24
residue id #3/A:26 number 26 index 25
residue id #3/A:27 number 27 index 26
residue id #3/A:28 number 28 index 27
residue id #3/A:29 number 29 index 28
residue id #3/A:30 number 30 index 29
residue id #3/A:31 number 31 index 30
residue id #3/A:32 number 32 index 31
residue id #3/A:33 number 33 index 32
residue id #3/A:34 number 34 index 33
residue id #3/A:35 number 35 index 34
residue id #3/A:36 number 36 index 35
residue id #3/A:37 number 37 index 36
residue id #3/A:38 number 38 index 37
residue id #3/A:39 number 39 index 38
residue id #3/A:40 number 40 index 39
residue id #3/A:41 number 41 index 40
residue id #3/A:42 number 42 index 41
residue id #3/A:43 number 43 index 42
residue id #3/A:44 number 44 index 43
residue id #3/A:45 number 45 index 44
residue id #3/A:46 number 46 index 45
residue id #3/A:47 number 47 index 46
residue id #3/A:48 number 48 index 47
residue id #3/A:49 number 49 index 48
residue id #3/A:50 number 50 index 49
residue id #3/A:51 number 51 index 50
residue id #3/A:209 number 209 index 184
residue id #3/A:210 number 210 index 185
residue id #3/A:211 number 211 index 186
residue id #3/A:212 number 212 index 187
residue id #3/A:213 number 213 index 188
residue id #3/A:214 number 214 index 189
residue id #3/A:215 number 215 index 190
residue id #3/A:216 number 216 index 191
residue id #3/A:217 number 217 index 192
residue id #3/A:218 number 218 index 193
residue id #3/A:219 number 219 index 194
residue id #3/A:220 number 220 index 195
residue id #3/A:221 number 221 index 196
residue id #3/A:222 number 222 index 197
residue id #3/A:223 number 223 index 198
residue id #3/A:224 number 224 index 199
residue id #3/A:225 number 225 index 200
residue id #3/A:226 number 226 index 201
residue id #3/A:167 number 167 index 150
residue id #3/A:168 number 168 index 151
residue id #3/A:169 number 169 index 152
residue id #3/A:170 number 170 index 153
residue id #3/A:171 number 171 index 154
residue id #3/A:172 number 172 index 155
residue id #3/A:173 number 173 index 156
residue id #3/A:174 number 174 index 157
residue id #3/A:175 number 175 index 158
residue id #3/A:176 number 176 index 159
residue id #3/A:177 number 177 index 160
residue id #3/A:178 number 178 index 161
residue id #3/A:179 number 179 index 162
residue id #3/A:180 number 180 index 163
residue id #3/A:181 number 181 index 164
residue id #3/A:182 number 182 index 165
residue id #3/A:183 number 183 index 166
residue id #3/A:194 number 194 index 169
residue id #3/A:195 number 195 index 170
residue id #3/A:196 number 196 index 171
residue id #3/A:197 number 197 index 172
residue id #3/A:198 number 198 index 173
residue id #3/A:199 number 199 index 174
residue id #3/A:200 number 200 index 175
residue id #3/A:201 number 201 index 176
residue id #3/A:202 number 202 index 177
residue id #3/A:203 number 203 index 178
residue id #3/A:204 number 204 index 179
residue id #3/A:205 number 205 index 180
residue id #3/A:206 number 206 index 181
residue id #3/A:207 number 207 index 182
residue id #3/A:208 number 208 index 183
> info residues #3/A &@@color='#b89a8c' attribute number
residue id #3/A:16 number 16 index 15
residue id #3/A:17 number 17 index 16
residue id #3/A:18 number 18 index 17
residue id #3/A:152 number 152 index 135
residue id #3/A:153 number 153 index 136
residue id #3/A:154 number 154 index 137
residue id #3/A:155 number 155 index 138
residue id #3/A:156 number 156 index 139
residue id #3/A:157 number 157 index 140
residue id #3/A:158 number 158 index 141
residue id #3/A:159 number 159 index 142
residue id #3/A:160 number 160 index 143
residue id #3/A:161 number 161 index 144
residue id #3/A:162 number 162 index 145
residue id #3/A:163 number 163 index 146
residue id #3/A:164 number 164 index 147
residue id #3/A:165 number 165 index 148
residue id #3/A:166 number 166 index 149
residue id #3/A:52 number 52 index 51
residue id #3/A:53 number 53 index 52
residue id #3/A:54 number 54 index 53
residue id #3/A:19 number 19 index 18
residue id #3/A:20 number 20 index 19
residue id #3/A:21 number 21 index 20
residue id #3/A:22 number 22 index 21
residue id #3/A:23 number 23 index 22
residue id #3/A:24 number 24 index 23
residue id #3/A:25 number 25 index 24
residue id #3/A:26 number 26 index 25
residue id #3/A:27 number 27 index 26
residue id #3/A:28 number 28 index 27
residue id #3/A:29 number 29 index 28
residue id #3/A:30 number 30 index 29
residue id #3/A:31 number 31 index 30
residue id #3/A:32 number 32 index 31
residue id #3/A:33 number 33 index 32
residue id #3/A:34 number 34 index 33
residue id #3/A:35 number 35 index 34
residue id #3/A:36 number 36 index 35
residue id #3/A:37 number 37 index 36
residue id #3/A:38 number 38 index 37
residue id #3/A:39 number 39 index 38
residue id #3/A:40 number 40 index 39
residue id #3/A:41 number 41 index 40
residue id #3/A:42 number 42 index 41
residue id #3/A:43 number 43 index 42
residue id #3/A:44 number 44 index 43
residue id #3/A:45 number 45 index 44
residue id #3/A:46 number 46 index 45
residue id #3/A:47 number 47 index 46
residue id #3/A:48 number 48 index 47
residue id #3/A:49 number 49 index 48
residue id #3/A:50 number 50 index 49
residue id #3/A:51 number 51 index 50
residue id #3/A:209 number 209 index 184
residue id #3/A:210 number 210 index 185
residue id #3/A:211 number 211 index 186
residue id #3/A:212 number 212 index 187
residue id #3/A:213 number 213 index 188
residue id #3/A:214 number 214 index 189
residue id #3/A:215 number 215 index 190
residue id #3/A:216 number 216 index 191
residue id #3/A:217 number 217 index 192
residue id #3/A:218 number 218 index 193
residue id #3/A:219 number 219 index 194
residue id #3/A:220 number 220 index 195
residue id #3/A:221 number 221 index 196
residue id #3/A:222 number 222 index 197
residue id #3/A:223 number 223 index 198
residue id #3/A:224 number 224 index 199
residue id #3/A:225 number 225 index 200
residue id #3/A:226 number 226 index 201
residue id #3/A:167 number 167 index 150
residue id #3/A:168 number 168 index 151
residue id #3/A:169 number 169 index 152
residue id #3/A:170 number 170 index 153
residue id #3/A:171 number 171 index 154
residue id #3/A:172 number 172 index 155
residue id #3/A:173 number 173 index 156
residue id #3/A:174 number 174 index 157
residue id #3/A:175 number 175 index 158
residue id #3/A:176 number 176 index 159
residue id #3/A:177 number 177 index 160
residue id #3/A:178 number 178 index 161
residue id #3/A:179 number 179 index 162
residue id #3/A:180 number 180 index 163
residue id #3/A:181 number 181 index 164
residue id #3/A:182 number 182 index 165
residue id #3/A:183 number 183 index 166
residue id #3/A:194 number 194 index 169
residue id #3/A:195 number 195 index 170
residue id #3/A:196 number 196 index 171
residue id #3/A:197 number 197 index 172
residue id #3/A:198 number 198 index 173
residue id #3/A:199 number 199 index 174
residue id #3/A:200 number 200 index 175
residue id #3/A:201 number 201 index 176
residue id #3/A:202 number 202 index 177
residue id #3/A:203 number 203 index 178
residue id #3/A:204 number 204 index 179
residue id #3/A:205 number 205 index 180
residue id #3/A:206 number 206 index 181
residue id #3/A:207 number 207 index 182
residue id #3/A:208 number 208 index 183
> show #!4 models
> hide #!3 models
> show #!3 models
> select #4/A:1-227
857 atoms, 885 bonds, 2 pseudobonds, 108 residues, 2 models selected
> ui tool show "Color Actions"
> color sel tan
> hide #!3 models
> show #!3 models
> select #4/A:425-436
Nothing selected
> hide #!3 models
> select #4/A:410-421
76 atoms, 77 bonds, 12 residues, 1 model selected
> color sel peru
> select #4/A:456-535
611 atoms, 624 bonds, 80 residues, 1 model selected
> show #!3 models
> hide #!3 models
> color sel violet
> select #4/A:572-685
908 atoms, 934 bonds, 114 residues, 1 model selected
> color sel light steel blue
> color sel powder blue
> color sel sky blue
> color sel medium orchid
> color sel light pink
> color sel light coral
> color sel light pink
> select #4/A:749-814
528 atoms, 540 bonds, 66 residues, 1 model selected
> color sel light coral
> show #!1 models
> show #!2.3 models
> show #!2.1 models
> hide #!2.1 models
> hide #!2.3 models
> show #!3 models
> hide #!3 models
> show #!2.1 models
> show #!2.3 models
> show #2.4 models
> show #2.5 models
> select #2/A:1-16
130 atoms, 132 bonds, 16 residues, 1 model selected
> hide sel cartoons
> select #2/A:1-16,54-58
170 atoms, 171 bonds, 21 residues, 1 model selected
> select #2/A:1-16,54-146
809 atoms, 828 bonds, 3 pseudobonds, 97 residues, 2 models selected
> hide sel cartoons
> select #2:SF4 :<3 /A-E
109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected
> hide #!1 models
> hide #!4 models
> show #!2.2 models
> show #!3 models
> select add #2.2
1804 atoms, 1850 bonds, 14 pseudobonds, 226 residues, 6 models selected
> show sel cartoons
> hide sel cartoons
> select subtract #2.2
93 atoms, 95 bonds, 9 pseudobonds, 14 residues, 4 models selected
> select #2/B:425-436
76 atoms, 77 bonds, 12 residues, 1 model selected
> show sel cartoons
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> select #2:SF4 :<3 /A-E
109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected
> select #2:SF4 :<3 /A-E
109 atoms, 108 bonds, 9 pseudobonds, 17 residues, 5 models selected
> show sel atoms
> color sel byhetero
> show sel cartoons
> show #!4 models
> select #4/A:456-535
611 atoms, 624 bonds, 80 residues, 1 model selected
> hide #!2.2 models
> hide #!2.1 models
> hide #2.4 models
> hide #2.5 models
> ui tool show Matchmaker
> matchmaker #!4 & sel to #2.3/C pairing bs showAlignment true
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PSI chains C, chain C (#2.3) with best.pdb, chain A (#4), sequence
alignment score = 401
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: PSI chains C #2.3/C, best.pdb
#4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 80 pruned atom pairs is 0.395 angstroms; (across all 80 pairs:
0.395)
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> show #!2.2 models
> select #4/A:CYS
84 atoms, 70 bonds, 14 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide #!2 models
> show #!2 models
> save "/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"
> split #2.1 atoms :SF4
Split PSI chains A (#2.1) into 2 models
Chain information for PSI chains A 2 #2.1.2
---
Chain | Description
A | No description available
> hide #!2.1.2 models
> split #2.3 atoms :SF4
Split PSI chains C (#2.3) into 2 models
Chain information for PSI chains C 2 #2.3.2
---
Chain | Description
C | No description available
Associated PSI chains C 2 (2.3.2) chain C to best.pdb, chain A with 0
mismatches
Chains used in RMSD evaluation for alignment 1: PSI chains C 2 #2.3.2/C,
best.pdb #4/A
> hide #2.3.2 models
> hide #2.3.1 models
> show #2.3.1 models
> hide #2.3.1 models
> show #2.3.1 models
> rename #3 id 20
> combine #2.1.1#2.3.1
> hide #!2 models
> rename #3 "Fe4S4 clusters"
> show #!1 models
> select #1 &!@@color='lime'
Expected a keyword
> select #1 &~@@color='lime'
669 atoms, 451 bonds, 8 pseudobonds, 151 residues, 2 models selected
> color sel orange
> color sel dark orange
> color sel byhetero
> select #1 &H
272 atoms, 48 residues, 1 model selected
> hide sel atoms
> select #1
762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected
> color sel byhetero
> select clear
> combine #1
> hide #!1 models
> ui tool show Matchmaker
> matchmaker #!18 to #4/B pairing bs showAlignment true
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker best.pdb, chain B (#4) with copy of 2fdn, chain M (#18), sequence
alignment score = 157.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: best.pdb #4/B, copy of 2fdn
#18/M
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 38 pruned atom pairs is 0.829 angstroms; (across all 51 pairs:
2.274)
> select #4:CYS
132 atoms, 110 bonds, 22 residues, 1 model selected
> select #4/B:CYS
48 atoms, 40 bonds, 8 residues, 1 model selected
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> save "/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"
> show #!5 models
> hide #!5 models
> help help:user
> color #5-18/A:1-227 tan
> color #5-18/A:410-421 peru
> color #5-18/A:456-535 violet
> color #5-18/A:572-685 light pink
> color #5-18/A:749-814 light coral
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> show #!9 models
> show #!7 models
> show #!8 models
> show #!6 models
> show #!5 models
> hide #3 models
> show #!4 models
> show #3 models
> show #!11 models
> show #!12 models
> show #13 models
> show #14 models
> show #15 models
> hide #15 models
> hide #14 models
> show #14 models
> hide #14 models
> hide #13 models
> close #13-17
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!18 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> select add #4
3337 atoms, 3419 bonds, 6 pseudobonds, 434 residues, 2 models selected
> select subtract #4
Nothing selected
> ui tool show Matchmaker
> help help:user
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #1:CYS
80 atoms, 72 bonds, 8 residues, 1 model selected
> align #18:CYS toAtoms #4:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.311 angstroms
> align #18:CYS toAtoms #1:CYS matchAtomNames true move nothing
RMSD between 80 atom pairs is 0.000 angstroms
> align #18:CYS toAtoms #5:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.316 angstroms
> align #18:CYS toAtoms #6:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.305 angstroms
> align #18:CYS toAtoms #7:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.308 angstroms
> align #18:CYS toAtoms #8:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.316 angstroms
> align #18:CYS toAtoms #9:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.306 angstroms
> align #18:CYS toAtoms #10:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.309 angstroms
> align #18:CYS toAtoms #11:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.311 angstroms
> align #18:CYS toAtoms #12:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 84 reference atoms
RMSD between 48 atom pairs is 8.309 angstroms
> select #5-12
26753 atoms, 27419 bonds, 48 pseudobonds, 3472 residues, 16 models selected
> select #5-12/B:CYS
384 atoms, 320 bonds, 64 residues, 8 models selected
> show sel atoms
> color sel byhetero
> align #18:CYS toAtoms #4/B:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.745 angstroms
> align #18:CYS toAtoms #5/B:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.738 angstroms
> align #18:CYS toAtoms #6/B:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.898 angstroms
> align #18:CYS toAtoms #7/B:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.823 angstroms
> align #18:CYS toAtoms #8/B:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.953 angstroms
> align #18:CYS toAtoms #9/B:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.867 angstroms
> align #18:CYS toAtoms #10/B:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.898 angstroms
> align #18:CYS toAtoms #11/B:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.745 angstroms
> align #18:CYS toAtoms #12/B:CYS matchAtomNames true move nothing
Pairing dropped 32 atoms and 0 reference atoms
RMSD between 48 atom pairs is 1.874 angstroms
> save "/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"
——— End of log from Tue Jun 4 18:24:08 2024 ———
opened ChimeraX session
> hide #!12 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> show #!18 models
> hide #!5 models
> hide #!4 models
> hide #!11 models
> select #18/A:CYS
Nothing selected
> select #18/A:CYS
Nothing selected
> select #18:CYS
80 atoms, 72 bonds, 8 residues, 1 model selected
> ui tool show "Color Actions"
> color sel cyan
> color sel byhetero
> select #4/B:CYS
48 atoms, 40 bonds, 8 residues, 1 model selected
> show #3#!18 atoms
> hide #3#!18 atoms
> select #3
24 atoms, 36 bonds, 3 residues, 1 model selected
> show sel atoms
> select #18:CYS
80 atoms, 72 bonds, 8 residues, 1 model selected
> show sel atoms
> select H
544 atoms, 96 residues, 2 models selected
> hide sel & #!18 atoms
> select #18:FS4
Nothing selected
> select #18:SF4
16 atoms, 24 bonds, 2 residues, 1 model selected
> show sel atoms
> select add #18
762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected
> select subtract #18
Nothing selected
> show #!4 models
> select #4/B:CYS
48 atoms, 40 bonds, 8 residues, 1 model selected
> hide #!4 models
> show #!5 models
> show #!11 models
> hide #!5 models
> show #!5 models
> show #!4 models
> save "/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"
——— End of log from Tue Jun 4 19:01:21 2024 ———
opened ChimeraX session
> hide #3 models
> hide #!5 models
> hide #!18 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> open "/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"
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
---
notes | Alignment identifier is design.fasta
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
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
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
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
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
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
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
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
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
11 messages similar to the above omitted
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
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
Showing conservation header ("seq_conservation" residue attribute) for
alignment design.fasta
Opened 64 sequences from design.fasta
> show #!11 models
> ui tool show Matchmaker
> matchmaker #11/B to #4/B pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker best.pdb, chain B (#4) with best_design1.pdb, chain B (#11),
sequence alignment score = 287.3
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: best.pdb #4/B,
best_design1.pdb #11/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 54 pruned atom pairs is 0.000 angstroms; (across all 54 pairs:
0.000)
> sequence header 2 consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment 2
> rename #4 "best (best design1).pdb"
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!2.1 models
> show #!2.1 models
> show #2.5 models
> show #!2.6 models
> hide #!2.6 models
> show #2.4 models
> hide #2.5 models
> hide #2.4 models
> show #3 models
> hide #!2 models
> select #4/B:53-54 #11/B:53-54
28 atoms, 26 bonds, 4 residues, 2 models selected
> select #4/B:24-54 #11/B:24-54
418 atoms, 418 bonds, 62 residues, 2 models selected
> select clear
[Repeated 1 time(s)]
> select add #11/B:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Models/PSI_Fdx Models/BFdx 8 designs with Fasta.cxs"
——— End of log from Thu Sep 19 17:01:48 2024 ———
opened ChimeraX session
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!11 models
> show #!1 models
> hide #!1 models
> show #!18 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> show #3 models
> close #2
Cell requested for row 10 is out of bounds for table with 14 rows! Resizing
table model.
> show #!11 models
> hide #!11 models
Cell requested for row 2 is out of bounds for table with 14 rows! Resizing
table model.
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #!5 models
> show #!11 models
> hide #!4 models
> show #!4 models
> show #!20 models
> hide #!20 models
> hide #!11 models
> close #5-12
> show #!1 models
> ui tool show Matchmaker
> matchmaker #1/M to #4/B pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker best (best design1).pdb, chain B (#4) with 2fdn, chain M (#1),
sequence alignment score = 157.4
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 2fdn #1/M, best (best
design1).pdb #4/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 40 pruned atom pairs is 0.905 angstroms; (across all 51 pairs:
2.218)
> sequence header 1 consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
> select #4/B:9
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/B:9
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/B:9
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/B:9
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel atoms
> select #4/B:9,23-30
64 atoms, 62 bonds, 9 residues, 1 model selected
> select #4/B:9,23-32
77 atoms, 75 bonds, 11 residues, 1 model selected
> hide #!18 models
> hide #3 models
> hide #!1 models
> ui tool show Contacts
> select #4/B
357 atoms, 359 bonds, 54 residues, 1 model selected
> contacts sel restrict #4/A resSeparation 5 interModel false intraMol false
> color #76d6ff radius 0.2 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
22 contacts
atom1 atom2 overlap distance
best (best design1).pdb #4/B ALA 7 CB best (best design1).pdb #4/A ARG 473 NH2 0.873 2.647
best (best design1).pdb #4/B GLU 16 OE1 best (best design1).pdb #4/A THR 802 CB 0.734 2.566
best (best design1).pdb #4/B GLU 16 OE1 best (best design1).pdb #4/A THR 802 OG1 0.578 1.902
best (best design1).pdb #4/B GLY 10 O best (best design1).pdb #4/A ILE 466 CD1 0.308 2.992
best (best design1).pdb #4/B GLU 16 CD best (best design1).pdb #4/A THR 802 OG1 0.249 3.091
best (best design1).pdb #4/B GLU 30 CG best (best design1).pdb #4/A LYS 489 CE 0.245 3.515
best (best design1).pdb #4/B ALA 7 CB best (best design1).pdb #4/A ARG 473 CZ 0.119 3.371
best (best design1).pdb #4/B CYS 11 CA best (best design1).pdb #4/A ILE 466 CD1 0.070 3.690
best (best design1).pdb #4/B GLU 16 CD best (best design1).pdb #4/A THR 802 CB -0.041 3.801
best (best design1).pdb #4/B ALA 7 CB best (best design1).pdb #4/A ARG 473 NH1 -0.058 3.578
best (best design1).pdb #4/B VAL 25 CG2 best (best design1).pdb #4/A VAL 776 CG1 -0.063 3.823
best (best design1).pdb #4/B GLU 30 CG best (best design1).pdb #4/A LYS 489 NZ -0.072 3.592
best (best design1).pdb #4/B GLU 30 OE1 best (best design1).pdb #4/A LYS 489 CE -0.103 3.403
best (best design1).pdb #4/B GLY 10 O best (best design1).pdb #4/A ILE 466 CG1 -0.116 3.416
best (best design1).pdb #4/B CYS 11 CB best (best design1).pdb #4/A CYS 468 SG -0.142 3.792
best (best design1).pdb #4/B GLU 30 CD best (best design1).pdb #4/A LYS 489 CE -0.168 3.928
best (best design1).pdb #4/B GLU 30 CD best (best design1).pdb #4/A LYS 489 NZ -0.185 3.705
best (best design1).pdb #4/B GLU 46 OE1 best (best design1).pdb #4/A ARG 12 NH1 -0.272 2.932
best (best design1).pdb #4/B GLU 26 CG best (best design1).pdb #4/A ALA 777 CB -0.283 4.043
best (best design1).pdb #4/B GLU 16 OE1 best (best design1).pdb #4/A THR 802 CA -0.299 3.599
best (best design1).pdb #4/B ALA 7 CA best (best design1).pdb #4/A ARG 473 NH2 -0.367 3.887
best (best design1).pdb #4/B VAL 25 CG1 best (best design1).pdb #4/A VAL 789 CG1 -0.391 4.151
22 contacts
> hide #4.2 models
> show #4.2 models
> select add #4.2
357 atoms, 359 bonds, 22 pseudobonds, 54 residues, 2 models selected
> select subtract #4.2
357 atoms, 359 bonds, 54 residues, 1 model selected
> hide #4.2 models
> show #4.2 models
> select #4/B:7,10-11,16,25-26,30/A:473,802,466,489,776-777,468,12,789
120 atoms, 107 bonds, 21 pseudobonds, 16 residues, 2 models selected
> style sel ball
Changed 120 atom styles
> color sel byhetero
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 16 items
> name frozen contacts sel
> select #4/B
357 atoms, 359 bonds, 54 residues, 1 model selected
> ui tool show Clashes
> clashes sel restrict #4/A resSeparation 5 interModel false intraMol false
> color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False
2 clashes
atom1 atom2 overlap distance
best (best design1).pdb #4/B ALA 7 CB best (best design1).pdb #4/A ARG 473 NH2 0.873 2.647
best (best design1).pdb #4/B GLU 16 OE1 best (best design1).pdb #4/A THR 802 CB 0.734 2.566
2 clashes
> select #4/B:7,16
14 atoms, 12 bonds, 2 residues, 1 model selected
> select #4/B
357 atoms, 359 bonds, 54 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0096ff restrict #4/A interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
4 best (best design1).pdb
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
best (best design1).pdb #4/A ARG 12 NH1 best (best design1).pdb #4/B GLU 46 OE1 no hydrogen 2.932 N/A
best (best design1).pdb #4/A LYS 489 NZ best (best design1).pdb #4/B GLU 26 O no hydrogen 3.483 N/A
best (best design1).pdb #4/A LYS 489 NZ best (best design1).pdb #4/B GLU 30 OE1 no hydrogen 3.116 N/A
best (best design1).pdb #4/A THR 802 OG1 best (best design1).pdb #4/B GLU 16 OE1 no hydrogen 1.902 N/A
4 hydrogen bonds found
> select #4/B:46,26,30,16/A:12,489,802
63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected
> style sel ball
Changed 63 atom styles
> hide #4.2 models
> hide #4.3 models
> select #4/B:46,26,30,16/A:12,489,802
63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected
> select clear
> select #4/B:1-6,10-23,33-48,51-54 #1/M:1-6,10-23,32-47,52-55
755 atoms, 754 bonds, 80 residues, 2 models selected
> select clear
> select #4/B:46,26,30,16/A:12,489,802
63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected
> select contacts &~#4/B:46,26,30,16/A:12,489,802
66 atoms, 58 bonds, 11 pseudobonds, 10 residues, 3 models selected
> style sel sphere
Changed 66 atom styles
> color sel byhetero
[Repeated 1 time(s)]
> select #4/B:26 &~backbone
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 5 atom styles
> show #4.2 models
> style sel ball
Changed 5 atom styles
> hide #4.4 models
> show #4.4 models
> hide #4.2 models
> show #4.2 models
> hide #4.2 models
> select #4/B:26 &~backbone
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 5 atom styles
> surface #4/A
> surface #4/B
> coulombic #4/B surfaces #4.6
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best (best design1).pdb_B SES surface #4.6: minimum,
-17.76, mean -5.37, maximum 4.03
> coulombic #4/A surfaces #4.5
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best (best design1).pdb_A SES surface #4.5: minimum,
-15.01, mean 1.13, maximum 14.51
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/PSI Fdx best MPNN .cxs"
> select clear
> open 6yez
6yez title:
Plant PSI-ferredoxin-plastocyanin supercomplex [more info...]
Chain information for 6yez #2
---
Chain | Description | UniProt
1 | Lhca1 |
2 | Chlorophyll a-b binding protein, chloroplastic | Q41038_PEA 58-265
3 | Chlorophyll a-b binding protein 3, chloroplastic | CB23_PEA 55-275
4 | Chlorophyll a-b binding protein P4, chloroplastic | CB24_PEA 52-249
A | Photosystem I P700 chlorophyll a apoprotein A1 | A0A0F6NFW5_PEA 16-758
B | Photosystem I P700 chlorophyll a apoprotein A2 | A0A0F6NGI2_PEA 2-734
C | Photosystem I iron-sulfur center | PSAC_PEA 2-81
D | PsaD |
E | PsaE |
F | PsaF |
G | PsaG |
H | PsaH |
I | Photosystem I reaction center subunit VIII | PSAI_PEA 2-32
J | PsaJ |
K | Photosystem I reaction center subunit X psaK | E1C9L3_PEA 46-126
L | PsaL |
N | Ferredoxin-1, chloroplastic | FER1_PEA 1-97
P | Plastocyanin, chloroplastic | PLAS_PEA 1-99
Non-standard residues in 6yez #2
---
3PH — 1,2-diacyl-glycerol-3-Sn-phosphate (phosphatidic acid)
BCR — β-carotene
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
CA — calcium ion
CHL — chlorophyll B
CL0 — chlorophyll A isomer
CLA — chlorophyll A
CU — copper (II) ion
DGD — digalactosyl diacyl glycerol (DGDG)
FES — FE2/S2 (inorganic) cluster
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
LMG — 1,2-distearoyl-monogalactosyl-diglyceride
LMT — dodecyl-β-D-maltoside
LUT — (3R,3'R,6S)-4,5-didehydro-5,6-dihydro-β,β-carotene-3,3'-diol
((3R,3'R)-β,β-carotene-3,3'-diol; lutein)
PQN — phylloquinone (vitamin K1; 2-methyl-3-phytyl-1,4-naphthoquinone)
SF4 — iron/sulfur cluster
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 (violaxanthin)
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
Associated 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
> select #2 &protein
26851 atoms, 27685 bonds, 3438 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> hide #4.6 models
> hide #4.5 models
> ui tool show Matchmaker
> matchmaker #2/C to #4/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker best (best design1).pdb, chain A (#4) with 6yez, chain C (#2),
sequence alignment score = 401
RMSD between 80 pruned atom pairs is 0.395 angstroms; (across all 80 pairs:
0.395)
> show #4.6 models
> hide #4.6 models
> show #4.6 models
> hide #4.6 models
> show #4.6 models
> hide #4.6 models
> show #4.5 models
> hide #4.5 models
> coulombic #2/E
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
6yez #2/E LYS 129 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6yez_E SES surface #2.2: minimum, -13.31, mean 0.69,
maximum 9.65
> hide #!4 models
> coulombic #2/C:2-81
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6yez_C SES surface #2.3: minimum, -12.54, mean -0.30,
maximum 9.66
> coulombic #2/D
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
6yez #2/D LEU 211 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 6yez_D SES surface #2.4: minimum, -11.93, mean 1.16,
maximum 13.86
> toolshed show
> volume showOutlineBox true
No volumes specified
> show #3 models
> show #!4 models
> select #2/N/P
1457 atoms, 1483 bonds, 7 pseudobonds, 198 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2:3001
8 atoms, 12 bonds, 1 residue, 1 model selected
> cofr sel
> select #4/A
2980 atoms, 3060 bonds, 6 pseudobonds, 380 residues, 2 models selected
> hide sel cartoons
> select contacts :<1 
128 atoms, 118 bonds, 17 residues, 1 model selected
> show sel atoms
> hide sel atoms
> hide #2.4 models
> hide #2.3 models
> hide #2.2 models
> select #4/A
2980 atoms, 3060 bonds, 7 pseudobonds, 380 residues, 3 models selected
> show sel cartoons
> show #4.5 models
> show #4.6 models
> select #2:CA,CU,DGD,3PH,C7Z,LHG
739 atoms, 735 bonds, 20 residues, 1 model selected
> select #2/1
2580 atoms, 2690 bonds, 61 pseudobonds, 214 residues, 2 models selected
> select #2/1-4
10673 atoms, 11130 bonds, 241 pseudobonds, 907 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/C-E
2288 atoms, 2352 bonds, 7 pseudobonds, 291 residues, 2 models selected
> hide sel cartoons
> set bgColor white
> select clear
> graphics silhouettes true
> hide #!4 models
> show #!4 models
> hide #4.4 models
> hide #4.5 models
> show #4.4 models
> hide #4.6 models
> show #4.5 models
> hide #4.5 models
> surface #2 enclose #2/A-B/F-L
> close #2.5
> select contacts :<1 
128 atoms, 118 bonds, 17 residues, 1 model selected
> select #4/A :<1 
3059 atoms, 3141 bonds, 4 pseudobonds, 382 residues, 2 models selected
> select #4/A :<1  &protein
2994 atoms, 3072 bonds, 381 residues, 1 model selected
> name frozen minAB sel
> select #2/A-B/F-L &~minAB
23858 atoms, 24789 bonds, 418 pseudobonds, 2167 residues, 2 models selected
> surface #2 enclose #2/A-B/F-L &~minAB
> show #4.5 models
> show #4.6 models
> hide #4.6 models
> select clear
> select #1:SF4
16 atoms, 24 bonds, 2 residues, 1 model selected
> show #!1 models
> select #1:1-55
652 atoms, 657 bonds, 55 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #4/A &contacts
71 atoms, 63 bonds, 9 residues, 1 model selected
> style sel stick
Changed 71 atom styles
> select :CL0,CLA
8422 atoms, 8990 bonds, 568 pseudobonds, 142 residues, 2 models selected
> color (#!2 & sel) lime
> color sel byhetero
> select clear
Cell requested for row 8 is out of bounds for table with 17 rows! Resizing
table model.
> select add #4.5
2980 atoms, 380 residues, 1 model selected
> transparency (#!4 & sel) 30
> transparency (#!4 & sel) 20
> select clear
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/PSI Fdx best MPNN .cxs"
> view name front
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx front .png" width 845 height 690 supersample 3
> transparentBackground true
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx front .png" width 1470 height 1200 supersample 3
> transparentBackground true
> select contacts
120 atoms, 107 bonds, 26 pseudobonds, 16 residues, 4 models selected
> style sel stick
Changed 120 atom styles
> show #4.6 models
> select clear
> select add #4.6
357 atoms, 54 residues, 1 model selected
> transparency (#!4 & sel) 20
> select clear
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx 2 surfaces front .png" width 1470 height 1200 supersample 3
> transparentBackground true
> hide #4.5 models
> hide #4.6 models
> select contacts
120 atoms, 107 bonds, 26 pseudobonds, 16 residues, 4 models selected
> style sel sphere
Changed 120 atom styles
> show #4.5 models
> hide #4.5 models
> show #4.5 models
> hide #4.5 models
> show #4.6 models
> select #4/B &contacts
49 atoms, 44 bonds, 7 residues, 1 model selected
> style sel stick
Changed 49 atom styles
> select clear
> view name back
> show #4.5 models
> hide #4.5 models
> hide #4.6 models
> show #4.6 models
> hide #4.6 models
> select #4/A:489
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show #4.6 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx back .png" width 1470 height 1200 supersample 3
> transparentBackground true
> select clear
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx back .png" width 1470 height 1200 supersample 3
> transparentBackground true
> view front
> select #4/A:12
11 atoms, 10 bonds, 1 residue, 1 model selected
> style sel stick
Changed 11 atom styles
> show #4.5 models
> select clear
> hide #4.6 models
> select #4/B:16,30,46
27 atoms, 24 bonds, 3 residues, 1 model selected
> style sel ball
Changed 27 atom styles
> select #4/B:26 &backbone
4 atoms, 3 bonds, 1 residue, 1 model selected
> style sel ball
Changed 4 atom styles
> view front
> select clear
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/PSI Fdx best MPNN .cxs"
> hide #4.5 models
> select #4/A &contacts &~489,802
Expected a keyword
> select #4/A &contacts &~:489,802
55 atoms, 49 bonds, 7 residues, 1 model selected
> style sel stick
Changed 55 atom styles
> select #4/A:12,489,802
27 atoms, 24 bonds, 3 residues, 1 model selected
> style sel ball
Changed 27 atom styles
> show #4.5 models
> select clear
> hide #4.5 models
> show #4.5 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/PSI Fdx best MPNN .cxs"
> hide #4.5 models
> show #4.5 models
> select #4/B:16,26,30,46/A:12,489,802
63 atoms, 56 bonds, 16 pseudobonds, 7 residues, 4 models selected
> name frozen hBonds sel
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/PSI Fdx best MPNN .cxs"
> select clear
> select #4/B &contacts &~hBonds
22 atoms, 19 bonds, 4 residues, 1 model selected
> style sel sphere
Changed 22 atom styles
> select #4/B:26 &~backbone
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 5 atom styles
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/PSI Fdx best MPNN .cxs"
> select clear
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx front .png" width 1568 height 1280 supersample 3
> transparentBackground true
> select #4/B &contacts &~hBonds
22 atoms, 19 bonds, 4 residues, 1 model selected
> style sel stick
Changed 22 atom styles
> select #4/B:26 &~backbone
5 atoms, 4 bonds, 1 residue, 1 model selected
> style sel stick
Changed 5 atom styles
> show #4.6 models
> select clear
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx 2 surfaces front .png" width 1568 height 1280 supersample 3
> transparentBackground true
> hide #4.6 models
> hide #4.5 models
> show #4.6 models
> view back
> select #4/A &contacts &~hBonds
44 atoms, 39 bonds, 6 residues, 1 model selected
> style sel sphere
Changed 44 atom styles
> select clear
> select minAB
3213 atoms, 3072 bonds, 410 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx 2 surfaces front .png" width 1568 height 1280 supersample 3
> transparentBackground true
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/PSI Fdx best MPNN .cxs"
——— End of log from Mon Sep 30 14:03:27 2024 ———
opened ChimeraX session
> open "/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"
Chain information for relaxed_structure.pdb #5
---
Chain | Description
A | No description available
B | No description available
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
> ui tool show Matchmaker
> hide #5 models
> show #5 models
> ui tool show Matchmaker
> matchmaker #5/A to #2/C pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6yez, chain C (#2) with relaxed_structure.pdb, chain A (#5),
sequence alignment score = 364.4
RMSD between 73 pruned atom pairs is 0.691 angstroms; (across all 80 pairs:
2.602)
> hide #!4 models
> hide #!2 models
> close #5
> show #!4 models
> open "/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"
Chain information for relaxed_structure.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
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
Associated 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
> select #5 &protein
28495 atoms, 28969 bonds, 1826 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> hide #!4 models
> hide #!1 models
> show #!2 models
> view front
> select clear
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on
> PSI.cxs"
> hide #2.5 models
> hide #!2 models
> surface #5
> show #!2 models
> coulombic #5/A surfaces #5.1
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for relaxed_structure.pdb_A SES surface #5.1: minimum,
-11.84, mean -0.24, maximum 17.92
> coulombic #5/B surfaces #5.2
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for relaxed_structure.pdb_B SES surface #5.2: minimum,
-13.17, mean 0.31, maximum 13.60
> coulombic #5/C surfaces #5.3
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for relaxed_structure.pdb_C SES surface #5.3: minimum,
-14.28, mean 0.87, maximum 12.27
> coulombic #5/D surfaces #5.4
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for relaxed_structure.pdb_D SES surface #5.4: minimum, -9.85,
mean 2.10, maximum 15.14
> coulombic #5/E surfaces #5.5
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for relaxed_structure.pdb_E SES surface #5.5: minimum,
-10.97, mean 1.53, maximum 12.30
> coulombic #5/F surfaces #5.6
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum,
-13.89, mean -3.67, maximum 7.01
> select add #5.1
11581 atoms, 743 residues, 1 model selected
> select add #5.2
23096 atoms, 1476 residues, 2 models selected
> select add #5.3
24310 atoms, 1556 residues, 3 models selected
> select add #5.4
26587 atoms, 1699 residues, 4 models selected
> select add #5.5
27646 atoms, 1765 residues, 5 models selected
> select subtract #5.4
25369 atoms, 1622 residues, 6 models selected
> select subtract #5.5
24310 atoms, 1556 residues, 5 models selected
> select add #5.6
25159 atoms, 1617 residues, 4 models selected
> select add #5.4
27436 atoms, 1760 residues, 5 models selected
> select add #5.5
28495 atoms, 1826 residues, 6 models selected
> transparency (#!5 & sel) 20
> show #!1 models
> hide #5.6 models
> select #5/C/F &:Cys &~H
102 atoms, 85 bonds, 17 residues, 1 model selected
> show sel atoms
> color sel byhetero
> style sel stick
Changed 102 atom styles
> select #5/F#1/M &:CYS
168 atoms, 152 bonds, 16 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #1/M & sel to #5/F & sel pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#1),
sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
1.008)
> select #5/A-E
27646 atoms, 28113 bonds, 1765 residues, 1 model selected
> ui tool show Clashes
> clashes sel restrict #5/F resSeparation 5 interModel false intraMol false
> color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False
0 clashes
atom1 atom2 overlap distance
No clashes
> ui tool show Contacts
> contacts sel restrict #15/B resSeparation 5 interModel false intraMol false
> color #76d6ff radius 0.2 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict #5/F resSeparation 5 interModel false intraMol false
> color #76d6ff radius 0.2 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
160 contacts
atom1 atom2 overlap distance
relaxed_structure.pdb #5/C ARG 18 HH11 relaxed_structure.pdb #5/F GLU 17 CD 0.421 2.279
relaxed_structure.pdb #5/D LYS 109 HZ2 relaxed_structure.pdb #5/F GLU 19 CD 0.387 2.313
relaxed_structure.pdb #5/E THR 54 HG1 relaxed_structure.pdb #5/F GLU 9 OE2 0.371 1.709
relaxed_structure.pdb #5/D LYS 109 HZ2 relaxed_structure.pdb #5/F GLU 19 OE1 0.357 1.723
relaxed_structure.pdb #5/A LYS 31 HZ2 relaxed_structure.pdb #5/F ASP 30 OD2 0.353 1.727
relaxed_structure.pdb #5/A ARG 27 HH21 relaxed_structure.pdb #5/F ASP 30 OD1 0.348 1.732
relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 CD 0.340 2.985
relaxed_structure.pdb #5/E ARG 43 HH21 relaxed_structure.pdb #5/F GLU 9 OE1 0.335 1.745
relaxed_structure.pdb #5/E THR 54 HG1 relaxed_structure.pdb #5/F GLU 9 CD 0.326 2.374
relaxed_structure.pdb #5/C ARG 18 HH22 relaxed_structure.pdb #5/F GLU 17 OE2 0.323 1.757
relaxed_structure.pdb #5/A ARG 27 HH11 relaxed_structure.pdb #5/F ASP 30 OD1 0.313 1.767
relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH22 0.308 1.772
relaxed_structure.pdb #5/E ARG 43 HH22 relaxed_structure.pdb #5/F ALA 7 O 0.213 1.867
relaxed_structure.pdb #5/C PRO 58 CB relaxed_structure.pdb #5/F ILE 11 CD1 0.169 3.231
relaxed_structure.pdb #5/A ARG 27 HH21 relaxed_structure.pdb #5/F ASP 30 CG 0.166 2.534
relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F THR 8 HA 0.161 2.464
relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 HE 0.158 1.942
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 N 0.152 3.098
relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 HH12 0.146 1.934
relaxed_structure.pdb #5/D LYS 109 HZ1 relaxed_structure.pdb #5/F PRO 18 O 0.146 1.934
relaxed_structure.pdb #5/C ARG 18 HH11 relaxed_structure.pdb #5/F GLU 17 OE1 0.136 1.944
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 HG2 0.085 2.540
relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 CD 0.062 3.263
relaxed_structure.pdb #5/A ARG 27 CZ relaxed_structure.pdb #5/F ASP 30 OD1 0.055 3.125
relaxed_structure.pdb #5/C ARG 18 HH11 relaxed_structure.pdb #5/F GLU 17 OE2 0.055 2.025
relaxed_structure.pdb #5/D LYS 109 HZ3 relaxed_structure.pdb #5/F GLU 19 OE2 0.047 2.033
relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 OD1 0.038 2.667
relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F SER 12 O 0.034 3.146
relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE1 0.032 2.673
relaxed_structure.pdb #5/C ALA 35 CB relaxed_structure.pdb #5/F VAL 51 HA 0.028 2.672
relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 OD2 0.025 2.680
relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 OD1 0.020 2.685
relaxed_structure.pdb #5/C LYS 34 C relaxed_structure.pdb #5/F GLY 50 O 0.019 3.161
relaxed_structure.pdb #5/C PRO 58 CG relaxed_structure.pdb #5/F ILE 11 CD1 0.015 3.385
relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F PRO 53 HB3 0.012 2.688
relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE2 0.011 2.694
relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 CD -0.001 3.201
relaxed_structure.pdb #5/A ARG 27 HH11 relaxed_structure.pdb #5/F ASP 30 CG -0.002 2.702
relaxed_structure.pdb #5/C THR 14 HG1 relaxed_structure.pdb #5/F ALA 15 HB3 -0.006 2.006
relaxed_structure.pdb #5/C CYS 13 O relaxed_structure.pdb #5/F ALA 15 HB3 -0.012 2.492
relaxed_structure.pdb #5/D LYS 109 HZ3 relaxed_structure.pdb #5/F GLU 19 CD -0.015 2.715
relaxed_structure.pdb #5/C PRO 58 HG3 relaxed_structure.pdb #5/F ILE 11 CD1 -0.017 2.717
relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 NH2 -0.023 2.728
relaxed_structure.pdb #5/C PRO 58 CB relaxed_structure.pdb #5/F ILE 11 HD11 -0.027 2.727
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 OE2 -0.028 2.733
relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F GLU 9 OE1 -0.044 2.749
relaxed_structure.pdb #5/C ARG 18 CZ relaxed_structure.pdb #5/F GLY 14 O -0.062 3.242
relaxed_structure.pdb #5/C ARG 18 HH22 relaxed_structure.pdb #5/F GLU 17 CD -0.064 2.764
relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 CG -0.076 3.401
relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 CZ -0.080 3.260
relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 OE2 -0.082 2.662
relaxed_structure.pdb #5/A ASP 34 CG relaxed_structure.pdb #5/F ARG 32 HH12 -0.083 2.783
relaxed_structure.pdb #5/A LYS 31 HZ2 relaxed_structure.pdb #5/F ASP 30 CG -0.084 2.784
relaxed_structure.pdb #5/E SER 53 C relaxed_structure.pdb #5/F GLU 9 OE2 -0.087 3.267
relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 HG3 -0.088 2.788
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F ALA 15 N -0.094 3.344
relaxed_structure.pdb #5/C ARG 18 HH21 relaxed_structure.pdb #5/F PRO 18 HG2 -0.099 2.099
relaxed_structure.pdb #5/C ARG 18 CZ relaxed_structure.pdb #5/F GLU 17 OE2 -0.103 3.283
relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F PRO 53 O -0.106 2.586
relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 HB2 -0.106 2.586
relaxed_structure.pdb #5/A ARG 27 HH21 relaxed_structure.pdb #5/F ASP 30 HA -0.109 2.109
relaxed_structure.pdb #5/E SER 53 H relaxed_structure.pdb #5/F GLU 9 OE2 -0.109 2.189
relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 HA -0.113 2.593
relaxed_structure.pdb #5/C THR 14 HG1 relaxed_structure.pdb #5/F ALA 15 CB -0.115 2.815
relaxed_structure.pdb #5/C PRO 58 CB relaxed_structure.pdb #5/F ILE 11 HD13 -0.120 2.820
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 C -0.122 3.447
relaxed_structure.pdb #5/C ILE 11 HG13 relaxed_structure.pdb #5/F PRO 53 CB -0.123 2.823
relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F PRO 18 O -0.123 2.828
relaxed_structure.pdb #5/C CYS 13 C relaxed_structure.pdb #5/F ALA 15 HB3 -0.125 2.825
relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE1 -0.132 2.837
relaxed_structure.pdb #5/C ILE 11 CG1 relaxed_structure.pdb #5/F PRO 53 CB -0.134 3.534
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 CG -0.138 3.463
relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 NH1 -0.139 2.844
relaxed_structure.pdb #5/C GLN 15 HG2 relaxed_structure.pdb #5/F SER 12 O -0.148 2.628
relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F MET 54 CE -0.150 3.350
relaxed_structure.pdb #5/C GLN 15 CG relaxed_structure.pdb #5/F SER 12 O -0.153 3.333
relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F ALA 7 O -0.157 2.862
relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 HA -0.159 2.784
relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F PRO 53 CB -0.177 3.577
relaxed_structure.pdb #5/C GLN 15 CG relaxed_structure.pdb #5/F CYS 13 HA -0.183 2.883
relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F THR 8 CA -0.185 3.510
relaxed_structure.pdb #5/C ALA 35 CA relaxed_structure.pdb #5/F VAL 51 HA -0.194 2.894
relaxed_structure.pdb #5/C GLN 15 HE21 relaxed_structure.pdb #5/F GLY 14 C -0.195 2.895
relaxed_structure.pdb #5/D LYS 109 HG2 relaxed_structure.pdb #5/F GLU 19 OE1 -0.202 2.682
relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE2 -0.203 2.908
relaxed_structure.pdb #5/E THR 54 O relaxed_structure.pdb #5/F MET 54 CE -0.206 3.386
relaxed_structure.pdb #5/C GLN 15 OE1 relaxed_structure.pdb #5/F SER 12 O -0.206 3.166
relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F GLY 14 N -0.207 3.532
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 CA -0.208 3.533
relaxed_structure.pdb #5/C PRO 58 HB2 relaxed_structure.pdb #5/F ILE 11 CD1 -0.211 2.911
relaxed_structure.pdb #5/E ARG 43 HH22 relaxed_structure.pdb #5/F ALA 7 C -0.212 2.912
relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 NE -0.215 2.940
relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F MET 54 SD -0.218 3.700
relaxed_structure.pdb #5/E THR 54 O relaxed_structure.pdb #5/F MET 54 HE2 -0.218 2.698
relaxed_structure.pdb #5/C LYS 34 CB relaxed_structure.pdb #5/F GLY 50 O -0.221 3.401
relaxed_structure.pdb #5/A THR 28 HG1 relaxed_structure.pdb #5/F ARG 32 HH21 -0.224 2.224
relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F PRO 53 HB3 -0.227 2.227
relaxed_structure.pdb #5/E ARG 43 HH22 relaxed_structure.pdb #5/F THR 8 HA -0.229 2.229
relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 CB -0.230 3.410
relaxed_structure.pdb #5/E THR 54 CG2 relaxed_structure.pdb #5/F GLU 9 OE1 -0.230 3.410
relaxed_structure.pdb #5/E SER 53 CA relaxed_structure.pdb #5/F GLU 9 OE2 -0.230 3.410
relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 CG -0.231 3.631
relaxed_structure.pdb #5/C PRO 58 CG relaxed_structure.pdb #5/F ILE 11 HD13 -0.233 2.933
relaxed_structure.pdb #5/C THR 14 HG1 relaxed_structure.pdb #5/F ALA 15 CA -0.234 2.934
relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 CG -0.235 3.560
relaxed_structure.pdb #5/C PRO 58 HB3 relaxed_structure.pdb #5/F ILE 11 HD11 -0.242 2.242
relaxed_structure.pdb #5/C ALA 35 CA relaxed_structure.pdb #5/F GLY 50 O -0.243 3.423
relaxed_structure.pdb #5/C ALA 35 HB3 relaxed_structure.pdb #5/F VAL 51 HA -0.244 2.244
relaxed_structure.pdb #5/A LYS 31 HZ1 relaxed_structure.pdb #5/F ASP 30 O -0.246 2.326
relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 CA -0.247 3.427
relaxed_structure.pdb #5/C CYS 13 HB2 relaxed_structure.pdb #5/F PRO 53 HG3 -0.250 2.250
relaxed_structure.pdb #5/A THR 28 HB relaxed_structure.pdb #5/F GLY 31 HA2 -0.251 2.251
relaxed_structure.pdb #5/C CYS 13 HB3 relaxed_structure.pdb #5/F PRO 53 CB -0.254 2.954
relaxed_structure.pdb #5/A ARG 27 HH21 relaxed_structure.pdb #5/F ASP 30 CA -0.255 2.955
relaxed_structure.pdb #5/C CYS 13 HB3 relaxed_structure.pdb #5/F PRO 53 HB2 -0.260 2.260
relaxed_structure.pdb #5/C PRO 58 HG3 relaxed_structure.pdb #5/F ILE 11 HD13 -0.265 2.265
relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 O -0.269 2.974
relaxed_structure.pdb #5/C PRO 58 HB2 relaxed_structure.pdb #5/F ILE 11 HD13 -0.269 2.269
relaxed_structure.pdb #5/C ALA 35 HA relaxed_structure.pdb #5/F VAL 51 HA -0.270 2.270
relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F PRO 53 C -0.274 2.974
relaxed_structure.pdb #5/E ARG 43 HH21 relaxed_structure.pdb #5/F GLU 9 CD -0.276 2.976
relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F GLY 14 H -0.276 2.976
relaxed_structure.pdb #5/A ASP 34 CG relaxed_structure.pdb #5/F ARG 32 HH22 -0.283 2.983
relaxed_structure.pdb #5/E THR 54 N relaxed_structure.pdb #5/F GLU 9 OE2 -0.285 2.990
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 H -0.288 2.913
relaxed_structure.pdb #5/D LYS 109 HZ1 relaxed_structure.pdb #5/F PRO 18 C -0.290 2.990
relaxed_structure.pdb #5/E ARG 43 CZ relaxed_structure.pdb #5/F GLU 9 OE1 -0.291 3.471
relaxed_structure.pdb #5/C THR 14 HG22 relaxed_structure.pdb #5/F ALA 15 CB -0.292 2.992
relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F MET 54 HE1 -0.299 2.799
relaxed_structure.pdb #5/E THR 54 CB relaxed_structure.pdb #5/F GLU 9 OE2 -0.302 3.482
relaxed_structure.pdb #5/C CYS 13 HA relaxed_structure.pdb #5/F PRO 53 HD3 -0.306 2.306
relaxed_structure.pdb #5/C ILE 11 CG1 relaxed_structure.pdb #5/F PRO 53 HB3 -0.311 3.011
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLY 14 O -0.312 3.017
relaxed_structure.pdb #5/A THR 28 HB relaxed_structure.pdb #5/F GLY 31 C -0.313 3.013
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 CD -0.314 3.639
relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 CA -0.317 3.642
relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 CB -0.318 3.718
relaxed_structure.pdb #5/C ILE 11 HG13 relaxed_structure.pdb #5/F PRO 53 HB2 -0.319 2.319
relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 HB2 -0.326 3.026
relaxed_structure.pdb #5/E VAL 52 HG21 relaxed_structure.pdb #5/F ILE 11 CG2 -0.326 3.026
relaxed_structure.pdb #5/C CYS 13 O relaxed_structure.pdb #5/F ALA 15 CB -0.332 3.512
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F CYS 13 C -0.336 3.661
relaxed_structure.pdb #5/D LYS 109 HZ2 relaxed_structure.pdb #5/F GLU 19 OE2 -0.338 2.418
relaxed_structure.pdb #5/C ALA 35 CB relaxed_structure.pdb #5/F VAL 51 CA -0.340 3.740
relaxed_structure.pdb #5/E SER 53 N relaxed_structure.pdb #5/F GLU 9 OE2 -0.349 3.054
relaxed_structure.pdb #5/A THR 28 HB relaxed_structure.pdb #5/F GLY 31 CA -0.353 3.053
relaxed_structure.pdb #5/C ARG 18 HH22 relaxed_structure.pdb #5/F PRO 18 HG2 -0.353 2.353
relaxed_structure.pdb #5/C ILE 11 HB relaxed_structure.pdb #5/F PRO 53 O -0.354 2.834
relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F MET 54 SD -0.357 3.139
relaxed_structure.pdb #5/C PRO 58 HB3 relaxed_structure.pdb #5/F ILE 11 CD1 -0.364 3.064
relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F CYS 13 HA -0.364 3.064
relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 CG -0.369 3.694
relaxed_structure.pdb #5/C THR 14 HG22 relaxed_structure.pdb #5/F ALA 15 HB3 -0.370 2.370
relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 CZ -0.377 3.577
relaxed_structure.pdb #5/C ALA 35 N relaxed_structure.pdb #5/F GLY 50 O -0.377 3.082
relaxed_structure.pdb #5/C GLN 15 HE21 relaxed_structure.pdb #5/F GLY 14 CA -0.381 3.081
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 CD -0.381 3.706
relaxed_structure.pdb #5/C ARG 18 HH22 relaxed_structure.pdb #5/F PRO 18 CG -0.386 3.086
relaxed_structure.pdb #5/C ILE 11 HD12 relaxed_structure.pdb #5/F PRO 53 CB -0.388 3.088
relaxed_structure.pdb #5/E THR 54 HG22 relaxed_structure.pdb #5/F GLU 9 OE1 -0.396 2.876
160 contacts
> color sel byhetero
> select #5/A-F
28495 atoms, 28969 bonds, 160 pseudobonds, 1826 residues, 2 models selected
> color sel byhetero
> coulombic #5/A surfaces #5.1
Coulombic values for relaxed_structure.pdb_A SES surface #5.1: minimum,
-11.84, mean -0.24, maximum 17.92
> coulombic #5/B surfaces #5.2
Coulombic values for relaxed_structure.pdb_B SES surface #5.2: minimum,
-13.17, mean 0.31, maximum 13.60
> coulombic #5/C surfaces #5.3
Coulombic values for relaxed_structure.pdb_C SES surface #5.3: minimum,
-14.28, mean 0.87, maximum 12.27
> coulombic #5/D surfaces #5.4
Coulombic values for relaxed_structure.pdb_D SES surface #5.4: minimum, -9.85,
mean 2.10, maximum 15.14
> coulombic #5/E surfaces #5.5
Coulombic values for relaxed_structure.pdb_E SES surface #5.5: minimum,
-10.97, mean 1.53, maximum 12.30
> select H
14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected
> hide sel & #!1,5 atoms
> select #5/A-E
27646 atoms, 28113 bonds, 1765 residues, 1 model selected
> hide #5.1 models
> hide #5.2 models
> hide #5.3 models
> hide #5.4 models
> hide #5.5 models
> hide #!2 models
> ui tool show H-Bonds
> hbonds sel color #0096ff restrict #5/F interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
5 relaxed_structure.pdb
18 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
18 hydrogen bonds found
> select #5/F:7,9,17-19,30,28,30,34
111 atoms, 106 bonds, 8 residues, 1 model selected
> style sel stick
Changed 111 atom styles
> select #5/F:28,34
30 atoms, 28 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 30 atom styles
> select #5/F:32
24 atoms, 23 bonds, 1 residue, 1 model selected
> style sel stick
Changed 24 atom styles
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54
167 atoms, 160 bonds, 9 residues, 1 model selected
> style sel stick
Changed 167 atom styles
> show sel atoms
> hide #5.8 models
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 9 items
> select #5/F:7,9,17-19,30,32
105 atoms, 101 bonds, 7 residues, 1 model selected
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 7 items
> select clear
> select :SF4
104 atoms, 156 bonds, 13 residues, 5 models selected
> style sel & #3#!1 ball
Changed 40 atom styles
> style sel & #3#!1 ball
Changed 40 atom styles
> select clear
> view front
[Repeated 1 time(s)]
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on
> PSI.cxs"
> view name hbond1
> view front
> view hbond1
> view name hbond2
> view name hbond3
> view front
> view back
> view front
[Repeated 1 time(s)]
> select #1/M:61@FE1
1 atom, 1 residue, 1 model selected
> select #1/M:61@FE2
1 atom, 1 residue, 1 model selected
> select #1/M:61@FE2#3/C:3003@FE2
2 atoms, 2 residues, 2 models selected
> ui tool show Distances
> distance style color #797979
[Repeated 2 time(s)]
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style radius 0.2
[Repeated 2 time(s)]
> distance #1/M:61@FE2 #3/C:3003@FE2
Distance between 2fdn #1/M SF4 61 FE2 and Fe4S4 clusters #3/C SF4 3003 FE2:
11.23Å
> ~distance #1/M:61@FE2 #3/C:3003@FE2
> select #1/M:61@FE2#3/C:3003@FE1
2 atoms, 2 residues, 2 models selected
> distance #1/M:61@FE2 #3/C:3003@FE1
Distance between 2fdn #1/M SF4 61 FE2 and Fe4S4 clusters #3/C SF4 3003 FE1:
8.79Å
> select clear
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Models/PSI_Fdx Models/BacetrioFdx PSI interface/Both best dock on
> PSI.cxs"
[Repeated 1 time(s)]
——— End of log from Thu Oct 3 09:47:21 2024 ———
opened ChimeraX session
> view front
> view back
> view hBond1
Expected an objects specifier or a view name or a keyword
> view hbond1
> hide #6.1 models
> view hbond2
> view hbond3
> view front
> show #5.1 models
> show #5.2 models
> show #5.3 models
> show #5.4 models
> show #5.5 models
> select add #5.5
1059 atoms, 66 residues, 1 model selected
> select add #5.4
3336 atoms, 209 residues, 2 models selected
> select add #5.3
4550 atoms, 289 residues, 3 models selected
> select add #5.2
16065 atoms, 1022 residues, 4 models selected
> select add #5.1
27646 atoms, 1765 residues, 5 models selected
> transparency (#!5 & sel) 20
> transparency (#!5 & sel) 30
> select clear
> graphics silhouettes false
> graphics silhouettes true
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2/F
1633 atoms, 1673 bonds, 9 pseudobonds, 164 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #2/J
528 atoms, 546 bonds, 5 pseudobonds, 46 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2:BCR
1080 atoms, 1107 bonds, 27 residues, 1 model selected
> select #2:BCR,LUT
1374 atoms, 1408 bonds, 34 residues, 1 model selected
> color sel orange
> color sel byhetero
> select clear
> show #5.6 models
> coulombic #5/F surfaces #5.6
Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum,
-13.89, mean -3.67, maximum 7.01
> select subtract #5.7
Nothing selected
> select add #5.6
849 atoms, 61 residues, 1 model selected
> transparency (#!5 & sel) 30
> select clear
> view front
> hide #5.6 models
> hide #5.5 models
> hide #5.4 models
> hide #5.3 models
> hide #5.2 models
> hide #5.1 models
> show #5.1 models
> show #5.2 models
> show #5.3 models
> show #5.4 models
> show #5.5 models
> hide #5.5 models
> show #5.5 models
> hide #5.5 models
> show #5.5 models
> show #5.6 models
> help help:user
> view name front
> turn x 180
> view front
> turn y 180
> hide #5.3 models
> hide #5.4 models
> hide #5.5 models
> hide #5.6 models
> show #5.3 models
> show #5.4 models
> show #5.5 models
> show #5.6 models
> hide #5.5 models
> hide #5.4 models
> hide #5.3 models
> show #5.4 models
> show #5.5 models
> hide #5.4 models
> hide #5.5 models
> show #5.4 models
> hide #5.4 models
> turn y 180
[Repeated 1 time(s)]
> view name back
> view front
> view back
> select #2/I/H/L
2569 atoms, 2652 bonds, 18 pseudobonds, 292 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide #5.6 models
> view name back
> show #5.6 models
> show #5.4 models
> hide #5.4 models
> hide #5.6 models
> view name back
> view front
> view back
> view front
> show #5.3 models
> show #5.4 models
> show #5.5 models
> hide #5.5 models
> hide #5.4 models
> hide #5.3 models
> show #5.3 models
> show #5.4 models
> show #5.5 models
> show #5.6 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
——— End of log from Thu Oct 3 21:28:49 2024 ———
opened ChimeraX session
> view front
> view backZoom
Expected an objects specifier or a view name or a keyword
> view hbond2
> view back
> hide #5.6 models
> show #5.6 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #5.6 models
> show #5.6 models
> hide #5.6 models
> show #5.6 models
> view front
> hide #5.6 models
> hide #!1 models
> show #!18 models
> rename #6 id #8
> select add #8
2569 atoms, 2652 bonds, 19 pseudobonds, 292 residues, 4 models selected
> hide #5.5 models
> hide #5.4 models
> hide #5.3 models
> show #!1 models
> show #8.1 models
> rename #1 id #6
> rename #2 id #1
> rename #3 id #2
> rename #4 id #3
> rename #18 id #4
> hide #!4 models
> ui tool show Matchmaker
> matchmaker #!6 to #5/B pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker relaxed_structure.pdb, chain B (#5) with 2fdn, chain M (#6),
sequence alignment score = 4
Fewer than 3 residues aligned; cannot match relaxed_structure.pdb, chain B
with 2fdn, chain M
> ui tool show Matchmaker
> matchmaker #!6 to #5/F pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
sequence alignment score = 170.3
RMSD between 41 pruned atom pairs is 0.850 angstroms; (across all 54 pairs:
2.909)
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> select #5@@draw_mode=0
28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected
> hide #5.1 models
> hide #5.7 models
> select subtract #5.7
28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 8 models selected
> select subtract #5.6
27425 atoms, 27831 bonds, 1756 residues, 7 models selected
> select subtract #5.5
26415 atoms, 26811 bonds, 1693 residues, 6 models selected
> select subtract #5.4
24160 atoms, 24526 bonds, 1551 residues, 5 models selected
> select subtract #5.3
23024 atoms, 23432 bonds, 1472 residues, 4 models selected
> select subtract #5.2
11509 atoms, 11705 bonds, 739 residues, 3 models selected
> select subtract #5.1
1 model selected
> hide #5.2 models
> select #5/A-F@@draw_mode=0
28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected
> select clear
> select subtract #5.7
Nothing selected
> hide #!5 models
> show #!5 models
> select #5/F:1-55@@draw_mode=0
600 atoms, 555 bonds, 48 residues, 1 model selected
> select #5 &protein &@@draw_mode=0
28121 atoms, 28483 bonds, 62 pseudobonds, 1810 residues, 2 models selected
> select #5/C:1-100 &@@draw_mode=0
1136 atoms, 1094 bonds, 79 residues, 1 model selected
> select #5/C:1-100@@draw_mode=0
1136 atoms, 1094 bonds, 79 residues, 1 model selected
> select subtract #5.3
1 model selected
> select #5/C:1-100@@draw_mode=0
1136 atoms, 1094 bonds, 79 residues, 1 model selected
> select #5/C:11,14-15,34-35/E:52/F:8,52-54
154 atoms, 149 bonds, 17 pseudobonds, 10 residues, 2 models selected
> select #5/C:11,14-15,34-35/E:52/F:8,51-54
170 atoms, 165 bonds, 22 pseudobonds, 11 residues, 2 models selected
> select #5/C:11,14-15,34-35/E:52/F:8,51,53,54
159 atoms, 153 bonds, 22 pseudobonds, 10 residues, 2 models selected
> select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54
169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 2 models selected
> select subtract #5.7
169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 5 models selected
> select subtract #5.6
98 atoms, 94 bonds, 6 residues, 4 models selected
> select subtract #5.5
82 atoms, 79 bonds, 5 residues, 3 models selected
> select subtract #5.3
1 model selected
> select #5/C:11,14-15,34-35/E:52/F:8,15,51,53,54
169 atoms, 162 bonds, 28 pseudobonds, 11 residues, 2 models selected
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> hide sel atoms
> select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54
202 atoms, 194 bonds, 40 pseudobonds, 13 residues, 2 models selected
> hide sel atoms
> show sel atoms
> select H
14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected
> hide sel & #!5-6 atoms
> style sel & #!5-6 stick
Changed 14343 atom styles
> select #5/C:11,14-15,34-35,58/E:52/F:8,11,15,51,53,54
202 atoms, 194 bonds, 40 pseudobonds, 13 residues, 2 models selected
> style sel stick
Changed 202 atom styles
> select #5/F:Cys
88 atoms, 80 bonds, 8 residues, 1 model selected
> select #5/F:Cys|#6:Cys
168 atoms, 152 bonds, 16 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!6 & sel to #5/B & sel pairing bs
No 'to' chains specified
> ui tool show Matchmaker
> matchmaker #!6 & sel to #5/F & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
1.008)
> select #6:Cys
80 atoms, 72 bonds, 8 residues, 1 model selected
> show sel atoms
> select #5:11-14
355 atoms, 352 bonds, 24 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 355 atom styles
> hide #!6 models
> select H
14615 atoms, 18 pseudobonds, 1922 residues, 4 models selected
> hide (#!5 & sel) target a
> show #!6 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
——— End of log from Fri Oct 4 09:37:44 2024 ———
opened ChimeraX session
> select #5/F:13
11 atoms, 10 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel CYH rotLib Dunbrack
relaxed_structure.pdb #5/F CYS 13: phi -84.1, psi 65.7 trans
Changed 9 bond radii
> swapaa #!5/F:13 CYH criteria 2 rotLib Dunbrack
Using Dunbrack library
relaxed_structure.pdb #!5/F CYS 13: phi -84.1, psi 65.7 trans
Applying CYS rotamer (chi angles: -178.7) to relaxed_structure.pdb #!5/F CYS
13
> select #6:Cys
80 atoms, 72 bonds, 8 residues, 1 model selected
> hide sel atoms
> view front
> hide #!6 models
> show #!6 models
> select #5/F:Cys|#6:Cys
165 atoms, 149 bonds, 16 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!6 & sel to #5/F & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
1.008)
> view front
> matchmaker #!6 & sel to #5/F & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
1.008)
> view front
> matchmaker #!6 & sel to #5/F & sel pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
sequence alignment score = 48
RMSD between 8 pruned atom pairs is 1.008 angstroms; (across all 8 pairs:
1.008)
> view name front
> turn y 180
> view front
> turn y 180
> turn x 30
> show #5.1 models
> show #5.2 models
> show #5.3 models
> show #5.4 models
> show #5.5 models
> hide #5.5 models
> show #5.5 models
> show #5.6 models
> hide #5.3 models
> hide #5.4 models
> coulombic #5/F surfaces #5.6
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for relaxed_structure.pdb_F SES surface #5.6: minimum,
-13.91, mean -3.63, maximum 7.03
> show #5.3 models
> show #5.4 models
> hide #5.4 models
> hide #5.3 models
> transparency (#!5-6 & sel) 30
> select clear
> select add #5.6
844 atoms, 61 residues, 1 model selected
> transparency (#!5 & sel) 30
> select clear
> view name back
> help help:user
> view list
Named views: back, front, hbond1, hbond2, hbond3
> view delete hbond1 hbond2 hbond3
Expected fewer arguments
> view list
Named views: back, front, hbond1, hbond2, hbond3
> help help:user
> view delete hbond1
> view delete hbond2
> view delete hbond3
> view list
Named views: back, front
> view front
> hide #5.5 models
> hide #5.6 models
> view back
> show #5.8 models
> select add #5.8
160 pseudobonds, 1 model selected
> select subtract #5.7
160 pseudobonds, 1 model selected
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
——— End of log from Fri Oct 4 10:09:32 2024 ———
opened ChimeraX session
> select #5/A-E
27646 atoms, 28113 bonds, 1765 residues, 1 model selected
> select #5/A-E &~H
13989 atoms, 14456 bonds, 1765 residues, 1 model selected
> ui tool show Contacts
> contacts sel setAttrs true restrict "#5/F &~H" resSeparation 5 interModel
> false intraMol false select true color #76d6ff radius 0.2 reveal true log
> true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
66 contacts
atom1 atom2 overlap distance
relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 CD 0.340 2.985
relaxed_structure.pdb #5/C PRO 58 CB relaxed_structure.pdb #5/F ILE 11 CD1 0.169 3.231
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 N 0.152 3.098
relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 CD 0.062 3.263
relaxed_structure.pdb #5/A ARG 27 CZ relaxed_structure.pdb #5/F ASP 30 OD1 0.055 3.125
relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 OD1 0.038 2.667
relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F SER 12 O 0.034 3.146
relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE1 0.032 2.673
relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 OD2 0.025 2.680
relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 OD1 0.020 2.685
relaxed_structure.pdb #5/C LYS 34 C relaxed_structure.pdb #5/F GLY 50 O 0.019 3.161
relaxed_structure.pdb #5/C PRO 58 CG relaxed_structure.pdb #5/F ILE 11 CD1 0.015 3.385
relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F GLU 19 OE2 0.011 2.694
relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 CD -0.001 3.201
relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 NH2 -0.023 2.728
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 OE2 -0.028 2.733
relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F GLU 9 OE1 -0.044 2.749
relaxed_structure.pdb #5/C ARG 18 CZ relaxed_structure.pdb #5/F GLY 14 O -0.062 3.242
relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 CG -0.076 3.401
relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 CZ -0.080 3.260
relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F GLU 9 OE2 -0.082 2.662
relaxed_structure.pdb #5/E SER 53 C relaxed_structure.pdb #5/F GLU 9 OE2 -0.087 3.267
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F ALA 15 N -0.094 3.344
relaxed_structure.pdb #5/C ARG 18 CZ relaxed_structure.pdb #5/F GLU 17 OE2 -0.103 3.283
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 C -0.122 3.447
relaxed_structure.pdb #5/D LYS 109 NZ relaxed_structure.pdb #5/F PRO 18 O -0.123 2.828
relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE1 -0.132 2.837
relaxed_structure.pdb #5/C ILE 11 CG1 relaxed_structure.pdb #5/F PRO 53 CB -0.134 3.534
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 CG -0.138 3.463
relaxed_structure.pdb #5/A ASP 34 OD2 relaxed_structure.pdb #5/F ARG 32 NH1 -0.139 2.844
relaxed_structure.pdb #5/E THR 54 OG1 relaxed_structure.pdb #5/F MET 54 CE -0.150 3.350
relaxed_structure.pdb #5/C GLN 15 CG relaxed_structure.pdb #5/F SER 12 O -0.153 3.333
relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F ALA 7 O -0.157 2.862
relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F PRO 53 CB -0.177 3.577
relaxed_structure.pdb #5/E ARG 43 NH2 relaxed_structure.pdb #5/F THR 8 CA -0.185 3.510
relaxed_structure.pdb #5/C ARG 18 NH1 relaxed_structure.pdb #5/F GLU 17 OE2 -0.203 2.908
relaxed_structure.pdb #5/E THR 54 O relaxed_structure.pdb #5/F MET 54 CE -0.206 3.386
relaxed_structure.pdb #5/C GLN 15 OE1 relaxed_structure.pdb #5/F SER 12 O -0.206 3.166
relaxed_structure.pdb #5/C GLN 15 CD relaxed_structure.pdb #5/F GLY 14 N -0.207 3.532
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F GLY 14 CA -0.208 3.533
relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 NE -0.215 2.940
relaxed_structure.pdb #5/C ILE 11 CD1 relaxed_structure.pdb #5/F MET 54 SD -0.218 3.700
relaxed_structure.pdb #5/C LYS 34 CB relaxed_structure.pdb #5/F GLY 50 O -0.221 3.401
relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 CB -0.230 3.410
relaxed_structure.pdb #5/E THR 54 CG2 relaxed_structure.pdb #5/F GLU 9 OE1 -0.230 3.410
relaxed_structure.pdb #5/E SER 53 CA relaxed_structure.pdb #5/F GLU 9 OE2 -0.230 3.410
relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 CG -0.231 3.631
relaxed_structure.pdb #5/A ARG 27 NH1 relaxed_structure.pdb #5/F ASP 30 CG -0.235 3.560
relaxed_structure.pdb #5/C ALA 35 CA relaxed_structure.pdb #5/F GLY 50 O -0.243 3.423
relaxed_structure.pdb #5/C ILE 11 O relaxed_structure.pdb #5/F PRO 53 CA -0.247 3.427
relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 O -0.269 2.974
relaxed_structure.pdb #5/E THR 54 N relaxed_structure.pdb #5/F GLU 9 OE2 -0.285 2.990
relaxed_structure.pdb #5/E ARG 43 CZ relaxed_structure.pdb #5/F GLU 9 OE1 -0.291 3.471
relaxed_structure.pdb #5/E THR 54 CB relaxed_structure.pdb #5/F GLU 9 OE2 -0.302 3.482
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLY 14 O -0.312 3.017
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F GLU 17 CD -0.314 3.639
relaxed_structure.pdb #5/A ARG 27 NH2 relaxed_structure.pdb #5/F ASP 30 CA -0.317 3.642
relaxed_structure.pdb #5/C CYS 13 CB relaxed_structure.pdb #5/F PRO 53 CB -0.318 3.718
relaxed_structure.pdb #5/C CYS 13 O relaxed_structure.pdb #5/F ALA 15 CB -0.332 3.512
relaxed_structure.pdb #5/C GLN 15 NE2 relaxed_structure.pdb #5/F CYS 13 C -0.336 3.661
relaxed_structure.pdb #5/C ALA 35 CB relaxed_structure.pdb #5/F VAL 51 CA -0.340 3.740
relaxed_structure.pdb #5/E SER 53 N relaxed_structure.pdb #5/F GLU 9 OE2 -0.349 3.054
relaxed_structure.pdb #5/A LYS 31 NZ relaxed_structure.pdb #5/F ASP 30 CG -0.369 3.694
relaxed_structure.pdb #5/A THR 28 OG1 relaxed_structure.pdb #5/F ARG 32 CZ -0.377 3.577
relaxed_structure.pdb #5/C ALA 35 N relaxed_structure.pdb #5/F GLY 50 O -0.377 3.082
relaxed_structure.pdb #5/C ARG 18 NH2 relaxed_structure.pdb #5/F PRO 18 CD -0.381 3.706
66 contacts
> style sel sphere
Changed 75 atom styles
> name frozen contacts sel
> select clear
> select contacts
16975 atoms, 38 bonds, 66 pseudobonds, 1093 residues, 2 models selected
> help help:user
> help help:user/selectcontacts.html
[Repeated 1 time(s)]
> interfaces select #5/A & ::polymer_type>0 contacting #5/F & ::polymer_type>0
> areaCutoff 0
4 contacting residues
> select contacts
16975 atoms, 38 bonds, 66 pseudobonds, 1093 residues, 2 models selected
> style sel stick
Changed 16975 atom styles
> hide #5.8 models
> select subtract #5.8
16975 atoms, 38 bonds, 1093 residues, 6 models selected
> close #5.8
> hide #5.9 models
> show #5.9 models
> close #5.9
> close #5.7
> ui tool show H-Bonds
> select #5/A-E
27646 atoms, 28113 bonds, 1765 residues, 1 model selected
> hbonds sel color #0096ff restrict #5/F interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
5 relaxed_structure.pdb
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_structure.pdb #5/F CYS 13 SG relaxed_structure.pdb #5/C CYS 13 O no hydrogen 3.816 N/A
relaxed_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
relaxed_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
relaxed_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
relaxed_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
19 hydrogen bonds found
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected
> select H
14612 atoms, 1922 residues, 3 models selected
> hide sel & #!5-6 atoms
> select #5/A-E
27646 atoms, 28113 bonds, 1765 residues, 1 model selected
> hbonds sel color #0096ff restrict #5/F interModel false intraMol false
> intraRes false reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
5 relaxed_structure.pdb
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_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
relaxed_structure.pdb #5/F CYS 13 SG relaxed_structure.pdb #5/C CYS 13 O no hydrogen 3.816 N/A
relaxed_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
relaxed_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
relaxed_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
relaxed_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
19 hydrogen bonds found
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected
> style sel ball
Changed 272 atom styles
> style sel stick
Changed 272 atom styles
> name frozen hBonds sel
[Repeated 1 time(s)]
> help help:user
> name delete all
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected
> name frozen Hbonds sel
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> view front
> interfaces select #5/A & ::polymer_type>0 contacting #5/F & ::polymer_type>0
> areaCutoff 0
4 contacting residues
> hide #5.1 models
> hide #5.2 models
> interfaces select #5/B & ::polymer_type>0 contacting #5/F & ::polymer_type>0
> areaCutoff 0
0 contacting residues
> interfaces select #5/C & ::polymer_type>0 contacting #5/F & ::polymer_type>0
> areaCutoff 0
9 contacting residues
> help help:user
> info residues sel
residue id #5/C:11 name ILE index 10
residue id #5/C:13 name CYS index 12
residue id #5/C:14 name THR index 13
residue id #5/C:15 name GLN index 14
residue id #5/C:18 name ARG index 17
residue id #5/C:34 name LYS index 33
residue id #5/C:35 name ALA index 34
residue id #5/C:37 name GLN index 36
residue id #5/C:58 name PRO index 57
> interfaces select #5/C#5/F & ::polymer_type>0 contacting #1/1 &
> ::polymer_type>0 areaCutoff 0
0 contacting residues
> interfaces select #5/F & ::polymer_type>0 contacting #5/C & ::polymer_type>0
> areaCutoff 0
10 contacting residues
> interfaces select #5/F & ::polymer_type>0 contacting #5/A#5/B#5/C#5/D &
> ::polymer_type>0 areaCutoff 0
15 contacting residues
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> info residues sel
residue id #5/F:11 name ILE index 10
residue id #5/F:12 name SER index 11
residue id #5/F:13 name CYS index 12
residue id #5/F:14 name GLY index 13
residue id #5/F:15 name ALA index 14
residue id #5/F:17 name GLU index 16
residue id #5/F:18 name PRO index 17
residue id #5/F:19 name GLU index 18
residue id #5/F:30 name ASP index 29
residue id #5/F:31 name GLY index 30
residue id #5/F:32 name ARG index 31
residue id #5/F:50 name GLY index 49
residue id #5/F:51 name VAL index 50
residue id #5/F:53 name PRO index 52
residue id #5/F:54 name MET index 53
> select #5/F:11-15,19,29,31,49,50,52,53
131 atoms, 126 bonds, 12 residues, 1 model selected
> select #5/F:11-15,29,31,49,50,52,53
116 atoms, 112 bonds, 11 residues, 1 model selected
> select #5/F:11-15,29,31,49,50,52,53
116 atoms, 112 bonds, 11 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 11 items
> select #5/F:11-15,29,31,49,50,52,53
116 atoms, 112 bonds, 11 residues, 1 model selected
> name frozen buriedFchain sel
> style sel sphere
Changed 116 atom styles
> interfaces select #5/A#5/B#5/C#5/D#5/E & ::polymer_type>0 contacting #5/F &
> ::polymer_type>0 areaCutoff 0
20 contacting residues
> info residues sel
residue id #5/A:27 name ARG index 26
residue id #5/A:28 name THR index 27
residue id #5/A:31 name LYS index 30
residue id #5/A:34 name ASP index 33
residue id #5/C:11 name ILE index 10
residue id #5/C:13 name CYS index 12
residue id #5/C:14 name THR index 13
residue id #5/C:15 name GLN index 14
residue id #5/C:18 name ARG index 17
residue id #5/C:34 name LYS index 33
residue id #5/C:35 name ALA index 34
residue id #5/C:37 name GLN index 36
residue id #5/C:58 name PRO index 57
residue id #5/D:109 name LYS index 108
residue id #5/E:41 name VAL index 40
residue id #5/E:43 name ARG index 42
residue id #5/E:51 name ASN index 50
residue id #5/E:52 name VAL index 51
residue id #5/E:54 name THR index 53
residue id #5/E:56 name ASN index 55
> select #5/C:11,13-15,34-37,58/E:41,51-52,56
206 atoms, 200 bonds, 13 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 206 atom styles
> select H
14612 atoms, 1922 residues, 3 models selected
> hide sel & #!5-6 atoms
> select clear
> select #5/C:11,13-15,34-37,58/E:41,51-52,56
206 atoms, 200 bonds, 13 residues, 1 model selected
> name frozen buriedA_Echain sel
> select clear
> select buriedA_Echain|buriedFChain
Expected an objects specifier or a keyword
> select buriedA_Echain | buriedFChain
Expected a keyword
> select buriedA_Echain
2273 atoms, 200 bonds, 146 residues, 1 model selected
> select buriedA_Echain | buriedFchain
3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected
> select buriedA_Echain
2273 atoms, 200 bonds, 146 residues, 1 model selected
> select buriedA_Echain | buriedFchain
3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected
> select Hbonds
16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected
> show sel atoms
> hide sel atoms
> select buriedA_Echain | buriedFchain
3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected
> name frozen A_EinterfaceF sel
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected
> show sel atoms
> select #5/C:Cys/F:Cys &~H &~/C:33
96 atoms, 157 bonds, 1 pseudobond, 16 residues, 2 models selected
> show sel atoms
> select buriedA_Echain | buriedFchain
3119 atoms, 312 bonds, 1 pseudobond, 207 residues, 2 models selected
> select buriedA_Echain
2273 atoms, 200 bonds, 146 residues, 1 model selected
> select #5/C:11,13-15,34-37,58/E:41,51-52,56
206 atoms, 200 bonds, 13 residues, 1 model selected
> select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53
322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected
> select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H
162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected
> show sel atoms
> view front
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> name delete all
> select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H
162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected
> name frozen interfaceNoHB sel
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected
> name frozen interfaceHB sel
> select interfaceHB
16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected
> style sel ball
Changed 16975 atom styles
> style sel sphere
Changed 16975 atom styles
> select interfaceHB
16975 atoms, 261 bonds, 18 pseudobonds, 1093 residues, 2 models selected
> style sel stick
Changed 16975 atom styles
> select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H
162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected
> style sel sphere
Changed 162 atom styles
> select clear
> view front
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> show #5.1 models
> show #5.2 models
> show #5.3 models
> show #5.4 models
> show #5.5 models
> show #5.6 models
> view front
> hide #8.1 models
> ui tool show "Color Key"
> ui mousemode right "color key"
> key blue-white-red :min : :+
> key blue-white-red :min :0 :+
> key blue-white-red :+ :0 :+
> key blue-white-red :+ :0 :-
> key bold true
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 19
> key fontSize 18
> key fontSize 17
> key fontSize 16
> key fontSize 15
> key fontSize 14
> key fontSize 13
> key fontSize 14
> key fontSize 15
> key fontSize 16
> key ticks true
> key tickLength 8.0
> key tickThickness 3.0
> key tickLength 6.0
> key tickLength 4.0
> key tickLength 2.0
> key tickLength 0.0
> key tickLength 2.0
> key tickLength 4.0
> key size 0.25000,0.04000
> key size 0.25000,0.03000
> key size 0.25000,0.02000
> key size 0.25000,0.01000
> key pos 0.71000,0.08000
> key pos 0.70000,0.08000
> key pos 0.69000,0.08000
> key pos 0.68000,0.08000
> key pos 0.67000,0.08000
> key pos 0.66000,0.08000
> key pos 0.65000,0.08000
> key pos 0.64000,0.08000
> key pos 0.63000,0.08000
> key pos 0.62000,0.08000
> key pos 0.61000,0.08000
> key pos 0.60000,0.08000
> key pos 0.59000,0.08000
> key pos 0.58000,0.08000
> key pos 0.57000,0.08000
> key pos 0.56000,0.08000
> key pos 0.55000,0.08000
> key pos 0.54000,0.08000
> key pos 0.53000,0.08000
> key pos 0.52000,0.08000
> key pos 0.51000,0.08000
> key pos 0.50000,0.08000
> key pos 0.49000,0.08000
> key pos 0.48000,0.08000
> key pos 0.47000,0.08000
> key pos 0.46000,0.08000
> key pos 0.45000,0.08000
> key pos 0.44000,0.08000
> key pos 0.43000,0.08000
> key pos 0.42000,0.08000
> key pos 0.41000,0.08000
> key pos 0.40000,0.08000
> key pos 0.39000,0.08000
> key pos 0.38000,0.08000
> key pos 0.37000,0.08000
> key pos 0.36000,0.08000
> key pos 0.35000,0.08000
> key pos 0.34000,0.08000
> key pos 0.33000,0.08000
> key pos 0.32000,0.08000
> key pos 0.31000,0.08000
> key pos 0.30000,0.08000
> key pos 0.29000,0.08000
> key pos 0.28000,0.08000
> key pos 0.27000,0.08000
> key pos 0.26000,0.08000
> key pos 0.25000,0.08000
> key pos 0.24000,0.08000
> key pos 0.23000,0.08000
> key pos 0.22000,0.08000
> key pos 0.21000,0.08000
> key pos 0.20000,0.08000
> key pos 0.19000,0.08000
> key pos 0.18000,0.08000
> key pos 0.17000,0.08000
> key pos 0.16000,0.08000
> key pos 0.15000,0.08000
> key pos 0.14000,0.08000
> key pos 0.13000,0.08000
> key pos 0.12000,0.08000
> key pos 0.11000,0.08000
> key pos 0.10000,0.08000
> key pos 0.09000,0.08000
> key pos 0.08000,0.08000
> key pos 0.07000,0.08000
> key pos 0.06000,0.08000
> key pos 0.05000,0.08000
> key pos 0.04000,0.08000
> key pos 0.03000,0.08000
> key pos 0.02000,0.08000
> key pos 0.02000,0.09000
> key pos 0.02000,0.10000
> key pos 0.02000,0.11000
> key pos 0.02000,0.12000
> key pos 0.02000,0.13000
> key pos 0.02000,0.14000
> key pos 0.02000,0.15000
> key pos 0.02000,0.16000
> key pos 0.02000,0.17000
> key pos 0.02000,0.18000
> key pos 0.02000,0.19000
> key pos 0.02000,0.20000
> key pos 0.02000,0.21000
> key pos 0.02000,0.22000
> key pos 0.02000,0.23000
> key pos 0.02000,0.24000
> key pos 0.02000,0.25000
> key pos 0.02000,0.26000
> key pos 0.02000,0.27000
> key pos 0.02000,0.28000
> key pos 0.02000,0.29000
> key pos 0.02000,0.30000
> key pos 0.02000,0.31000
> key pos 0.02000,0.32000
> key pos 0.02000,0.33000
> key pos 0.02000,0.34000
> key pos 0.02000,0.35000
> key pos 0.02000,0.36000
> key pos 0.02000,0.37000
> key pos 0.02000,0.38000
> key pos 0.02000,0.39000
> key pos 0.02000,0.40000
> key pos 0.02000,0.41000
> key pos 0.02000,0.42000
> key pos 0.02000,0.43000
> key pos 0.02000,0.44000
> key pos 0.02000,0.45000
> key pos 0.02000,0.46000
> key pos 0.02000,0.47000
> key pos 0.02000,0.48000
> key pos 0.02000,0.49000
> key pos 0.02000,0.50000
> key pos 0.02000,0.51000
> key pos 0.02000,0.52000
> key pos 0.02000,0.53000
> key pos 0.02000,0.54000
> key pos 0.02000,0.55000
> key pos 0.02000,0.56000
> key pos 0.02000,0.57000
> key pos 0.02000,0.58000
> key pos 0.02000,0.59000
> key pos 0.02000,0.60000
> key pos 0.02000,0.61000
> key pos 0.02000,0.62000
> key pos 0.02000,0.63000
> key pos 0.02000,0.64000
> key pos 0.02000,0.65000
> key pos 0.02000,0.66000
> key pos 0.02000,0.67000
> key pos 0.02000,0.68000
> key pos 0.02000,0.69000
> key pos 0.02000,0.70000
> key pos 0.02000,0.71000
> key pos 0.02000,0.72000
> key pos 0.02000,0.73000
> key pos 0.02000,0.74000
> key pos 0.02000,0.75000
> key pos 0.02000,0.76000
> key pos 0.02000,0.77000
> key pos 0.02000,0.78000
> key pos 0.02000,0.79000
> key pos 0.02000,0.80000
> key pos 0.02000,0.81000
> key pos 0.02000,0.82000
> key pos 0.02000,0.83000
> key pos 0.02000,0.84000
> key pos 0.02000,0.85000
> key pos 0.02000,0.86000
> key pos 0.02000,0.87000
> key pos 0.02000,0.88000
> key pos 0.02000,0.89000
> key pos 0.02000,0.90000
> key pos 0.02000,0.91000
> key pos 0.02000,0.92000
> key pos 0.02000,0.93000
> key pos 0.02000,0.94000
> key pos 0.02000,0.95000
> key pos 0.02000,0.96000
> key pos 0.02000,0.97000
> key pos 0.02000,0.98000
> key pos 0.03000,0.98000
> key pos 0.04000,0.98000
> key pos 0.05000,0.98000
> key pos 0.06000,0.98000
> key pos 0.07000,0.98000
> key pos 0.08000,0.98000
> key pos 0.09000,0.98000
> key pos 0.10000,0.98000
> key pos 0.11000,0.98000
> key pos 0.12000,0.98000
> key pos 0.13000,0.98000
> key pos 0.14000,0.98000
> key pos 0.15000,0.98000
> key pos 0.16000,0.98000
> key pos 0.17000,0.98000
> key pos 0.18000,0.98000
> key pos 0.19000,0.98000
> key pos 0.20000,0.98000
> key pos 0.21000,0.98000
> key pos 0.22000,0.98000
> key pos 0.23000,0.98000
> key pos 0.24000,0.98000
> key pos 0.25000,0.98000
> key pos 0.26000,0.98000
> key pos 0.27000,0.98000
> key pos 0.28000,0.98000
> key pos 0.29000,0.98000
> key pos 0.30000,0.98000
> key pos 0.31000,0.98000
> key pos 0.32000,0.98000
> key pos 0.33000,0.98000
> key pos 0.34000,0.98000
> key pos 0.35000,0.98000
> key pos 0.36000,0.98000
> key pos 0.37000,0.98000
> key pos 0.38000,0.98000
> key pos 0.39000,0.98000
> key pos 0.40000,0.98000
> key pos 0.41000,0.98000
> key pos 0.42000,0.98000
> key pos 0.43000,0.98000
> key pos 0.44000,0.98000
> key pos 0.45000,0.98000
> key pos 0.46000,0.98000
> key pos 0.47000,0.98000
> key pos 0.48000,0.98000
> key pos 0.49000,0.98000
> key pos 0.50000,0.98000
> key pos 0.51000,0.98000
> key pos 0.52000,0.98000
> key pos 0.53000,0.98000
> key pos 0.54000,0.98000
> key pos 0.55000,0.98000
> key pos 0.56000,0.98000
> key pos 0.57000,0.98000
> key pos 0.58000,0.98000
> key pos 0.59000,0.98000
> key pos 0.60000,0.98000
> key pos 0.61000,0.98000
> key pos 0.62000,0.98000
> key pos 0.63000,0.98000
> key pos 0.64000,0.98000
> key pos 0.65000,0.98000
> key pos 0.66000,0.98000
> key pos 0.67000,0.98000
> key pos 0.68000,0.98000
> key pos 0.69000,0.98000
> key pos 0.70000,0.98000
> key pos 0.71000,0.98000
> key pos 0.72000,0.98000
> key pos 0.73000,0.98000
> key pos 0.74000,0.98000
> key pos 0.73000,0.98000
> ui mousemode right translate
> hide #7 models
> show #7 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> hide #5.6 models
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54/F:7,9,17-19,30,32
272 atoms, 261 bonds, 18 pseudobonds, 16 residues, 2 models selected
> select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53 &~H
162 atoms, 152 bonds, 1 pseudobond, 24 residues, 2 models selected
> transparency (#!5 & sel) 80
> transparency (#!5 & sel) 100
> select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53
322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected
> transparency (#!5 & sel) 100
> select clear
> select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53
322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected
> transparency (#!5 & sel) 90
> transparency (#!5 & sel) 70
> transparency (#!5 & sel) 100
> hide #5.5 models
> show #5.5 models
> hide #5.5 models
> show #5.5 models
> hide #5.5 models
> show #5.5 models
> hide #5.5 models
> select clear
> show #5.6 models
> hide #5.6 models
> show #5.5 models
> select add #5.6
844 atoms, 61 residues, 1 model selected
> select add #5.5
1903 atoms, 127 residues, 2 models selected
> select add #5.4
4180 atoms, 270 residues, 3 models selected
> select add #5.3
5394 atoms, 350 residues, 4 models selected
> select add #5.2
16909 atoms, 1083 residues, 5 models selected
> select add #5.1
28490 atoms, 1826 residues, 6 models selected
> show #5.6 models
> transparency (#!5 & sel) 30
> select #5/C:11,13-15,34-37,58/E:41,51-52,56/F:11-15,29,31,49,50,52,53
322 atoms, 312 bonds, 1 pseudobond, 24 residues, 2 models selected
> style sel stick
Changed 322 atom styles
> view front
> select clear
> hide #5.6 models
> show #5.6 models
> hide #5.6 models
> show #5.6 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx Alt All surfaces front .png" width 1508 height 1200 supersample
> 3 transparentBackground true
> hide #5.6 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx Alt no F surface front .png" width 1508 height 1200 supersample
> 3 transparentBackground true
> show #5.6 models
> hide #5.5 models
> hide #5.4 models
> hide #5.3 models
> view back
> show #5.3 models
> hide #5.3 models
> show #5.5 models
> hide #5.5 models
> trurn y 90
Unknown command: trurn y 90
> turn y 90
> show #5.3 models
> turn y 30
> view back
[Repeated 1 time(s)]
> turn y 30
[Repeated 1 time(s)]
> turn y 10
> turn x 10
[Repeated 1 time(s)]
> turn y -10
[Repeated 1 time(s)]
> view back
> turn x 10
> turn y 30
[Repeated 1 time(s)]
> turn x 10
> view back
> turn x 60
> turn y 60
> turn y -30
> view back
> turn x 10
> turn y 40
> turn y 10
> turn x 10
> view back
> turn y 50
> turn x 20
> show #5.4 models
> show #5.5 models
> view name side
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> hide #5.6 models
> hide #5.5 models
> hide #5.4 models
> hide #5.3 models
> show #5.5 models
> hide #5.5 models
> show #5.5 models
> show #5.6 models
> show #5.4 models
> show #5.3 models
> view front
> view side
> view front
> hide #5.5 models
> show #5.5 models
> view side
> view front
> hide #5.6 models
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54
167 atoms, 160 bonds, 9 residues, 1 model selected
> transparency (#!5 & sel) 80
> select clear
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54
167 atoms, 160 bonds, 9 residues, 1 model selected
> transparency (#!5 & sel) 90
> select clear
> turn x 10
> turn x -10
> turn x 5
> turn x -5
> view side
> view front
[Repeated 1 time(s)]
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> turn x 5
> turn y 5
> turn x 5
[Repeated 1 time(s)]
> turn y -5
> view front
> turn x 15
> show #5.6 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> select add #5.6
844 atoms, 61 residues, 1 model selected
> select add #5.5
1903 atoms, 127 residues, 2 models selected
> select add #5.4
4180 atoms, 270 residues, 3 models selected
> select add #5.3
5394 atoms, 350 residues, 4 models selected
> select add #5.2
16909 atoms, 1083 residues, 5 models selected
> select add #5.1
28490 atoms, 1826 residues, 6 models selected
> transparency (#!5 & sel) 20
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> hide #5.7 models
> show #5.7 models
> hide #5.6 models
> select clear
> show #5.6 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> view name front
> turn y 50
> hide #5.4 models
> show #5.4 models
> hide #5.5 models
> show #5.5 models
> view front
> view side
> hide #5.5 models
> show #5.5 models
> hide #5.4 models
> show #5.4 models
> view front
> turn y 60
> hide #5.4 models
> show #5.4 models
> view side
> hide #5.4 models
> view front
> turn y 60
> turn y -60
[Repeated 1 time(s)]
> show #5.4 models
> view front
> hide #5.5 models
> show #5.5 models
> view side
> view front
> view side
> view front
> turn y 90
> hide #5.6 models
> show #5.6 models
> hide #5.6 models
> show #5.6 models
> hide #5.6 models
> show #5.6 models
> view front
> turn x 90
> hide #5.6 models
> show #5.6 models
> view front
> turn 30
Expected an axis vector or a keyword
> turn y 30
> hide #5.6 models
> show #5.6 models
> hide #5.4 models
> show #5.4 models
> hide #5.5 models
> show #5.5 models
> turn y -30
[Repeated 3 time(s)]
> turn x 30
> turn x 10
> turn x 5
> view front
> turn x 45
> turn x -45
> turn y 30
> view front
> turn y 30
> view front
> turn y -30
> turn x -45
> turn x 45
[Repeated 1 time(s)]
> view front
> turn y -45
> view front
> turn y -45
> turn x 45
> view front
> turn y -50
> turn x -45
> view front
> turn y -50
> turn x 45
> turn x -15
> view front
> turn y -50
> turn x 30
> view front
> turn y -60
> view front
[Repeated 1 time(s)]
> help help:user
> trun 1,1,0 45
Unknown command: trun 1,1,0 45
> turn 1,1,0 45
> turn 1,1,0 -45
> turn -1,1,0 45
> view front
> turn -1,1,0 -45
> turn y 60
> turn y -60
[Repeated 1 time(s)]
> view front
> view back
> view front
> turn y 180
> turn x 45
> hide #5.4 models
> show #5.4 models
> view front
> turn y 180
> turn x 45
[Repeated 1 time(s)]
> turn x 15
> view front
> turn y 180
> turn x 60
> view front
> turn y 180
> turn x 60
> turn x 30
> view front
> turn x 90
> hide #5.6 models
> show #5.6 models
> view front
> turn x 60
> view front
[Repeated 1 time(s)]
> turn y 180
> turn x 90
> turn x 30
> view front
> turn y 180
> turn x 120
> view front
> turn y 190
> turn x 130
> turn y 10
[Repeated 2 time(s)]
> view front
> turn y 200
> turn x 145
> view front
> turn x 145
> turn y 200
> view front
> view name side
> view front
> hide #5.6 models
> select add #8
1 pseudobond, 2 models selected
> select subtract #8
Nothing selected
> select add #8
1 pseudobond, 2 models selected
> select subtract #8
Nothing selected
> select add #8
1 pseudobond, 2 models selected
> select subtract #8
Nothing selected
> select add #8
1 pseudobond, 2 models selected
> select subtract #8
Nothing selected
> select add #8
1 pseudobond, 2 models selected
> select subtract #8
Nothing selected
> show #8.1 models
> hide #8.1 models
> select #5/A:27,28,31,34/C:18/D:109/E:43,53,54
167 atoms, 160 bonds, 9 residues, 1 model selected
> transparency (#!5 & sel) 90
> select clear
> hide #7 models
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> view name HbondsZoom
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
> view HbondsZoom
> select #5/C:11,13-15,34-37,58
146 atoms, 143 bonds, 9 residues, 1 model selected
> select #5/C:11,13-15
61 atoms, 59 bonds, 4 residues, 1 model selected
> select #5/C:13-15
42 atoms, 41 bonds, 3 residues, 1 model selected
> transparency (#!5 & sel) 90
> view HbondsZoom
> select #5/C:13-15
42 atoms, 41 bonds, 3 residues, 1 model selected
> transparency (#!5 & sel) 20
> select #5/C:11
19 atoms, 18 bonds, 1 residue, 1 model selected
> transparency (#!5 & sel) 90
> select clear
> graphics silhouettes false
> graphics silhouettes true
> view name HbondsZoom
> view front
> view side
> view HbondsZoom
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
——— End of log from Fri Oct 4 15:14:28 2024 ———
opened ChimeraX session
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx Alt zoom hbonds.png" width 1506 height 1200 supersample 3
> transparentBackground true
> hide #!8 models
> show #!8 models
> select #6:1-2,8-24,30-47
447 atoms, 448 bonds, 37 residues, 1 model selected
> select #3/B:1
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/B:1-2
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #6:1-2,8-24,30-47
447 atoms, 448 bonds, 37 residues, 1 model selected
> select #3/B:1-2
17 atoms, 17 bonds, 2 residues, 1 model selected
> select #6:1-2,8-24,30-47
447 atoms, 448 bonds, 37 residues, 1 model selected
> select #6:1-2,8-24,30-47#5/F:1-2
480 atoms, 481 bonds, 39 residues, 2 models selected
> select #6:1-2,8-24,30-47#5/F:1-2,8-24
695 atoms, 697 bonds, 56 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #!6 to #5/F pairing bs showAlignment true
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker relaxed_structure.pdb, chain F (#5) with 2fdn, chain M (#6),
sequence alignment score = 170.3
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: relaxed_structure.pdb #5/F,
2fdn #6/M
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 41 pruned atom pairs is 0.850 angstroms; (across all 54 pairs:
2.909)
> sequence header 1 consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
> select #6:1-2,8-24,30-47#5/F:1-2,10-26
696 atoms, 698 bonds, 56 residues, 2 models selected
> select #6:1-2,8-24,30-47#5/F:1-2,10-26,35-52
925 atoms, 927 bonds, 74 residues, 2 models selected
> show sel cartoons
> select #5
28492 atoms, 28966 bonds, 19 pseudobonds, 1826 residues, 2 models selected
> hide sel cartoons
> show sel cartoons
> select #6
762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected
> hide sel cartoons
> select #5/F:1-2,10-26,35-52
478 atoms, 479 bonds, 37 residues, 1 model selected
> color (#!5 & sel) orange
> color sel byhetero
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx Alt zoom hbonds.png" width 1506 height 1200 supersample 3
> transparentBackground true
> select clear
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Figures/Fdx_PSI
> MPNN/PSI-Fdx Alt zoom hbonds.png" width 1506 height 1200 supersample 3
> transparentBackground true
> save "/Users/drornoy/OneDrive - Migal/NSF-BSF grant 2024/Models/PSI_Fdx
> Models/BacetrioFdx PSI interface/Both best dock on PSI.cxs"
——— End of log from Sun Oct 6 13:38:31 2024 ———
opened ChimeraX session
> hide #!1 models
> close #20
> close #8
> close #7
> hide #5.5 models
> hide #5.3 models
> hide #5.2 models
> hide #5.1 models
> hide #5.4 models
> hide #2 models
> show #2 models
> select #2
24 atoms, 36 bonds, 3 residues, 1 model selected
> select #2 :<3 /A-C:Cys
132 atoms, 120 bonds, 12 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select #2 :<3 /A-C:Cys &H
60 atoms, 12 residues, 1 model selected
> hide sel atoms
> select #2 :<3 /A-C:Cys
132 atoms, 120 bonds, 12 residues, 1 model selected
> style sel stick
Changed 132 atom styles
> show #!1 models
> hide #2 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> select #1/B:549
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel cartoons
> show #!5 models
> hide #!5 models
> select #1/A-B
18021 atoms, 18789 bonds, 361 pseudobonds, 1592 residues, 2 models selected
> show sel cartoons
> show #!5 models
> hide #!1 models
> hide #!5 models
> show #!1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> close #1
> show #2 models
> close #3-4
> show #!5 models
> ui mousemode right "translate selected atoms"
> ui mousemode right "translate selected models"
> rename #2 "PSI Fx Fa Fb clusters"
> rename #5 id #1
> rename #6 id #3
> rename #1 "relaxed PsaABCDE BFd(F) complex"
> show #1.1 models
> show #1.2 models
> show #1.3 models
> show #1.4 models
> show #1.5 models
> show #1.6 models
> hide #1.5 models
> hide #1.4 models
> hide #1.3 models
> hide #1.2 models
> hide #1.1 models
> hide #1.6 models
> rename #5/F
No name or id option specified for renaming
> select #5/F
Nothing selected
> select #1/F
846 atoms, 853 bonds, 61 residues, 1 model selected
> color sel bychain
> color sel byhetero
> help help:user
> color #1 chains pal sett3-9
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color bychain #1 pal sett3-9
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sequential #1 chains
> color sequential #1 chains palette set3-9
> color sel byhetero
> ~select
Nothing selected
> color byhetero
> color sequential #1 chains palette pastel1
> color byhetero
> color sequential #1 chains palette accent
> color byhetero
> save "/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"
> rename #3 "BFd (2fdn)"
> save "/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"
> close #1.1-7
> save "/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"
——— End of log from Tue Oct 8 17:54:27 2024 ———
opened ChimeraX session
> open "/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"
Chain information for PSI_BFd.opt.pdb #4
---
Chain | Description
? | No description available
> 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 PSI_BFd.opt.pdb (#4) into 6 models
Chain information for PSI_BFd.opt.pdb 1 #4.1
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 2 #4.2
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 3 #4.3
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 4 #4.4
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 5 #4.5
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 6 #4.6
---
Chain | Description
? | No description available
> combine #4.1#4.2#4.3#4.4#4.5#4.6
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'B'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'C'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'D'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 6 #4.6 to 'E'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'F'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> combine #4.1
Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'A'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> combine #4.2#4.3
Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'B'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> combine #4.2#4.4
Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'B'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> combine #4.2#4.5
Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'B'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> combine #4.2
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> combine #4
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'B'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'C'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'D'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 6 #4.6 to 'E'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'F'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> close #4
> open "/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"
Chain information for PSI_BFd.opt.pdb #4
---
Chain | Description
? | No description available
> 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 PSI_BFd.opt.pdb (#4) into 6 models
Chain information for PSI_BFd.opt.pdb 1 #4.1
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 2 #4.2
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 3 #4.3
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 4 #4.4
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 5 #4.5
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 6 #4.6
---
Chain | Description
? | No description available
> combine #4.2
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> combine #4
Remapping chain ID ' ' in PSI_BFd.opt.pdb 2 #4.2 to 'A'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 3 #4.3 to 'B'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 4 #4.4 to 'C'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 5 #4.5 to 'D'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 6 #4.6 to 'E'
Remapping chain ID ' ' in PSI_BFd.opt.pdb 1 #4.1 to 'F'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> changechains #4.2 B
Chain IDs of 733 residues changed
> changechains #4.3 C
Chain IDs of 82 residues changed
> changechains #4.4 D
Chain IDs of 143 residues changed
> changechains #4.5 E
Chain IDs of 67 residues changed
> changechains #4.6 F
Chain IDs of 62 residues changed
> renumber #4.1:1829 start 3001
1 residues renumbered
> renumber #4.2 start 1
733 residues renumbered
> renumber #4.3 start 1
82 residues renumbered
> renumber #4.3:354-355 start 3002
2 residues renumbered
> renumber #4.4 start 1
143 residues renumbered
> renumber #4.5 start 1
67 residues renumbered
> renumber #4.6 start 1
62 residues renumbered
> save "/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" models #4
> open "/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"
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
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR 36 ALA 44 1 9
Start residue of secondary structure not found: HELIX 2 2 PHE 49 HIE 52 1 4
Start residue of secondary structure not found: HELIX 3 3 LEU 56 GLY 85 1 30
Start residue of secondary structure not found: HELIX 4 4 TYR 91 ASN 96 1 6
Start residue of secondary structure not found: HELIX 5 5 GLN 114 LEU 117 1 4
180 messages similar to the above omitted
Chain information for PSI_BFd_SF4_opt.pdb
---
Chain | Description
5.1/? | No description available
5.2/B | No description available
5.3/C | No description available
5.4/D | No description available
5.5/E | No description available
5.6/F | No description available
> combine #5.1#5.2#5.3#5.4#5.5#5.6
Remapping chain ID ' ' in PSI_BFd_SF4_opt.pdb #5.1 to 'A'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> close #5
> save "/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" models #4
> save "/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" models #4.1
> save "/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" models #4.2
> open "/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"
> "/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"
Chain information for PSI_BFd_SF4_opt_A.pdb #5
---
Chain | Description
? | No description available
Chain information for PSI_BFd_SF4_opt_B.pdb #6
---
Chain | Description
B | No description available
> combine #5#6
Remapping chain ID ' ' in PSI_BFd_SF4_opt_A.pdb #5 to 'A'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/cmd.py", line 144, in combine_cmd
residues[residues.chain_ids == chain_id].chain_ids = new_id
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
cset(self._c_pointers, n, v)
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
ValueError: Cannot set polymeric chain ID directly from Residue; must use
Chain
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
cset(self._c_pointers, n, v)
See log for complete Python traceback.
> close #6#4-5
> open "/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"
Chain information for PSI_BFd.opt.pdb #4
---
Chain | Description
? | No description available
> split #4 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699
> atoms :1700-1766 atoms :1767-1826
Split PSI_BFd.opt.pdb (#4) into 7 models
Chain information for PSI_BFd.opt.pdb 1 #4.1
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 2 #4.2
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 3 #4.3
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 4 #4.4
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 5 #4.5
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 6 #4.6
---
Chain | Description
? | No description available
> hide #!4.7 models
> hide #1 models
> hide #2 models
> hide #!3 models
> changechains #4.2 B
Chain IDs of 733 residues changed
> changechains #4.3 C
Chain IDs of 80 residues changed
> changechains #4.4 D
Chain IDs of 143 residues changed
> changechains #4.5 E
Chain IDs of 67 residues changed
> changechains #4.6 F
Chain IDs of 60 residues changed
> renumber #4.2 start 1
733 residues renumbered
> renumber #4.3 start 1
80 residues renumbered
> renumber #4.4 start 1
143 residues renumbered
> renumber #4.5 start 1
67 residues renumbered
> renumber #4.6 start 1
60 residues renumbered
> changechains #4.1 A
Chain IDs of 743 residues changed
> changechains #4.7 X
Chain IDs of 5 residues changed
> combine #4.1#4.2#4.3#4.4#4.5#4.6
> hide #!4 models
> show #!4 models
> combine #4.7
> combine #5#6
> hide #!6 models
> hide #5 models
> hide #!4 models
> color sequential #7 chains palette accent
> show #1 models
> hide #1 models
> color #!7 byhetero
> select #7/X:1827@F2
1 atom, 1 residue, 1 model selected
> close #5#4,6
> rename #7 PSI_BFD_SF4_opt.pdb
> rename #7 id #4
> show #1 models
> hide #!4 models
> show #!3 models
> select add #3
763 atoms, 681 bonds, 8 pseudobonds, 152 residues, 3 models selected
> select subtract #3
1 atom, 1 residue, 1 model selected
> select #3
762 atoms, 681 bonds, 8 pseudobonds, 151 residues, 2 models selected
> show sel cartoons
> select #3:cys
80 atoms, 72 bonds, 8 residues, 1 model selected
> show sel atoms
> color sel byhetero
> hide #!3 models
> show #!4 models
> hide #1 models
> show #!3 models
> align #3:SF4 toAtoms #4:1827-1828
RMSD between 16 atom pairs is 0.346 angstroms
> hide #!3 models
> show #1 models
> hide #1 models
> select #4/X:1831 @<9 /X:1827
Nothing selected
> select #4/X:1831 @<10 /X:1827
2 atoms, 1 pseudobond, 1 residue, 2 models selected
> select #4/X:1831 @<9.2 /X:1827
Nothing selected
> select #4/X:1831 @<9.5 /X:1827
Nothing selected
> select #4/X:1831 @<9.8 /X:1827
2 atoms, 1 pseudobond, 1 residue, 2 models selected
> select #4/X:1831 @<9.7 /X:1827
1 atom, 1 residue, 1 model selected
> select #4/X:1827 @<9.7 /X:1831
1 atom, 1 residue, 1 model selected
> select #4/X:1831 @<9.7 /X:1827
1 atom, 1 residue, 1 model selected
> select #4/X:1831@F2:1827@F1
2 atoms, 2 residues, 1 model selected
> select #4/X:1831@F1:1827@F2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #4/X:1827@F2 #4/X:1831@F1
Distance between PSI_BFD_SF4_opt.pdb #4/X SF4 1827 F2 and SF4 1831 F1: 9.521Å
> select #4/A-F
28475 atoms, 28948 bonds, 1826 residues, 1 model selected
> select #4/A-F
28475 atoms, 28948 bonds, 1826 residues, 1 model selected
> show sel surfaces
> coulombic #4/A
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge +1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpzcprkc0n/ante.in.mol2);
atoms read (22), bonds read (21).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 92; net charge: 1`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for PSI_BFD_SF4_opt.pdb_A SES surface #4.2: minimum, -12.49,
mean 0.00, maximum 20.13
> coulombic #4/B
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpwjns68s7/ante.in.mol2);
atoms read (22), bonds read (21).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 94; net charge: -1`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for PSI_BFD_SF4_opt.pdb_B SES surface #4.3: minimum, -15.85,
mean -0.16, maximum 13.13
> coulombic #4/C
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp8vgevu6e/ante.in.mol2);
atoms read (22), bonds read (21).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 94; net charge: -1`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for PSI_BFD_SF4_opt.pdb_C SES surface #4.4: minimum, -22.24,
mean -4.06, maximum 8.43
> coulombic #4/D
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for PSI_BFD_SF4_opt.pdb_D SES surface #4.5: minimum, -11.15,
mean 2.11, maximum 15.26
> coulombic #4/E
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for PSI_BFD_SF4_opt.pdb_E SES surface #4.6: minimum, -11.38,
mean 1.55, maximum 11.87
> coulombic #4/F
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpaverh6fg/ante.in.mol2);
atoms read (23), bonds read (22).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 94; net charge: 0`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for PSI_BFD_SF4_opt.pdb_F SES surface #4.7: minimum, -16.02,
mean -3.74, maximum 7.04
> save "/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"
——— End of log from Wed Oct 9 21:29:02 2024 ———
opened ChimeraX session
> hide #4.7 models
> hide #4.6 models
> hide #4.5 models
> hide #4.4 models
> show #4.4 models
> hide #4.4 models
> hide #4.3 models
> hide #4.2 models
> select #4/F
829 atoms, 836 bonds, 60 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false
> intraRes false reveal true log true
Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt.pdb #4/A CYF 575
SG
Wrong number of grandchild atoms for phi/psi acceptor PSI_BFD_SF4_opt.pdb #4/A
CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
4 PSI_BFD_SF4_opt.pdb
21 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
21 hydrogen bonds found
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 60 items
> select #4:SF4
40 atoms, 91 pseudobonds, 5 residues, 3 models selected
> style sel sphere
Changed 40 atom styles
> save "/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"
> select #4/F
829 atoms, 836 bonds, 60 residues, 1 model selected
> ui tool show Contacts
> select #4/F &~H
430 atoms, 437 bonds, 60 residues, 1 model selected
> contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol
> false color #76d6ff radius 0.2 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
88 contacts
atom1 atom2 overlap distance
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 2.060 1.340
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.981 2.479
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA 0.878 2.462
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.466 2.254
PSI_BFD_SF4_opt.pdb #4/F TYR 1 C PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.397 3.063
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.361 2.819
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.215 3.025
PSI_BFD_SF4_opt.pdb #4/F GLY 13 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 0.214 3.036
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG 0.203 3.197
PSI_BFD_SF4_opt.pdb #4/F TYR 1 C PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.161 3.019
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 C 0.154 3.026
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 C 0.095 3.085
PSI_BFD_SF4_opt.pdb #4/F GLU 18 CD PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ 0.059 3.266
PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1 PSI_BFD_SF4_opt.pdb #4/C PRO 58 CB 0.048 3.352
PSI_BFD_SF4_opt.pdb #4/F THR 7 CA PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 0.005 3.320
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 CZ -0.006 3.186
PSI_BFD_SF4_opt.pdb #4/F ALA 38 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA -0.013 3.193
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.014 2.719
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 O -0.032 3.212
PSI_BFD_SF4_opt.pdb #4/F TYR 1 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 C -0.032 3.272
PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1 PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ -0.032 2.737
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.033 2.738
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.040 2.745
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2 PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ -0.041 2.746
PSI_BFD_SF4_opt.pdb #4/F THR 7 C PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.042 3.367
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.049 3.449
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 CG2 -0.052 3.232
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 CB -0.054 3.234
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1 -0.055 2.760
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ -0.060 3.240
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.075 2.780
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.079 2.784
PSI_BFD_SF4_opt.pdb #4/F GLY 13 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.080 3.405
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1 -0.086 2.666
PSI_BFD_SF4_opt.pdb #4/F ALA 38 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB -0.088 3.268
PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 -0.100 3.425
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA -0.103 3.283
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1 PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 -0.107 2.812
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 CB -0.122 3.302
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 C -0.130 3.530
PSI_BFD_SF4_opt.pdb #4/F GLY 13 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.134 3.459
PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.136 3.316
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.143 2.848
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB -0.146 3.486
PSI_BFD_SF4_opt.pdb #4/F GLY 13 O PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ -0.147 3.327
PSI_BFD_SF4_opt.pdb #4/F CYF 12 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.148 3.473
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG -0.162 3.562
PSI_BFD_SF4_opt.pdb #4/F MET 53 SD PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1 -0.167 3.649
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE -0.170 2.875
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 -0.177 2.902
PSI_BFD_SF4_opt.pdb #4/F GLU 8 N PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.182 3.432
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.182 3.507
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ -0.183 3.363
PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.187 3.512
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 CB -0.188 3.368
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 CA -0.188 3.368
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.189 2.894
PSI_BFD_SF4_opt.pdb #4/F ASP 43 CG PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.197 3.522
PSI_BFD_SF4_opt.pdb #4/F PRO 17 O PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ -0.212 2.917
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 CG1 -0.215 3.615
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.219 3.619
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1 -0.225 3.625
PSI_BFD_SF4_opt.pdb #4/F PRO 17 CG PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.230 3.555
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.238 3.503
PSI_BFD_SF4_opt.pdb #4/F GLY 13 O PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.254 2.959
PSI_BFD_SF4_opt.pdb #4/F ALA 14 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.256 3.506
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 N -0.272 2.977
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1 -0.275 2.980
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CB PSI_BFD_SF4_opt.pdb #4/E ALA 67 C -0.275 3.735
PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1 PSI_BFD_SF4_opt.pdb #4/C PRO 58 CG -0.291 3.691
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1 -0.299 3.499
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1 -0.301 3.626
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 CB -0.316 3.716
PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD PSI_BFD_SF4_opt.pdb #4/E SER 53 CB -0.323 3.723
PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.332 3.657
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.337 3.662
PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 -0.342 3.542
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CA PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.346 3.671
PSI_BFD_SF4_opt.pdb #4/F CYF 12 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.353 3.753
PSI_BFD_SF4_opt.pdb #4/F GLY 13 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.355 3.680
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ -0.356 3.536
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ -0.363 3.688
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 O -0.366 3.546
PSI_BFD_SF4_opt.pdb #4/F VAL 50 CA PSI_BFD_SF4_opt.pdb #4/C ALA 35 CB -0.371 3.771
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 O -0.372 3.332
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB -0.376 3.776
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CG PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB -0.389 3.789
PSI_BFD_SF4_opt.pdb #4/F PRO 17 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.394 3.719
88 contacts
> contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol
> false select true color #ff85ff radius 0.2 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
88 contacts
atom1 atom2 overlap distance
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 2.060 1.340
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.981 2.479
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA 0.878 2.462
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.466 2.254
PSI_BFD_SF4_opt.pdb #4/F TYR 1 C PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.397 3.063
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.361 2.819
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.215 3.025
PSI_BFD_SF4_opt.pdb #4/F GLY 13 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 0.214 3.036
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG 0.203 3.197
PSI_BFD_SF4_opt.pdb #4/F TYR 1 C PSI_BFD_SF4_opt.pdb #4/E ALA 67 O 0.161 3.019
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 C 0.154 3.026
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 C 0.095 3.085
PSI_BFD_SF4_opt.pdb #4/F GLU 18 CD PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ 0.059 3.266
PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1 PSI_BFD_SF4_opt.pdb #4/C PRO 58 CB 0.048 3.352
PSI_BFD_SF4_opt.pdb #4/F THR 7 CA PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 0.005 3.320
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 CZ -0.006 3.186
PSI_BFD_SF4_opt.pdb #4/F ALA 38 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA -0.013 3.193
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.014 2.719
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 O -0.032 3.212
PSI_BFD_SF4_opt.pdb #4/F TYR 1 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 C -0.032 3.272
PSI_BFD_SF4_opt.pdb #4/F GLU 18 OE1 PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ -0.032 2.737
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.033 2.738
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.040 2.745
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD2 PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ -0.041 2.746
PSI_BFD_SF4_opt.pdb #4/F THR 7 C PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.042 3.367
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.049 3.449
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 CG2 -0.052 3.232
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 CB -0.054 3.234
PSI_BFD_SF4_opt.pdb #4/F ASP 29 OD1 PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1 -0.055 2.760
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ -0.060 3.240
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.075 2.780
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH2 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.079 2.784
PSI_BFD_SF4_opt.pdb #4/F GLY 13 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.080 3.405
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1 -0.086 2.666
PSI_BFD_SF4_opt.pdb #4/F ALA 38 O PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB -0.088 3.268
PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 -0.100 3.425
PSI_BFD_SF4_opt.pdb #4/F ASP 43 OD2 PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA -0.103 3.283
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE1 PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH1 -0.107 2.812
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 CB -0.122 3.302
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 C -0.130 3.530
PSI_BFD_SF4_opt.pdb #4/F GLY 13 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.134 3.459
PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.136 3.316
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.143 2.848
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CB -0.146 3.486
PSI_BFD_SF4_opt.pdb #4/F GLY 13 O PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ -0.147 3.327
PSI_BFD_SF4_opt.pdb #4/F CYF 12 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.148 3.473
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 CG -0.162 3.562
PSI_BFD_SF4_opt.pdb #4/F MET 53 SD PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1 -0.167 3.649
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE1 PSI_BFD_SF4_opt.pdb #4/E ARG 43 NE -0.170 2.875
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NE PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 -0.177 2.902
PSI_BFD_SF4_opt.pdb #4/F GLU 8 N PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.182 3.432
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.182 3.507
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 CZ -0.183 3.363
PSI_BFD_SF4_opt.pdb #4/F GLU 16 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.187 3.512
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 CB -0.188 3.368
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E SER 53 CA -0.188 3.368
PSI_BFD_SF4_opt.pdb #4/F ARG 31 NH1 PSI_BFD_SF4_opt.pdb #4/A ASP 34 OD2 -0.189 2.894
PSI_BFD_SF4_opt.pdb #4/F ASP 43 CG PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.197 3.522
PSI_BFD_SF4_opt.pdb #4/F PRO 17 O PSI_BFD_SF4_opt.pdb #4/D LYS 109 NZ -0.212 2.917
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 CG1 -0.215 3.615
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CB PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.219 3.619
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 CD1 -0.225 3.625
PSI_BFD_SF4_opt.pdb #4/F PRO 17 CG PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.230 3.555
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 N -0.238 3.503
PSI_BFD_SF4_opt.pdb #4/F GLY 13 O PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.254 2.959
PSI_BFD_SF4_opt.pdb #4/F ALA 14 N PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.256 3.506
PSI_BFD_SF4_opt.pdb #4/F GLU 8 OE2 PSI_BFD_SF4_opt.pdb #4/E THR 54 N -0.272 2.977
PSI_BFD_SF4_opt.pdb #4/F ALA 6 O PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH1 -0.275 2.980
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CB PSI_BFD_SF4_opt.pdb #4/E ALA 67 C -0.275 3.735
PSI_BFD_SF4_opt.pdb #4/F ILE 10 CD1 PSI_BFD_SF4_opt.pdb #4/C PRO 58 CG -0.291 3.691
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 OG1 -0.299 3.499
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH1 -0.301 3.626
PSI_BFD_SF4_opt.pdb #4/F MET 53 CE PSI_BFD_SF4_opt.pdb #4/E THR 54 CB -0.316 3.716
PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD PSI_BFD_SF4_opt.pdb #4/E SER 53 CB -0.323 3.723
PSI_BFD_SF4_opt.pdb #4/F GLU 8 CD PSI_BFD_SF4_opt.pdb #4/E ARG 43 NH2 -0.332 3.657
PSI_BFD_SF4_opt.pdb #4/F CYF 12 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.337 3.662
PSI_BFD_SF4_opt.pdb #4/F ARG 31 CZ PSI_BFD_SF4_opt.pdb #4/A THR 28 OG1 -0.342 3.542
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CA PSI_BFD_SF4_opt.pdb #4/A ARG 27 NH2 -0.346 3.671
PSI_BFD_SF4_opt.pdb #4/F CYF 12 C PSI_BFD_SF4_opt.pdb #4/C GLN 15 CD -0.353 3.753
PSI_BFD_SF4_opt.pdb #4/F GLY 13 CA PSI_BFD_SF4_opt.pdb #4/C GLN 15 NE2 -0.355 3.680
PSI_BFD_SF4_opt.pdb #4/F GLU 16 OE2 PSI_BFD_SF4_opt.pdb #4/C ARG 18 CZ -0.356 3.536
PSI_BFD_SF4_opt.pdb #4/F ASP 29 CG PSI_BFD_SF4_opt.pdb #4/A LYS 31 NZ -0.363 3.688
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C ILE 11 O -0.366 3.546
PSI_BFD_SF4_opt.pdb #4/F VAL 50 CA PSI_BFD_SF4_opt.pdb #4/C ALA 35 CB -0.371 3.771
PSI_BFD_SF4_opt.pdb #4/F GLY 49 O PSI_BFD_SF4_opt.pdb #4/C LYS 34 O -0.372 3.332
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CB PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB -0.376 3.776
PSI_BFD_SF4_opt.pdb #4/F PRO 52 CG PSI_BFD_SF4_opt.pdb #4/C CYF 13 CB -0.389 3.789
PSI_BFD_SF4_opt.pdb #4/F PRO 17 CD PSI_BFD_SF4_opt.pdb #4/C ARG 18 NH2 -0.394 3.719
88 contacts
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone true
Assigning ribbon_hide_backbone attribute to 35 items
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 35 items
> hide #4.8 models
> ui tool show Clashes
> select #4/F
829 atoms, 836 bonds, 60 residues, 1 model selected
> clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false
> color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False
4 clashes
atom1 atom2 overlap distance
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 2.060 1.340
PSI_BFD_SF4_opt.pdb #4/F TYR 1 CA PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.981 2.479
PSI_BFD_SF4_opt.pdb #4/F TYR 1 N PSI_BFD_SF4_opt.pdb #4/E ALA 67 CA 0.878 2.462
PSI_BFD_SF4_opt.pdb #4/F TYR 1 H PSI_BFD_SF4_opt.pdb #4/E ALA 67 C 0.727 2.033
4 clashes
> hide #4.9 models
> select #4/E
1071 atoms, 1082 bonds, 67 residues, 1 model selected
> show #1 models
> hide #!4 models
> open "/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"
Chain information for PSI_BFd.opt.pdb #6
---
Chain | Description
? | No description available
> split #6 atoms :1-743 atoms :744-1476 atoms :1477-1556 atoms :1557-1699
> atoms :1700-1765 atoms :1766-1826
Split PSI_BFd.opt.pdb (#6) into 7 models
Chain information for PSI_BFd.opt.pdb 1 #6.1
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 2 #6.2
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 3 #6.3
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 4 #6.4
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 5 #6.5
---
Chain | Description
? | No description available
Chain information for PSI_BFd.opt.pdb 6 #6.6
---
Chain | Description
? | No description available
> changechains #6.1 A
Chain IDs of 743 residues changed
> changechains #6.2 B
Chain IDs of 733 residues changed
> changechains #6.3 C
Chain IDs of 80 residues changed
> changechains #6.4 D
Chain IDs of 143 residues changed
> changechains #6.5 E
Chain IDs of 66 residues changed
> changechains #6.6 F
Chain IDs of 61 residues changed
> changechains #6.7 X
Chain IDs of 5 residues changed
> 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#6.7
> help help:user
> renumber #8/A-E seqStart 1
1022 residues renumbered
> hide #!6 models
> hide #4.1 models
> hide #1 models
> hide #7 models
> renumber #8/A start 1
0 residues renumbered
> renumber #8/B start 1
0 residues renumbered
> renumber #8/C start 1
0 residues renumbered
> renumber #8/D start 1
0 residues renumbered
> renumber #8/E start 1
0 residues renumbered
> renumber #8/F start 1
61 residues renumbered
> select #8/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false
> color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False
0 clashes
atom1 atom2 overlap distance
No clashes
> clashes sel restrict #8/A-E resSeparation 5 interModel false intraMol false
> color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False
0 clashes
atom1 atom2 overlap distance
No clashes
> close #7#4-6
> rename #8 id #4
> close #9
> select #4/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> clashes sel restrict #4/A-E resSeparation 5 interModel false intraMol false
> color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False
0 clashes
atom1 atom2 overlap distance
No clashes
> color sequential #4 chains palette accent
> color sel byhetero
> select #4/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> select #4/F &~H
435 atoms, 442 bonds, 61 residues, 1 model selected
> contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol
> false color #ff85ff radius 0.2 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
71 contacts
atom1 atom2 overlap distance
combination #4/F GLY 14 N combination #4/C GLN 15 NE2 0.214 3.036
combination #4/F CYF 13 CB combination #4/C GLN 15 CG 0.203 3.197
combination #4/F GLU 9 OE2 combination #4/E SER 53 C 0.154 3.026
combination #4/F GLY 50 O combination #4/C LYS 34 C 0.095 3.085
combination #4/F GLU 19 CD combination #4/D LYS 109 NZ 0.059 3.266
combination #4/F ILE 11 CD1 combination #4/C PRO 58 CB 0.048 3.352
combination #4/F THR 8 CA combination #4/E ARG 43 NH2 0.005 3.320
combination #4/F ASP 30 OD1 combination #4/A ARG 27 CZ -0.006 3.186
combination #4/F ASP 30 OD1 combination #4/A ARG 27 NH2 -0.014 2.719
combination #4/F MET 54 CE combination #4/E THR 54 O -0.032 3.212
combination #4/F GLU 19 OE1 combination #4/D LYS 109 NZ -0.032 2.737
combination #4/F GLU 9 OE1 combination #4/E ARG 43 NH2 -0.033 2.738
combination #4/F ASP 30 OD2 combination #4/A LYS 31 NZ -0.041 2.746
combination #4/F THR 8 C combination #4/E ARG 43 NH2 -0.042 3.367
combination #4/F CYF 13 CA combination #4/C GLN 15 CD -0.049 3.449
combination #4/F GLU 9 OE2 combination #4/E THR 54 CG2 -0.052 3.232
combination #4/F GLY 50 O combination #4/C LYS 34 CB -0.054 3.234
combination #4/F ASP 30 OD1 combination #4/A ARG 27 NH1 -0.055 2.760
combination #4/F GLU 9 OE1 combination #4/E ARG 43 CZ -0.060 3.240
combination #4/F GLU 17 OE2 combination #4/C ARG 18 NH2 -0.075 2.780
combination #4/F ARG 32 NH2 combination #4/A ASP 34 OD2 -0.079 2.784
combination #4/F GLY 14 N combination #4/C GLN 15 CD -0.080 3.405
combination #4/F GLU 9 OE2 combination #4/E THR 54 OG1 -0.086 2.666
combination #4/F GLU 17 CD combination #4/C ARG 18 NH1 -0.100 3.425
combination #4/F GLU 17 OE1 combination #4/C ARG 18 NH1 -0.107 2.812
combination #4/F GLU 9 OE2 combination #4/E THR 54 CB -0.122 3.302
combination #4/F MET 54 CE combination #4/E THR 54 C -0.130 3.530
combination #4/F GLY 14 C combination #4/C GLN 15 NE2 -0.134 3.459
combination #4/F ARG 32 CZ combination #4/A ASP 34 OD2 -0.136 3.316
combination #4/F ALA 7 O combination #4/E ARG 43 NH2 -0.143 2.848
combination #4/F GLY 14 O combination #4/C ARG 18 CZ -0.147 3.327
combination #4/F CYF 13 C combination #4/C GLN 15 NE2 -0.148 3.473
combination #4/F CYF 13 CA combination #4/C GLN 15 CG -0.162 3.562
combination #4/F MET 54 SD combination #4/C ILE 11 CD1 -0.167 3.649
combination #4/F GLU 9 OE1 combination #4/E ARG 43 NE -0.170 2.875
combination #4/F ARG 32 NE combination #4/A THR 28 OG1 -0.177 2.902
combination #4/F GLU 9 N combination #4/E ARG 43 NH2 -0.182 3.432
combination #4/F ASP 30 CG combination #4/A ARG 27 NH2 -0.182 3.507
combination #4/F ALA 7 O combination #4/E ARG 43 CZ -0.183 3.363
combination #4/F GLU 17 CD combination #4/C ARG 18 NH2 -0.187 3.512
combination #4/F GLU 9 OE2 combination #4/E SER 53 CB -0.188 3.368
combination #4/F GLU 9 OE2 combination #4/E SER 53 CA -0.188 3.368
combination #4/F ARG 32 NH1 combination #4/A ASP 34 OD2 -0.189 2.894
combination #4/F PRO 18 O combination #4/D LYS 109 NZ -0.212 2.917
combination #4/F PRO 53 CB combination #4/C ILE 11 CG1 -0.215 3.615
combination #4/F CYF 13 CB combination #4/C GLN 15 CD -0.219 3.619
combination #4/F PRO 53 CB combination #4/C ILE 11 CD1 -0.225 3.625
combination #4/F PRO 18 CG combination #4/C ARG 18 NH2 -0.230 3.555
combination #4/F GLY 14 O combination #4/C ARG 18 NH2 -0.254 2.959
combination #4/F ALA 15 N combination #4/C GLN 15 NE2 -0.256 3.506
combination #4/F GLU 9 OE2 combination #4/E THR 54 N -0.272 2.977
combination #4/F ALA 7 O combination #4/E ARG 43 NH1 -0.275 2.980
combination #4/F ILE 11 CD1 combination #4/C PRO 58 CG -0.291 3.691
combination #4/F MET 54 CE combination #4/E THR 54 OG1 -0.299 3.499
combination #4/F ASP 30 CG combination #4/A ARG 27 NH1 -0.301 3.626
combination #4/F MET 54 CE combination #4/E THR 54 CB -0.316 3.716
combination #4/F GLU 9 CD combination #4/E SER 53 CB -0.323 3.723
combination #4/F GLU 9 CD combination #4/E ARG 43 NH2 -0.332 3.657
combination #4/F CYF 13 CA combination #4/C GLN 15 NE2 -0.337 3.662
combination #4/F ARG 32 CZ combination #4/A THR 28 OG1 -0.342 3.542
combination #4/F ASP 30 CA combination #4/A ARG 27 NH2 -0.346 3.671
combination #4/F CYF 13 C combination #4/C GLN 15 CD -0.353 3.753
combination #4/F GLY 14 CA combination #4/C GLN 15 NE2 -0.355 3.680
combination #4/F GLU 17 OE2 combination #4/C ARG 18 CZ -0.356 3.536
combination #4/F ASP 30 CG combination #4/A LYS 31 NZ -0.363 3.688
combination #4/F PRO 53 CB combination #4/C ILE 11 O -0.366 3.546
combination #4/F VAL 51 CA combination #4/C ALA 35 CB -0.371 3.771
combination #4/F GLY 50 O combination #4/C LYS 34 O -0.372 3.332
combination #4/F PRO 53 CB combination #4/C CYF 13 CB -0.376 3.776
combination #4/F PRO 53 CG combination #4/C CYF 13 CB -0.389 3.789
combination #4/F PRO 18 CD combination #4/C ARG 18 NH2 -0.394 3.719
71 contacts
> select #4/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false
> intraRes false reveal true log true
Skipping possible acceptor with bad geometry: combination #4/A CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor combination #4/A CYF 575
SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
4 combination
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
combination #4/A ARG 27 NH1 combination #4/F ASP 30 OD1 combination #4/A ARG 27 HH11 2.760 1.842
combination #4/A ARG 27 NH2 combination #4/F ASP 30 OD1 combination #4/A ARG 27 HH21 2.719 1.800
combination #4/A LYS 31 NZ combination #4/F ASP 30 O combination #4/A LYS 31 HZ1 3.148 2.456
combination #4/A LYS 31 NZ combination #4/F ASP 30 OD2 combination #4/A LYS 31 HZ2 2.746 1.778
combination #4/C ARG 18 NH1 combination #4/F GLU 17 OE1 combination #4/C ARG 18 HH11 2.812 1.825
combination #4/C ARG 18 NH1 combination #4/F GLU 17 OE2 combination #4/C ARG 18 HH11 3.358 2.560
combination #4/C ARG 18 NH2 combination #4/F GLU 17 OE2 combination #4/C ARG 18 HH22 2.780 1.765
combination #4/D LYS 109 NZ combination #4/F PRO 18 O combination #4/D LYS 109 HZ1 2.917 2.045
combination #4/D LYS 109 NZ combination #4/F GLU 19 OE1 combination #4/D LYS 109 HZ2 2.737 1.813
combination #4/E ARG 43 NE combination #4/F GLU 9 OE1 combination #4/E ARG 43 HE 2.875 1.950
combination #4/E ARG 43 NH1 combination #4/F ALA 7 O combination #4/E ARG 43 HH12 2.980 2.103
combination #4/E ARG 43 NH2 combination #4/F ALA 7 O combination #4/E ARG 43 HH22 2.848 1.943
combination #4/E ARG 43 NH2 combination #4/F GLU 9 OE1 combination #4/E ARG 43 HH21 2.738 1.784
combination #4/E THR 54 OG1 combination #4/F GLU 9 OE2 combination #4/E THR 54 HG1 2.666 1.685
combination #4/E ASN 56 ND2 combination #4/F PRO 53 O combination #4/E ASN 56 HD22 3.598 2.755
combination #4/F ARG 32 NE combination #4/A THR 28 OG1 combination #4/F ARG 32 HE 2.902 1.898
combination #4/F ARG 32 NH1 combination #4/A ASP 34 OD2 combination #4/F ARG 32 HH12 2.894 1.970
combination #4/F ARG 32 NH2 combination #4/A THR 28 OG1 combination #4/F ARG 32 HH21 3.324 2.539
combination #4/F ARG 32 NH2 combination #4/A ASP 34 OD2 combination #4/F ARG 32 HH22 2.784 1.818
19 hydrogen bonds found
> select #4
28515 atoms, 28949 bonds, 180 pseudobonds, 1831 residues, 4 models selected
> color sel byhetero
> hide #4.3 models
> rename #4 PSI_BFd_SF4_opt.pdb
> select #4
28515 atoms, 28949 bonds, 180 pseudobonds, 1831 residues, 4 models selected
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 1831 items
> coulombic #4/A
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge +1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmploxhgeh0/ante.in.mol2);
atoms read (22), bonds read (21).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 92; net charge: 1`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for PSI_BFd_SF4_opt.pdb_A SES surface #4.5: minimum, -12.49,
mean 0.00, maximum 20.13
> coulombic #4/B
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmpmbbrltbe/ante.in.mol2);
atoms read (22), bonds read (21).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 94; net charge: -1`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for PSI_BFd_SF4_opt.pdb_B SES surface #4.6: minimum, -15.84,
mean -0.16, maximum 13.13
> coulombic #4/C
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmprnh8u1d7/ante.in.mol2);
atoms read (25), bonds read (24).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 102; net charge: -1`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for PSI_BFd_SF4_opt.pdb_C SES surface #4.7: minimum, -21.93,
mean -4.05, maximum 8.44
> coulombic #4/D
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for PSI_BFd_SF4_opt.pdb_D SES surface #4.8: minimum, -11.15,
mean 2.11, maximum 15.26
> coulombic #4/E
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for PSI_BFd_SF4_opt.pdb_E SES surface #4.9: minimum, -11.38,
mean 1.55, maximum 11.87
> coulombic #4/F
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp2k4_gr13/ante.in.mol2);
atoms read (22), bonds read (21).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 94; net charge: -1`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.8.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for PSI_BFd_SF4_opt.pdb_F SES surface #4.10: minimum, -24.55,
mean -9.44, maximum 5.59
> save "/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"
> hide #4.10 models
> select #4/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark orange target acpf
> color sel byhetero target acpf
> select #4/X:1831@F1:1827@F2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #4/X:1827@F2 #4/X:1831@F1
Distance between PSI_BFd_SF4_opt.pdb #4/X SF4 1827 F2 and SF4 1831 F1: 9.521Å
> distance style color #011993
[Repeated 2 time(s)]
> distance style decimalPlaces 4
[Repeated 2 time(s)]
> distance style decimalPlaces 5
[Repeated 2 time(s)]
> distance style decimalPlaces 6
[Repeated 2 time(s)]
> distance style decimalPlaces 5
[Repeated 2 time(s)]
> distance style decimalPlaces 4
[Repeated 2 time(s)]
> distance style decimalPlaces 3
[Repeated 2 time(s)]
> distance style decimalPlaces 2
[Repeated 2 time(s)]
> distance style decimalPlaces 1
[Repeated 2 time(s)]
> distance style radius 0.3
[Repeated 2 time(s)]
> distance style radius 0.2
[Repeated 2 time(s)]
> hide #!5 models
> select #4/F:3-9,27-34,53-61
368 atoms, 369 bonds, 24 residues, 1 model selected
> show #1 models
> ui tool show Matchmaker
> select #2:1-2,8-24,30-47 :<0.1 /F
Nothing selected
> select #3:1-2,8-24,30-47 :<0.1 /F
Nothing selected
> select #3:1-2,8-24,30-47
447 atoms, 448 bonds, 37 residues, 1 model selected
> show #!3 models
> select #3:1-2,8-24,30-47
447 atoms, 448 bonds, 37 residues, 1 model selected
> select #3 &~:1-2,8-24,30-47
315 atoms, 228 bonds, 114 residues, 1 model selected
> color sel cyan target acpf
> hide #!3 models
> show #!3 models
> hide #1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show Matchmaker
> matchmaker #!3 to #4/F pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with BFd (2fdn), chain M (#3),
sequence alignment score = 115.9
RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs:
3.340)
> matchmaker #!3 to #4/F pairing bs showAlignment true
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with BFd (2fdn), chain M (#3),
sequence alignment score = 115.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M,
PSI_BFd_SF4_opt.pdb #4/F
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs:
3.340)
> sequence header consensus show
Showing consensus header ("seq_consensus" residue attribute) for alignment 1
> select #4:3-9,27-34,53-61
2226 atoms, 2237 bonds, 35 pseudobonds, 144 residues, 3 models selected
> select #4/F:3-9,27-34,53-61
368 atoms, 369 bonds, 24 residues, 1 model selected
> color sel cyan target acpf
> color sel byhetero target acpf
> show #4.10 models
> hide #4.10 models
> select #4/A:27,28,31,34
72 atoms, 69 bonds, 4 residues, 1 model selected
> transparency (#!4 & sel) 20
> transparency (#!4 & sel) 10
> transparency (#!4 & sel) 90
> select clear
> select #4/C:18/D:109/E:43,54,56,67
98 atoms, 93 bonds, 5 residues, 1 model selected
> transparency (#!4 & sel) 90
> select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
170 atoms, 162 bonds, 9 residues, 1 model selected
> transparency (#!4 & sel) 0
> select #4/A-F
28475 atoms, 28949 bonds, 90 pseudobonds, 1826 residues, 3 models selected
> show #4.10 models
> transparency (#!4 & sel) 30
> transparency (#!4 & sel) 20
> transparency (#!4 & sel) 10
> select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
170 atoms, 162 bonds, 9 residues, 1 model selected
> transparency (#!4 & sel) 90
> hide #4.10 models
> select clear
> transparency #4.1-2,4-9#!4 80
> transparency #4.1-2,4-9#!4 10
> select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
170 atoms, 162 bonds, 9 residues, 1 model selected
> transparency (#!4 & sel) 80
> select clear
> hide #4.7 models
> select #4/X
40 atoms, 91 pseudobonds, 5 residues, 3 models selected
> style sel sphere
Changed 40 atom styles
> style sel ball
Changed 40 atom styles
> show #1 models
> hide #!4 models
> show #!4 models
> show #!5 models
> hide #1 models
> style sel sphere
Changed 40 atom styles
> select clear
> show #4.10 models
> hide #4.10 models
> show #4.7 models
> select #4/A-E
27634 atoms, 28101 bonds, 1765 residues, 1 model selected
> transparency (#!4 & sel) 30
> hide #4.9 models
> hide #4.8 models
> hide #4.7 models
> hide #4.6 models
> hide #4.5 models
> show #4.5 models
> show #4.6 models
> show #4.7 models
> show #4.8 models
> show #4.9 models
> show #4.10 models
> select add #4.10
28475 atoms, 28101 bonds, 1826 residues, 6 models selected
> select subtract #4.10
27634 atoms, 28101 bonds, 1765 residues, 7 models selected
> select add #4.10
28475 atoms, 28101 bonds, 1826 residues, 6 models selected
> select subtract #4.10
27634 atoms, 28101 bonds, 1765 residues, 7 models selected
> select add #4.10
28475 atoms, 28101 bonds, 1826 residues, 6 models selected
> select #4/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> transparency (#!4 & sel) 30
> select clear
> save "/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"
> hide #4.10 models
> show #4.10 models
> hide #4.10 models
> hide #4.7 models
> save "/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"
> hide #4.9 models
> hide #4.8 models
> hide #4.6 models
> hide #4.5 models
> select #4:SF4
40 atoms, 91 pseudobonds, 5 residues, 3 models selected
> style sel stick
Changed 40 atom styles
> style sel ball
Changed 40 atom styles
> select #4/F:42@SG
1 atom, 1 residue, 1 model selected
> select #4/X:1828@F1
1 atom, 1 residue, 1 model selected
> ui tool show "Build Structure"
> select clear
[Repeated 1 time(s)]
> help help:user
> hide #4.1 models
> show #4.1 models
> hide #4.1 models
> show #4.1 models
> select #4:1828@F1
1 atom, 1 residue, 1 model selected
> bond #4:1828@F1 reasonable true
Must specify two or more atoms
> select #4:1828@F1,S2,S3,S4
4 atoms, 3 pseudobonds, 1 residue, 2 models selected
> bond #4:1828@F1,S2,S3,S4
Created 3 bonds
> bond #4:1828@F3,S1,S3,S2
Created 2 bonds
> bond #4:1828@F3,S4
Created 1 bond
> select #4:1828@F2,S4
2 atoms, 1 pseudobond, 1 residue, 2 models selected
> select #4:1828@F2,S4,S1,S3
4 atoms, 3 pseudobonds, 1 residue, 2 models selected
> bond #4:1828@F2,S4,S1,S3
Created 3 bonds
> select #4:1828@F4,S2,S1,S3
4 atoms, 3 pseudobonds, 1 residue, 2 models selected
> bond #4:1828@F4,S2,S1,S3
Created 3 bonds
> bond #4:1828
Created 6 bonds
> ~bond sel
> bond #4:SF4
Created 78 bonds
> ~bond #4:SF4@F1,F2,F3,F4
> hide #4.1 models
> select #4:SF4
40 atoms, 60 bonds, 91 pseudobonds, 5 residues, 3 models selected
> style sel ball
Changed 40 atom styles
> select clear
> save "/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"
> windowsize
window size 806 684
> windowsize 750
> windowsize 800
> windowsize 800 600
> windowsize 800 800
> windowsize 800 700
> windowsize 800 670
> windowsize 800 675
> show #4.10 models
> show #4.9 models
> show #4.8 models
> show #4.7 models
> show #4.6 models
> show #4.5 models
> view list
Named views: HbondsZoom, back, front, side
> view front
> view side
> view HbondsZoom
> hide #4.10 models
> save "/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"
> select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
170 atoms, 162 bonds, 9 residues, 1 model selected
> transparency (#!4 & sel) 80
> select clear
> hide #4.9 models
> show #4.3 models
> save "/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"
> ui tool show Contacts
> select #4/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> select #4/F &~H
435 atoms, 442 bonds, 61 residues, 1 model selected
> contacts sel restrict "#4/A-E &~H" resSeparation 5 interModel false intraMol
> false color #ff85ff radius 0.2 log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
71 contacts
atom1 atom2 overlap distance
PSI_BFd_SF4_opt.pdb #4/F GLY 14 N PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 0.214 3.036
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CB PSI_BFd_SF4_opt.pdb #4/C GLN 15 CG 0.203 3.197
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E SER 53 C 0.154 3.026
PSI_BFd_SF4_opt.pdb #4/F GLY 50 O PSI_BFd_SF4_opt.pdb #4/C LYS 34 C 0.095 3.085
PSI_BFd_SF4_opt.pdb #4/F GLU 19 CD PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ 0.059 3.266
PSI_BFd_SF4_opt.pdb #4/F ILE 11 CD1 PSI_BFd_SF4_opt.pdb #4/C PRO 58 CB 0.048 3.352
PSI_BFd_SF4_opt.pdb #4/F THR 8 CA PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 0.005 3.320
PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1 PSI_BFd_SF4_opt.pdb #4/A ARG 27 CZ -0.006 3.186
PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1 PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2 -0.014 2.719
PSI_BFd_SF4_opt.pdb #4/F MET 54 CE PSI_BFd_SF4_opt.pdb #4/E THR 54 O -0.032 3.212
PSI_BFd_SF4_opt.pdb #4/F GLU 19 OE1 PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ -0.032 2.737
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1 PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.033 2.738
PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD2 PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ -0.041 2.746
PSI_BFd_SF4_opt.pdb #4/F THR 8 C PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.042 3.367
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD -0.049 3.449
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E THR 54 CG2 -0.052 3.232
PSI_BFd_SF4_opt.pdb #4/F GLY 50 O PSI_BFd_SF4_opt.pdb #4/C LYS 34 CB -0.054 3.234
PSI_BFd_SF4_opt.pdb #4/F ASP 30 OD1 PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1 -0.055 2.760
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1 PSI_BFd_SF4_opt.pdb #4/E ARG 43 CZ -0.060 3.240
PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2 PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.075 2.780
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH2 PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2 -0.079 2.784
PSI_BFd_SF4_opt.pdb #4/F GLY 14 N PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD -0.080 3.405
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1 -0.086 2.666
PSI_BFd_SF4_opt.pdb #4/F GLU 17 CD PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1 -0.100 3.425
PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE1 PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH1 -0.107 2.812
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E THR 54 CB -0.122 3.302
PSI_BFd_SF4_opt.pdb #4/F MET 54 CE PSI_BFd_SF4_opt.pdb #4/E THR 54 C -0.130 3.530
PSI_BFd_SF4_opt.pdb #4/F GLY 14 C PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.134 3.459
PSI_BFd_SF4_opt.pdb #4/F ARG 32 CZ PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2 -0.136 3.316
PSI_BFd_SF4_opt.pdb #4/F ALA 7 O PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.143 2.848
PSI_BFd_SF4_opt.pdb #4/F GLY 14 O PSI_BFd_SF4_opt.pdb #4/C ARG 18 CZ -0.147 3.327
PSI_BFd_SF4_opt.pdb #4/F CYF 13 C PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.148 3.473
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA PSI_BFd_SF4_opt.pdb #4/C GLN 15 CG -0.162 3.562
PSI_BFd_SF4_opt.pdb #4/F MET 54 SD PSI_BFd_SF4_opt.pdb #4/C ILE 11 CD1 -0.167 3.649
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE1 PSI_BFd_SF4_opt.pdb #4/E ARG 43 NE -0.170 2.875
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NE PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1 -0.177 2.902
PSI_BFd_SF4_opt.pdb #4/F GLU 9 N PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.182 3.432
PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2 -0.182 3.507
PSI_BFd_SF4_opt.pdb #4/F ALA 7 O PSI_BFd_SF4_opt.pdb #4/E ARG 43 CZ -0.183 3.363
PSI_BFd_SF4_opt.pdb #4/F GLU 17 CD PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.187 3.512
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E SER 53 CB -0.188 3.368
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E SER 53 CA -0.188 3.368
PSI_BFd_SF4_opt.pdb #4/F ARG 32 NH1 PSI_BFd_SF4_opt.pdb #4/A ASP 34 OD2 -0.189 2.894
PSI_BFd_SF4_opt.pdb #4/F PRO 18 O PSI_BFd_SF4_opt.pdb #4/D LYS 109 NZ -0.212 2.917
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB PSI_BFd_SF4_opt.pdb #4/C ILE 11 CG1 -0.215 3.615
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CB PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD -0.219 3.619
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB PSI_BFd_SF4_opt.pdb #4/C ILE 11 CD1 -0.225 3.625
PSI_BFd_SF4_opt.pdb #4/F PRO 18 CG PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.230 3.555
PSI_BFd_SF4_opt.pdb #4/F GLY 14 O PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.254 2.959
PSI_BFd_SF4_opt.pdb #4/F ALA 15 N PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.256 3.506
PSI_BFd_SF4_opt.pdb #4/F GLU 9 OE2 PSI_BFd_SF4_opt.pdb #4/E THR 54 N -0.272 2.977
PSI_BFd_SF4_opt.pdb #4/F ALA 7 O PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH1 -0.275 2.980
PSI_BFd_SF4_opt.pdb #4/F ILE 11 CD1 PSI_BFd_SF4_opt.pdb #4/C PRO 58 CG -0.291 3.691
PSI_BFd_SF4_opt.pdb #4/F MET 54 CE PSI_BFd_SF4_opt.pdb #4/E THR 54 OG1 -0.299 3.499
PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH1 -0.301 3.626
PSI_BFd_SF4_opt.pdb #4/F MET 54 CE PSI_BFd_SF4_opt.pdb #4/E THR 54 CB -0.316 3.716
PSI_BFd_SF4_opt.pdb #4/F GLU 9 CD PSI_BFd_SF4_opt.pdb #4/E SER 53 CB -0.323 3.723
PSI_BFd_SF4_opt.pdb #4/F GLU 9 CD PSI_BFd_SF4_opt.pdb #4/E ARG 43 NH2 -0.332 3.657
PSI_BFd_SF4_opt.pdb #4/F CYF 13 CA PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.337 3.662
PSI_BFd_SF4_opt.pdb #4/F ARG 32 CZ PSI_BFd_SF4_opt.pdb #4/A THR 28 OG1 -0.342 3.542
PSI_BFd_SF4_opt.pdb #4/F ASP 30 CA PSI_BFd_SF4_opt.pdb #4/A ARG 27 NH2 -0.346 3.671
PSI_BFd_SF4_opt.pdb #4/F CYF 13 C PSI_BFd_SF4_opt.pdb #4/C GLN 15 CD -0.353 3.753
PSI_BFd_SF4_opt.pdb #4/F GLY 14 CA PSI_BFd_SF4_opt.pdb #4/C GLN 15 NE2 -0.355 3.680
PSI_BFd_SF4_opt.pdb #4/F GLU 17 OE2 PSI_BFd_SF4_opt.pdb #4/C ARG 18 CZ -0.356 3.536
PSI_BFd_SF4_opt.pdb #4/F ASP 30 CG PSI_BFd_SF4_opt.pdb #4/A LYS 31 NZ -0.363 3.688
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB PSI_BFd_SF4_opt.pdb #4/C ILE 11 O -0.366 3.546
PSI_BFd_SF4_opt.pdb #4/F VAL 51 CA PSI_BFd_SF4_opt.pdb #4/C ALA 35 CB -0.371 3.771
PSI_BFd_SF4_opt.pdb #4/F GLY 50 O PSI_BFd_SF4_opt.pdb #4/C LYS 34 O -0.372 3.332
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CB PSI_BFd_SF4_opt.pdb #4/C CYF 13 CB -0.376 3.776
PSI_BFd_SF4_opt.pdb #4/F PRO 53 CG PSI_BFd_SF4_opt.pdb #4/C CYF 13 CB -0.389 3.789
PSI_BFd_SF4_opt.pdb #4/F PRO 18 CD PSI_BFd_SF4_opt.pdb #4/C ARG 18 NH2 -0.394 3.719
71 contacts
> select #4/F:14,9,50,19,11,8,30,54,19,9,17,32,7,18,53,51
199 atoms, 193 bonds, 14 residues, 1 model selected
> hide sel atoms
> select #4/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone true
Assigning ribbon_hide_backbone attribute to 61 items
> select #4/F &H
406 atoms, 61 residues, 1 model selected
> hide sel atoms
> ui tool show H-Bonds
> select #4/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> hbonds sel color #0096ff restrict #4/A-E interModel false intraMol false
> intraRes false select true reveal true log true
Skipping possible acceptor with bad geometry: PSI_BFd_SF4_opt.pdb #4/A CYF 575
SG
Wrong number of grandchild atoms for phi/psi acceptor PSI_BFd_SF4_opt.pdb #4/A
CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
4 PSI_BFd_SF4_opt.pdb
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
19 hydrogen bonds found
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone true
Assigning ribbon_hide_backbone attribute to 17 items
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 17 items
> hide #4.3 models
> show #4.9 models
> show #4.10 models
> hide #4.10 models
> select clear
> save "/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"
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom
> hbonds.png" width 1600 height 1350 supersample 3 transparentBackground true
> show #4.10 models
> hide #5.1 models
> select add #4.10
841 atoms, 61 residues, 1 model selected
> select add #4.9
1900 atoms, 127 residues, 2 models selected
> select add #4.8
4177 atoms, 270 residues, 3 models selected
> select add #4.7
5383 atoms, 350 residues, 4 models selected
> select add #4.6
16896 atoms, 1083 residues, 5 models selected
> select add #4.5
28475 atoms, 1826 residues, 6 models selected
> transparency (#!4 & sel) 20
> view front
> select clear
> save "/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" width 1600 height 1350 supersample 3 transparentBackground true
> view side
> view front
> ui tool show "Color Key"
> ui mousemode right "color key"
> key blue-white-red :min : :-
> key blue-white-red :min :0 :-
> key blue-white-red :+ :0 :-
> key size 0.25000,0.02000
> key size 0.25000,0.01000
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 19
> key fontSize 18
> key ticks true
> key tickThickness 5.0
> key tickThickness 4.0
> key labelOffset -1.0
> key labelOffset -2.0
> key labelOffset -3.0
> key labelOffset -4.0
> key labelOffset -5.0
> key labelOffset -6.0
> key labelOffset -7.0
> key labelOffset -8.0
> key labelOffset -9.0
> key labelOffset -10.0
> key labelOffset -11.0
> key labelOffset -12.0
> key labelOffset -13.0
> key labelOffset -14.0
> key labelOffset -15.0
> key labelOffset -16.0
> key labelOffset -17.0
> key labelOffset -16.0
> key labelOffset -15.0
> key fontSize 17
> key bold true
> key pos 0.1,0.08000
> key pos 0.70000,0.08000
> key pos 0.75000,0.08000
> key pos 0.75000,0.8000
> key pos 0.75000,0.9000
> key pos 0.75000,0.95000
> windowsize 800 675
> key pos 0.75000,0.90000
> key pos 0.75000,0.98000
> key pos 0.75000,0.9000
> key pos 0.75000,0.97000
> key pos 0.72000,0.97000
> ui mousemode right translate
> windowsize 800 675
> select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
170 atoms, 162 bonds, 9 residues, 1 model selected
> select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
170 atoms, 162 bonds, 9 residues, 1 model selected
> view HbondsZoom
> hide #4.10 models
> transparency (#!4 & sel) 80
> select clear
> hide #6 models
> show #6 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom
> hbonds.png" width 1600 height 1350 supersample 3 transparentBackground true
> select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
170 atoms, 162 bonds, 9 residues, 1 model selected
> transparency (#!4 & sel) 20
> select clear
> show #4.10 models
> view front
> save "/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" width 1600 height 1350 supersample 3 transparentBackground true
> view side
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png"
> width 1600 height 1350 supersample 3 transparentBackground true
> save "/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"
——— End of log from Thu Oct 10 08:30:31 2024 ———
opened ChimeraX session
> windowsize 900 675
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt side view.png"
> width 1800 height 1350 supersample 3 transparentBackground true
> view list
Named views: HbondsZoom, back, front, side
> view front
> save "/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" width 1800 height 1350 supersample 3 transparentBackground true
> select #4/A:27,28,31,34/C:18/D:109/E:43,54,56,67
170 atoms, 162 bonds, 9 residues, 1 model selected
> transparency (#!4 & sel) 80
> view HbondsZoom
> hide #4.10 models
> select clear
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Figures/Fdx_PSI MPNN/AMBER min with clusters/PSI-Fdx Alt zoom
> hbonds.png" width 1800 height 1350 supersample 3 transparentBackground true
> save "/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"
——— End of log from Fri Oct 11 10:32:45 2024 ———
opened ChimeraX session
> hide #4.9 models
> hide #4.7 models
> hide #4.8 models
> hide #4.6 models
> hide #4.5 models
> hide #4.4 models
> show #4.4 models
> open "/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"
Chain information for Dock_PS1_Fd_test_output.pdb #7
---
Chain | Description
Y | No description available
Z | No description available
> ui tool show Matchmaker
> matchmaker #7/Z to #4/C pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PSI_BFd_SF4_opt.pdb, chain C (#4) with Dock_PS1_Fd_test_output.pdb,
chain Z (#7), sequence alignment score = 342.4
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: PSI_BFd_SF4_opt.pdb #4/C,
Dock_PS1_Fd_test_output.pdb #7/Z
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 80 pruned atom pairs is 0.300 angstroms; (across all 80 pairs:
0.300)
> select #9:1183@S4:1741@F1
Nothing selected
> select #7:1183@S4:1741@F1
2 atoms, 2 residues, 1 model selected
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> ui tool show Distances
> ~distance #4/X:1827@F2 #4/X:1831@F1
> distance #7/Z:1741@F1 #7/Y:1183@S4
Distance between Dock_PS1_Fd_test_output.pdb #7/Z SF4 1741 F1 and /Y SF4 1183
S4: 11.458Å
> select #7/Z
13593 atoms, 13984 bonds, 54 pseudobonds, 1741 residues, 2 models selected
> ui tool show Clashes
> clashes sel restrict #7/Y resSeparation 5 interModel false intraMol false
> color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False
9 clashes
atom1 atom2 overlap distance
Dock_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
Dock_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
Dock_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
Dock_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
Dock_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
Dock_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
Dock_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
Dock_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
Dock_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
9 clashes
> hide #!4 models
> open "/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"
Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif
#8
---
Chain | Description
A | .
> ui tool show Matchmaker
> matchmaker #8/A to #7/Y pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
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
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains 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
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 7 pruned atom pairs is 1.406 angstroms; (across all 441 pairs:
35.668)
> hide #!7 models
> close #8
> show #!7 models
> open "/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"
Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif
#8
---
Chain | Description
A | .
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
Chains 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
> view
> hide #8 models
> save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"
——— End of log from Mon Oct 14 17:57:44 2024 ———
opened ChimeraX session
> open 1hfe
1hfe title:
1.6 A resolution structure of the Fe-ONLY hydrogenase from desulfovibrio
desulfuricans [more info...]
Chain information for 1hfe #9
---
Chain | Description | UniProt
L M | PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) | PHFL_DESVH 1-421
S T | PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) | PHFS_DESVH 1-123
Non-standard residues in 1hfe #9
---
CMO — carbon monoxide
CYN — cyanide ion
CYS — cysteine
FE2 — Fe (II) ion
PDT — 1,3-propanedithiol
SF4 — iron/sulfur cluster
ZN — zinc ion
1hfe mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| software_defined_assembly
351 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Associated 1hfe chain L to
fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 25
mismatches
Associated 1hfe chain M to
fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A with 25
mismatches
> view
> show #8 models
> open 6sdv
Summary of feedback from opening 6sdv fetched from pdb
---
note | Fetching compressed mmCIF 6sdv from http://files.rcsb.org/download/6sdv.cif
6sdv title:
W-formate dehydrogenase from Desulfovibrio vulgaris - Formate reduced form
[more info...]
Chain information for 6sdv #10
---
Chain | Description | UniProt
A | Formate dehydrogenase, alpha subunit, selenocysteine-containing,Formate dehydrogenase, alpha subunit, selenocysteine-containing,W-formate dehydrogenase - alpha subunit | Q72EJ1_DESVH 1-1005
B | Formate dehydrogenase, beta subunit, putative | Q72EJ0_DESVH 1-236
Non-standard residues in 6sdv #10
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
H2S — hydrosulfuric acid (hydrogen sulfide)
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 (molybdopterin guanosine dinucleotide)
NO3 — nitrate ion
PEG — di(hydroxyethyl)ether
SEC — selenocysteine
SF4 — iron/sulfur cluster
W — tungsten ion
> hide #8 models
> hide #!9 models
> open "/Users/drornoy/Documents/Protein Designs/PSI H2ase/Prabir optimized
> structures/Dock_PS1_Fd_test_output.pdb"
Chain information for Dock_PS1_Fd_test_output.pdb #11
---
Chain | Description
Y | No description available
Z | No description available
Associated Dock_PS1_Fd_test_output.pdb chain Z to Dock_PS1_Fd_test_output.pdb,
chain Z with 0 mismatches
Associated Dock_PS1_Fd_test_output.pdb chain Y to Dock_PS1_Fd_test_output.pdb,
chain Y with 0 mismatches
> show #!9 models
> hide #!10 models
> hide #!7 models
> close #11
> show #!10 models
> save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"
——— End of log from Mon Oct 14 18:11:28 2024 ———
opened ChimeraX session
> show #!4 models
> ui tool show Matchmaker
> matchmaker #9/L to #4/F pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PSI_BFd_SF4_opt.pdb, chain F (#4) with 1hfe, chain L (#9), sequence
alignment score = 28.8
RMSD between 22 pruned atom pairs is 0.734 angstroms; (across all 52 pairs:
15.360)
> select #9/M/T
4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected
> hide #!4 models
> hide sel cartoons
> hide sel atoms
> show #!4 models
> hide #!4 models
> show #1 models
> hide #1 models
> show #!4 models
> hide #!4 models
> show #!7 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> hide #!10 models
> show #!10 models
No reference and/or match structure/chain chosen
> show #!4 models
> hide #!10 models
> hide #!7 models
> show #!7 models
> show #!10 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> matchmaker #10/B to #7/Y pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 6sdv, chain B (#10),
sequence alignment score = 1014
RMSD between 123 pruned atom pairs is 1.190 angstroms; (across all 214 pairs:
3.455)
> matchmaker #9/L to #10/B pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6sdv, chain B (#10) with 1hfe, chain L (#9), sequence alignment
score = 64.3
RMSD between 6 pruned atom pairs is 1.458 angstroms; (across all 188 pairs:
28.430)
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!7 models
> hide #!4 models
> select #7/Y:1-73
585 atoms, 600 bonds, 73 residues, 1 model selected
> show #!9 models
> hide #!7 models
> select #9/Y:25-84
Nothing selected
> select #9/S:25-84
393 atoms, 400 bonds, 49 residues, 1 model selected
> select #9/L:25-84
450 atoms, 461 bonds, 60 residues, 1 model selected
> select #7/Y:1-73#9/L:25-84
1035 atoms, 1061 bonds, 133 residues, 2 models selected
> show #!10 models
> hide #!10 models
> show #!7 models
> matchmaker #9/L & sel to #7/Y & sel pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 1hfe, chain L (#9),
sequence alignment score = 34.8
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: Dock_PS1_Fd_test_output.pdb
#7/Y, 1hfe #9/L
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 8 pruned atom pairs is 1.316 angstroms; (across all 51 pairs:
12.843)
> matchmaker #9/L & sel to #10/B pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6sdv, chain B (#10) with 1hfe, chain L (#9), sequence alignment
score = 34.1
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 1hfe #9/L, 6sdv #10/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 4 pruned atom pairs is 1.059 angstroms; (across all 59 pairs:
15.580)
> hide #!7 models
> show #!10 models
> show #!7 models
> hide #!10 models
> hide #!9 models
> show #!10 models
> hide #!7 models
> show #!7 models
> select #7/Y:75-137#9/L:25-84
910 atoms, 928 bonds, 123 residues, 2 models selected
> matchmaker #9/L & sel to #10/B & sel pairing ss showAlignment true
No 'to' chains specified
> matchmaker #9/L & sel to #7/Y & sel pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with 1hfe, chain L (#9),
sequence alignment score = 52.2
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains used in RMSD evaluation for alignment 4: Dock_PS1_Fd_test_output.pdb
#7/Y, 1hfe #9/L
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 22 pruned atom pairs is 1.074 angstroms; (across all 46 pairs:
6.759)
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!3 models
> hide #!3 models
> select #7/Y
9266 atoms, 9474 bonds, 90 pseudobonds, 1186 residues, 2 models selected
> color (#!7 & sel) gray
> color sel byhetero
> show #!3 models
> hide #!3 models
> show #!9 models
> hide #!7 models
> show #!3 models
> hide #!3 models
> hide #!9 models
> show #!7 models
> show #!9 models
> hide #!7 models
> hide #!9 models
> show #!7 models
> align #9/L:422-423 toAtoms #7/Y:1183-1184
RMSD between 16 atom pairs is 1.724 angstroms
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!7 models
> show #!9 models
> select #9/L:35,38,41,76, 45,66,69,72#7/Y:73,76,81,120,85,110,113,116
96 atoms, 80 bonds, 16 residues, 2 models selected
> hide #!9 models
> show #!7 models
> select #9/L:35-41 #7/Y:73-81
114 atoms, 115 bonds, 16 residues, 2 models selected
> show #!9 models
> hide #!7 models
> show #!3 models
> hide #!9 models
> show #!9 models
> select ~sel & ##selected
31473 atoms, 31085 bonds, 193 pseudobonds, 5083 residues, 6 models selected
> align #9/L:422-423 toAtoms #3:61,62
RMSD between 16 atom pairs is 2.679 angstroms
> select #9/S:25-84
393 atoms, 400 bonds, 49 residues, 1 model selected
> hide #!3 models
> select #9/L:25-84
450 atoms, 461 bonds, 60 residues, 1 model selected
> select #9/L:27-84
432 atoms, 442 bonds, 58 residues, 1 model selected
> select #9/L:27-84
432 atoms, 442 bonds, 58 residues, 1 model selected
> color sel lime
> color sel byhetero
> hide #!9 models
> show #!7 models
> select #7/Y:63-121
434 atoms, 443 bonds, 59 residues, 1 model selected
> select #7/Y:72-121
354 atoms, 358 bonds, 50 residues, 1 model selected
> show #!9 models
> hide #!9 models
> combine #3
Associated copy of BFd (2fdn) chain M to BFd (2fdn), chain M with 0 mismatches
Chains used in RMSD evaluation for alignment 1: BFd (2fdn) #3/M,
PSI_BFd_SF4_opt.pdb #4/F, copy of BFd (2fdn) #11/M
> matchmaker #11/M to #7/Y & sel pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Dock_PS1_Fd_test_output.pdb, chain Y (#7) with copy of BFd (2fdn),
chain M (#11), sequence alignment score = 86.5
RMSD between 25 pruned atom pairs is 1.276 angstroms; (across all 42 pairs:
3.792)
> hide #!7 models
> show #!9 models
> select #9/L:25-84
450 atoms, 461 bonds, 60 residues, 1 model selected
> matchmaker #9/L & sel to #11/M pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker copy of BFd (2fdn), chain M (#11) with 1hfe, chain L (#9), sequence
alignment score = 104.3
RMSD between 43 pruned atom pairs is 1.236 angstroms; (across all 55 pairs:
2.501)
> show #!3 models
> hide #!9 models
> select #3:61/11:61
8 atoms, 12 bonds, 1 residue, 1 model selected
> select #3:61#11:61
16 atoms, 24 bonds, 2 residues, 2 models selected
> color sel cornflower blue
> show #!9 models
> hide #!9 models
> select #9/L:25-84
450 atoms, 461 bonds, 60 residues, 1 model selected
> hide #!11 models
> show #!9 models
> matchmaker #9/L & sel to #3/M pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker BFd (2fdn), chain M (#3) with 1hfe, chain L (#9), sequence
alignment score = 104.3
RMSD between 43 pruned atom pairs is 1.232 angstroms; (across all 55 pairs:
2.484)
> show #!4 models
> show #8 models
> matchmaker #8/A to #9/L pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1hfe, chain L (#9) with
fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A (#8),
sequence alignment score = 2066.5
RMSD between 390 pruned atom pairs is 0.207 angstroms; (across all 396 pairs:
1.636)
> hide #!9 models
> show #!9 models
> select #9/S
860 atoms, 733 bonds, 1 pseudobond, 235 residues, 2 models selected
> color (#!9 & sel) cyan
> hide #!9 models
> select #8:467-477
92 atoms, 96 bonds, 11 residues, 1 model selected
> hide sel cartoons
> show #!9 models
> select add #8
3677 atoms, 3770 bonds, 477 residues, 1 model selected
> select subtract #8
Nothing selected
> hide #8 models
> hide #!9 models
> show #8 models
> close #9-10
> save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Compare PSI-BFd PSI-DdHyd.cxs"
> open "/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"
Chain information for fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif #9
---
Chain | Description
A | .
B | .
> hide #8 models
> hide #!3 models
> hide #!4 models
> view
> select #9:59-150 &:Cys
78 atoms, 65 bonds, 13 residues, 1 model selected
> select #9:59-140 &:Cys
66 atoms, 55 bonds, 11 residues, 1 model selected
> select #9/B:59-140 &:Cys
48 atoms, 40 bonds, 8 residues, 1 model selected
> show #!11 models
> matchmaker #9/B & sel to #11/M pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
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
RMSD between 8 pruned atom pairs is 0.685 angstroms; (across all 8 pairs:
0.685)
> view
> show #!7 models
> hide #!7 models
> show #!4 models
> hide #!11 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
> PSI-BFd PSI-DdHyd.cxs"
> select #9/B:112-137
195 atoms, 196 bonds, 26 residues, 1 model selected
> show #!7 models
> hide #!4 models
> select #9/B:59-140 &:Cys
48 atoms, 40 bonds, 8 residues, 1 model selected
> show sel atoms
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
> PSI-BFd PSI-DdHyd.cxs"
——— End of log from Mon Oct 14 21:44:01 2024 ———
opened ChimeraX session
> hide #!5 models
> hide #5.1 models
> hide #6 models
> hide #!7 models
> hide #9 models
> show #!4 models
> open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-
> DFG/DdHyd_PSI.opt.pdb
Chain information for DdHyd_PSI.opt.pdb #10
---
Chain | Description
? | No description available
> ui tool show Matchmaker
> matchmaker #!10 to #4 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PSI_BFd_SF4_opt.pdb, chain A (#4) with DdHyd_PSI.opt.pdb, chain
(blank) (#10), sequence alignment score = 3958.5
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: PSI_BFd_SF4_opt.pdb #4/A,
DdHyd_PSI.opt.pdb #10/?
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 743 pruned atom pairs is 0.000 angstroms; (across all 743 pairs:
0.000)
> hide #!4 models
> 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 DdHyd_PSI.opt.pdb (#10) into 6 models
Chain information for DdHyd_PSI.opt.pdb 1 #10.1
---
Chain | Description
? | No description available
Chain information for DdHyd_PSI.opt.pdb 2 #10.2
---
Chain | Description
? | No description available
Chain information for DdHyd_PSI.opt.pdb 3 #10.3
---
Chain | Description
? | No description available
Chain information for DdHyd_PSI.opt.pdb 4 #10.4
---
Chain | Description
? | No description available
Chain information for DdHyd_PSI.opt.pdb 5 #10.5
---
Chain | Description
? | No description available
Chain information for DdHyd_PSI.opt.pdb 6 #10.6
---
Chain | Description
? | No description available
Associated DdHyd_PSI.opt.pdb 1 (10.1) chain (blank) to PSI_BFd_SF4_opt.pdb,
chain A with 0 mismatches
Associated DdHyd_PSI.opt.pdb 2 (10.2) chain (blank) to DdHyd_PSI.opt.pdb,
chain (blank) with 0 mismatches
Associated DdHyd_PSI.opt.pdb 3 (10.3) chain (blank) to DdHyd_PSI.opt.pdb,
chain (blank) with 0 mismatches
Associated DdHyd_PSI.opt.pdb 4 (10.4) chain (blank) to DdHyd_PSI.opt.pdb,
chain (blank) with 0 mismatches
Associated DdHyd_PSI.opt.pdb 5 (10.5) chain (blank) to DdHyd_PSI.opt.pdb,
chain (blank) with 0 mismatches
Associated DdHyd_PSI.opt.pdb 6 (10.6) chain (blank) to DdHyd_PSI.opt.pdb,
chain (blank) with 0 mismatches
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 427, in <lambda>
self.associate([s for s in models if isinstance(s, AtomicStructure)],
force=False))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 394, in associate
self._notify_observers(note_name, note_data)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 826, in _notify_observers
self._notify_rmsd_change()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 835, in _notify_rmsd_change
self._notify_observers(self.NOTE_RMSD_UPDATE, None)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 823, in _notify_observers
recipient.alignment_notification(note_name, note_data)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alignment_headers/rmsd.py", line 52, in
alignment_notification
self.reevaluate()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alignment_headers/rmsd.py", line 126, in reevaluate
new_eval_chains = self.alignment.rmsd_chains
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 670, in rmsd_chains
rmsd = self._eval_rmsd([c1, c2])
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 769, in _eval_rmsd
for coords in self._gather_coords(chains, pa_name):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/alignment.py", line 794, in _gather_coords
pa = r.find_atom(pa_name)
^^^^^^^^^^^^^^^^^^^^
File "atomic_cpp/cymol.pyx", line 1651, in
chimerax.atomic.cymol.CyResidue.find_atom
RuntimeError: Residue already deleted
Error processing trigger "add models":
RuntimeError: Residue already deleted
File "atomic_cpp/cymol.pyx", line 1651, in
chimerax.atomic.cymol.CyResidue.find_atom
See log for complete Python traceback.
> hide #!10.1 models
> hide #10.2 models
> hide #!10.3 models
> hide #10.4 models
> hide #10.5 models
> hide #!10.6 models
> show #!10.1 models
> hide #!10.1 models
> show #10.2 models
> show #!10.1 models
> hide #10.2 models
> hide #!10.1 models
> show #!10.1 models
> show #10.2 models
> show #!10.3 models
> show #10.4 models
> hide #!10.3 models
> hide #10.2 models
> hide #!10.1 models
> hide #10.4 models
> show #10.5 models
> hide #10.5 models
> show #!10.6 models
> show #10.2 models
> show #!10.1 models
> show #!10.3 models
> show #10.4 models
> show #10.5 models
> ui tool show "Change Chain IDs"
> select add #10.1
11635 atoms, 11818 bonds, 18 pseudobonds, 752 residues, 3 models selected
> changechains sel A
Cannot reassign chain ID to only part of polymeric chain
(fold_clj_fdhf_hycb_2024_09_20_17_20_model_0.cif #9/B)
> select clear
> select add #10.1
11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected
> changechains sel A
Chain IDs of 744 residues changed
> select subtract #10.1
Nothing selected
> select add #10.2
11513 atoms, 11725 bonds, 733 residues, 1 model selected
> changechains sel B
Chain IDs of 733 residues changed
> select subtract #10.2
Nothing selected
> select add #10.3
1222 atoms, 1219 bonds, 36 pseudobonds, 82 residues, 2 models selected
> changechains sel C
Chain IDs of 82 residues changed
> select subtract #10.3
Nothing selected
> select add #10.4
2277 atoms, 2308 bonds, 143 residues, 1 model selected
> changechains sel D
Chain IDs of 143 residues changed
> select subtract #10.4
Nothing selected
> select add #10.5
1059 atoms, 1071 bonds, 66 residues, 1 model selected
> changechains sel E
Chain IDs of 66 residues changed
> select add #10.6
8232 atoms, 8313 bonds, 54 pseudobonds, 542 residues, 3 models selected
> select subtract #10.5
7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected
> changechains sel F
Chain IDs of 476 residues changed
> select add #10
34831 atoms, 35343 bonds, 108 pseudobonds, 2244 residues, 10 models selected
> color sel bychain
> color sel byhetero
[Repeated 1 time(s)]
> select clear
> combine #10.1#10.2#10.3#10.4#10.5#10.6
Associated combination chain A to PSI_BFd_SF4_opt.pdb, chain A with 0
mismatches
Associated combination chain B to DdHyd_PSI.opt.pdb, chain (blank) with 0
mismatches
Associated combination chain F to DdHyd_PSI.opt.pdb, chain (blank) with 0
mismatches
Associated combination chain D to DdHyd_PSI.opt.pdb, chain (blank) with 0
mismatches
Associated combination chain C to DdHyd_PSI.opt.pdb, chain (blank) with 0
mismatches
Associated combination chain E to DdHyd_PSI.opt.pdb, chain (blank) with 0
mismatches
> hide #!10 models
> show #!10 models
> rename #12 "DdHyd_PSI.opt.pdb split to chains"
> close #10
> rename #12 id #10
> select #10/A-E
27658 atoms, 28101 bonds, 54 pseudobonds, 1768 residues, 2 models selected
> ui tool show Clashes
> clashes sel restrict #10/F resSeparation 5 interModel false intraMol false
> color #fffb00 reveal true log true
Allowed overlap: 0.6
H-bond overlap reduction: 0.4
Ignore clashes between atoms separated by 4 bonds or less
Ignore clashes between atoms in residues less than 5 apart in sequence
Detect intra-residue clashes: False
Detect intra-molecule clashes: False
0 clashes
atom1 atom2 overlap distance
No clashes
> ui tool show Contacts
> select #10/A-E &~H
14013 atoms, 14456 bonds, 54 pseudobonds, 1768 residues, 2 models selected
> contacts sel restrict "#10/F &~H" resSeparation 5 interModel false intraMol
> false color #ff85ff radius 0.2 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Ignore contacts between atoms in residues less than 5 apart in sequence
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
61 contacts
atom1 atom2 overlap distance
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
61 contacts
> hide #10.3 models
> ui tool show H-Bonds
> hbonds sel color #0096ff restrict #10/F interModel false intraMol false
> intraRes false reveal true log true
Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.pdb split to
chains #10/A CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.pdb split
to chains #10/A CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
10 DdHyd_PSI.opt.pdb split to chains
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
13 hydrogen bonds found
> select #10/A-E
27658 atoms, 28101 bonds, 54 pseudobonds, 1768 residues, 2 models selected
> hbonds sel color #0096ff restrict #10/F interModel false intraMol false
> intraRes false reveal true log true
Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.pdb split to
chains #10/A CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.pdb split
to chains #10/A CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
10 DdHyd_PSI.opt.pdb split to chains
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
13 hydrogen bonds found
> select #10/A-F
34831 atoms, 35343 bonds, 182 pseudobonds, 2244 residues, 4 models selected
> hide sel cartoons
> hide #10.1 models
> help help:user
> bonds #10:2239-2244@F4@F2
Unknown command: bonds #10:2239-2244@F4@F2
> bond #10:2239-2244@F4@F2
Created 6 bonds
> select #10:2239-2244
48 atoms, 6 bonds, 108 pseudobonds, 6 residues, 2 models selected
> style sel stick
Changed 48 atom styles
> ~bond #10:2239-2244@F4@F2
> ~bond #10:2239-2244@F4@S1
> bond #10:2239-2244@F4@S1
Created 6 bonds
> bond #10:2239-2244@F3@S1
Created 6 bonds
> bond #10:2239-2244@F3@S2
Created 6 bonds
> bond #10:2239-2244@F4@S2
Created 6 bonds
> bond #10:2239-2244@F3@S4
Created 6 bonds
> bond #10:2239-2244@F2@S4
Created 6 bonds
> bond #10:2239-2244@F2@S1
Created 6 bonds
> bond #10:2239-2244@F2@S3
Created 6 bonds
> bond #10:2239-2244@F4@S3
Created 6 bonds
> bond #10:2239-2244@F1@S2
Created 6 bonds
> bond #10:2239-2244@F1@S3
Created 6 bonds
> bond #10:2239-2244@F1@S4
Created 6 bonds
> select #10:SF4
48 atoms, 72 bonds, 108 pseudobonds, 6 residues, 2 models selected
> style sel ball
Changed 48 atom styles
> select #10:SF4 &Fe
24 atoms, 36 pseudobonds, 6 residues, 2 models selected
> style sel sphere
Changed 24 atom styles
> select #10
34831 atoms, 35415 bonds, 183 pseudobonds, 2244 residues, 5 models selected
> show sel cartoons
> show #!4 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/PSI-DdHyd
> PSI-BFd AMBER opt.cxs"
——— End of log from Mon Oct 21 23:18:11 2024 ———
opened ChimeraX session
> hide #!4 models
> show #!4 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/NSF-BSF grant
> 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb" models #4
> close session
> open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-
> DFG/DdHyd_PSI.opt.chains.pdb "/Users/drornoy/Library/CloudStorage/OneDrive-
> Migal/NSF-BSF grant 2024/Models/PSI_Fdx Models/PSI_BFD_SF4_opt_chains.pdb"
Chain information for DdHyd_PSI.opt.chains.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
Chain information for PSI_BFD_SF4_opt_chains.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> select protein
63258 atoms, 64292 bonds, 4064 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> color sel bychain
> color sel byhetero
> ~select
Nothing selected
> color byhetero
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
> PSI-BFd PSI-DdHyd AMBER minimized chain split.cxs"
——— End of log from Tue Oct 22 09:43:01 2024 ———
opened ChimeraX session
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> rename #1 id #3
> rename #2 id #1
> rename #3 id #2
> open /Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-
> DFG/ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb
Chain information for ClFdh_HycB_PSI_optdock_WMGD_embedded.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
> select #3 &protein
34578 atoms, 35179 bonds, 2662 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select #3/Y:1183-1187,1200
41 atoms, 12 bonds, 72 pseudobonds, 6 residues, 2 models selected
> hide #!2 models
> hide #!1 models
> style sel sphere
Changed 41 atom styles
> color sel byhetero
> select #3/Z:SF4
24 atoms, 54 pseudobonds, 3 residues, 2 models selected
> color sel byhetero
> select #3
34737 atoms, 35295 bonds, 130 pseudobonds, 2673 residues, 2 models selected
> color sel bychain
> color sel byhetero
> select #13/Y:1188-1189
Nothing selected
> select #3/Y:1188-1189
94 atoms, 104 bonds, 2 residues, 1 model selected
> color sel magenta
> color sel byhetero
> show #!2 models
> show #!1 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
> PSI-BFd PSI-DdHyd PSI-FdhF.cxs"
——— End of log from Tue Oct 22 11:39:31 2024 ———
opened ChimeraX session
> select add #3
34737 atoms, 35295 bonds, 130 pseudobonds, 2673 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!3 models
> hide #!2 models
> show #!3 models
> show #!2 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Compare
> PSI-BFd PSI-DdHyd PSI-FdhF.cxs"
——— End of log from Tue Oct 22 11:40:52 2024 ———
> view name session-start
opened ChimeraX session
> hide #!2 models
> hide #!3 models
> open 2fdn
2fdn title:
2[4FE-4S] ferredoxin from clostridium acidi-urici [more info...]
Chain information for 2fdn #4
---
Chain | Description | UniProt
A | FERREDOXIN | FER_CLOAC 1-55
Non-standard residues in 2fdn #4
---
SF4 — iron/sulfur cluster
74 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PSI_BFD_SF4_opt_chains.pdb, chain F (#1) with 2fdn, chain A (#4),
sequence alignment score = 115.9
RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs:
3.340)
> select #1/A-E
27634 atoms, 28101 bonds, 1765 residues, 1 model selected
> hide sel cartoons
> select #1/X
40 atoms, 90 pseudobonds, 5 residues, 2 models selected
> hide sel atoms
> undo
> select #1/X:1829-1831
24 atoms, 54 pseudobonds, 3 residues, 2 models selected
> hide sel atoms
> select #1/X:1827-1828
16 atoms, 36 pseudobonds, 2 residues, 2 models selected
> style sel stick
Changed 16 atom styles
> hide #!4 models
> select #1/F:Cys
Nothing selected
> select #1/F:Cyf
80 atoms, 72 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 80 atom styles
> select H
45159 atoms, 5877 residues, 4 models selected
> hide sel & #!1 atoms
> show #!4 models
> select #1/X:1827-1828
16 atoms, 36 pseudobonds, 2 residues, 2 models selected
> style sel sphere
Changed 16 atom styles
> hide #!1 models
> select #4:61-62
16 atoms, 24 bonds, 2 residues, 1 model selected
> style sel sphere
Changed 16 atom styles
> hide #4.1 models
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!4 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PSI_BFD_SF4_opt_chains.pdb, chain F (#1) with 2fdn, chain A (#4),
sequence alignment score = 115.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: PSI_BFD_SF4_opt_chains.pdb
#1/F, 2fdn #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 42 pruned atom pairs is 0.827 angstroms; (across all 54 pairs:
3.340)
> select #1/F:3
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/F:3-8
96 atoms, 96 bonds, 6 residues, 1 model selected
> select #1/F:3
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/F:3-8 #4/A:3-8
168 atoms, 167 bonds, 12 residues, 2 models selected
MatchMaker Alignment [ID: 1] region chain F..chain A [3-8] RMSD: 6.436
> color sel cyan
> select #1/F:9
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/F:9
15 atoms, 14 bonds, 1 residue, 1 model selected
> color sel cyan
> select #4/A:25
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/F:27-34 #4/A:25-29
160 atoms, 159 bonds, 13 residues, 2 models selected
MatchMaker Alignment [ID: 1] region chain F..chain A [27-34] RMSD: 4.473
> color sel cyan
> select #4/A:48
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/F:53-61 #4/A:48-55
240 atoms, 242 bonds, 17 residues, 2 models selected
MatchMaker Alignment [ID: 1] region chain F..chain A [53-62] RMSD: 5.761
> color sel cyan
> hide #!4 models
> show #!4 models
> hide #!1 models
> color sel & #!4 byhetero
> select clear
> color #!4 byhetero
> select #1/F:3
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/F:3-9 #4/A:3-8
183 atoms, 182 bonds, 13 residues, 2 models selected
MatchMaker Alignment [ID: 1] region chain F..chain A [3-9] RMSD: 6.436
> show sel & #!4 atoms
> style sel & #!4 stick
Changed 72 atom styles
> select #4/A:1-2,8-24,30-47
447 atoms, 448 bonds, 37 residues, 1 model selected
> select #4/A:1-55 &~:1-2,8-24,30-47
205 atoms, 204 bonds, 18 residues, 1 model selected
> show sel atoms
> select H
45159 atoms, 5877 residues, 4 models selected
> hide sel & #!4 atoms
> select #4/A:1-55 &~:1-2,8-24,30-47
205 atoms, 204 bonds, 18 residues, 1 model selected
> select #1/F:3
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #1/F:3-9
111 atoms, 111 bonds, 7 residues, 1 model selected
> select #4/A:1-55 &~:1-2,8-24,30-47#1/F:3-9
205 atoms, 204 bonds, 18 residues, 1 model selected
> select #4/A:1-55 &~:1-2,8-24,30-47 |#1/F:3-9
205 atoms, 209 bonds, 18 residues, 1 model selected
> select #1/F:3-9,27-34,53-61
368 atoms, 369 bonds, 24 residues, 1 model selected
> show #!1 models
> show sel atoms
> style sel stick
Changed 368 atom styles
> color sel byhetero
> select H
45159 atoms, 5877 residues, 4 models selected
> hide sel & #!1,4 atoms
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 5877 items
> select @N,O
13656 atoms, 6875 residues, 4 models selected
> hide sel & #!1,4 atoms
> hide #!4 models
> select clear
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> select #4/A:1-2,8-24,30-47
447 atoms, 448 bonds, 37 residues, 1 model selected
> show #!4 models
> hide #!1 models
> ui tool show "Color Actions"
> color sel light slate gray
> color sel steel blue
> color sel olive drab
> color sel steel blue
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/Compare BFd to ModBFd.cxs"
——— End of log from Sat Sep 13 22:23:04 2025 ———
> view name session-start
opened ChimeraX session
> select #1/A-E
27634 atoms, 28101 bonds, 1765 residues, 1 model selected
> show sel cartoons
> select #1/X:1827-1828
16 atoms, 36 pseudobonds, 2 residues, 2 models selected
> select #1/X
40 atoms, 90 pseudobonds, 5 residues, 2 models selected
> show sel atoms
> select #1/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0096ff showDist true interModel false intraMol false
> intraRes false select true log true
Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A
CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor
PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 PSI_BFD_SF4_opt_chains.pdb
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
19 hydrogen bonds found
> show sel atoms
> style sel stick
Changed 31 atom styles
> ui tool show H-Bonds
> hbonds sel color #0096ff showDist true interModel false intraMol false
> intraRes false select true reveal true log true
Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A
CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor
PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 PSI_BFD_SF4_opt_chains.pdb
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
19 hydrogen bonds found
> select #1/F
841 atoms, 848 bonds, 61 residues, 1 model selected
> hbonds sel color #0096ff showDist true interModel false intraMol false
> intraRes false select true reveal true log true
Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A
CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor
PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 PSI_BFD_SF4_opt_chains.pdb
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
19 hydrogen bonds found
> hbonds sel color #0096ff showDist true interModel false intraMol false
> intraRes false reveal true log true
Skipping possible acceptor with bad geometry: PSI_BFD_SF4_opt_chains.pdb #1/A
CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor
PSI_BFD_SF4_opt_chains.pdb #1/A CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 PSI_BFD_SF4_opt_chains.pdb
19 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
PSI_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
19 hydrogen bonds found
> select #1/A:27,28,31,34/C:18/D:109/E:43,54,56
170 atoms, 162 bonds, 9 residues, 1 model selected
> select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &~H
81 atoms, 73 bonds, 9 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 81 atom styles
> hide #1.2.1 models
> select clear
> select #1/X:1829-1831
24 atoms, 54 pseudobonds, 3 residues, 2 models selected
> style sel ball
Changed 24 atom styles
> style sel sphere
Changed 24 atom styles
> select #1/X:1829-1831 &S
12 atoms, 3 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> color sel goldenrod
> color sel gold
> color sel green yellow
> color sel yellow green
> color sel green yellow
> color sel pale goldenrod
> color sel wheat
[Repeated 1 time(s)]
> color sel beige
> color sel light goldenrod yellow
> select clear
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Graphics/Designs/BFD design on PSI H-bonds.png" width
> 1800 height 1355 supersample 3 transparentBackground true
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs"
> view name zoom1
> ui tool show "Color Actions"
> select #1/A &protein
11579 atoms, 11778 bonds, 743 residues, 1 model selected
> color sel thistle target c
> color sel lavender target c
> color sel light pink target c
> color sel thistle target c
> color sel plum target c
> select #1/B &protein
11513 atoms, 11725 bonds, 733 residues, 1 model selected
> color sel light pink target c
> select #1/C &protein
1206 atoms, 1219 bonds, 80 residues, 1 model selected
> color sel pale green target c
> color sel dark sea green target c
> select #1/C &protein
1206 atoms, 1219 bonds, 80 residues, 1 model selected
> color sel dark gray target c
> color sel gray target c
> color sel teal target c
> color sel green target c
> color sel maroon target c
> color sel dark salmon target c
> color sel dark goldenrod target c
> color sel brown target c
> select #1/D &protein
2277 atoms, 2308 bonds, 143 residues, 1 model selected
> color sel dark khaki target c
> color sel wheat target c
> color sel peach puff target c
> color sel pale goldenrod target c
> color sel light salmon target c
> color sel burly wood target c
> select #1/E &protein
1059 atoms, 1071 bonds, 66 residues, 1 model selected
> view zoom1
> view name zoom2
> select #1/E &protein
1059 atoms, 1071 bonds, 66 residues, 1 model selected
> color sel sandy brown target c
> color sel peach puff target c
> color sel light salmon target c
[Repeated 1 time(s)]
> color sel sandy brown target c
> color sel light salmon target c
> view name zoom2
> select #1/F:17-18
29 atoms, 29 bonds, 2 residues, 1 model selected
> select #1/F:17-18 &~H
16 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> select #1/F:17-19 &~H
25 atoms, 25 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 25 atom styles
> select #1/C
1206 atoms, 1219 bonds, 80 residues, 1 model selected
> select #1/C &protein
1206 atoms, 1219 bonds, 80 residues, 1 model selected
> color sel brown target ac
> color sel byhetero
> color sel orange red target c
> color sel dark orange target c
> color sel coral target c
> color sel chocolate target c
> select #1/A:27,28,31,34/C:18/D:109/E:43,54,56 &~H
81 atoms, 73 bonds, 9 residues, 1 model selected
> color sel steel blue target c
> color sel steel blue target ac
> color sel byhetero
> color sel medium orchid target ac
> color sel byhetero
> color sel medium purple target ac
> color sel byhetero
> name frozen Hbonding sel
> color sel medium violet red target ac
> color sel deep pink target ac
> color sel byhetero
> select #1/E &protein
1059 atoms, 1071 bonds, 66 residues, 1 model selected
> color sel bisque target c
> color sel pink target c
> color sel peach puff target c
> select #1/C &protein
1206 atoms, 1219 bonds, 80 residues, 1 model selected
> color sel wheat target c
> color sel burly wood target c
> color sel tan target c
[Repeated 1 time(s)]
> select #1/D &protein
2277 atoms, 2308 bonds, 143 residues, 1 model selected
> color sel burly wood target c
> select clear
> select #1/F:9,17-19 &~H
34 atoms, 33 bonds, 4 residues, 1 model selected
> show sel atoms
> select clear
> view name zoom2
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-BFd design H-bonds.cxs"
——— End of log from Sun Sep 14 07:49:27 2025 ———
> view name session-start
opened ChimeraX session
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> ui tool show "Selection Inspector"
> select #1/A:393
16 atoms, 15 bonds, 1 residue, 1 model selected
> show #!2 models
> select #2/A
11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected
> help help:user
> color #2/A DDA0DD target c
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #2/A #DDA0DD target c
> select #1/B:393
20 atoms, 20 bonds, 1 residue, 1 model selected
> color #2/B #FFB6C1 target c
> select #1/C:40
11 atoms, 10 bonds, 1 residue, 1 model selected
> color #2/C #D2B48C target c
> view session_start
Expected an objects specifier or a view name or a keyword
> view list
Named views: session-start, zoom1, zoom2
> view session-start
> select #1/D:40
14 atoms, 14 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #2/D:40
Nothing selected
> hide #!1 models
> view list
Named views: session-start, zoom1, zoom2
> view session-start
> select #1/D:40
14 atoms, 14 bonds, 1 residue, 1 model selected
> color #2/D #DEB887 target c
> select #1/E:40
16 atoms, 15 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> color #2/D #FFDAB9 target c
> color #2/D #DEB887 target c
> color #2/E #FFDAB9 target c
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #1/X:1829@S1
1 atom, 1 residue, 1 model selected
> select #2:2239-2241
24 atoms, 54 pseudobonds, 3 residues, 2 models selected
> select #2:2239-2241 &S
12 atoms, 3 residues, 1 model selected
> select #1/X:1829@S1
1 atom, 1 residue, 1 model selected
> select #2:2239-2241 &S
12 atoms, 3 residues, 1 model selected
> color #2:2239-2241 &S #FAFAD2
> view session-start
> view name viewH2ase
> open 1hfe
1hfe title:
1.6 A resolution structure of the Fe-ONLY hydrogenase from desulfovibrio
desulfuricans [more info...]
Chain information for 1hfe #5
---
Chain | Description | UniProt
L M | PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT)) | PHFL_DESVH 1-421
S T | PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT)) | PHFS_DESVH 1-123
Non-standard residues in 1hfe #5
---
CMO — carbon monoxide
CYN — cyanide ion
CYS — cysteine
FE2 — Fe (II) ion
PDT — 1,3-propanedithiol
SF4 — iron/sulfur cluster
ZN — zinc ion
1hfe mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
3| software_defined_assembly
351 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!5 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5),
sequence alignment score = 1795.1
RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs:
2.105)
> select #5/M/T
4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected
> select #5/L/S
4358 atoms, 3871 bonds, 19 pseudobonds, 1080 residues, 2 models selected
> select #5/M/T
4370 atoms, 3871 bonds, 18 pseudobonds, 1092 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #5/S
860 atoms, 733 bonds, 1 pseudobond, 235 residues, 2 models selected
> color (#!5 & sel) orange
> color sel byhetero
> select #2/F:2157
21 atoms, 21 bonds, 1 residue, 1 model selected
> select #2/F:2157-2238
1309 atoms, 1329 bonds, 82 residues, 1 model selected
> ui tool show "Color Actions"
> color sel steel blue
> color sel slate gray
> color sel light slate gray
> color sel steel blue
> color sel light steel blue
> select #2/F:2150-2151
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5:386
8 atoms, 6 bonds, 2 residues, 1 model selected
> select #5:388
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #2/F:2152-2153
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #2/F:2152-2156
65 atoms, 65 bonds, 5 residues, 1 model selected
> color sel cyan
> select #2/F:388-390
Nothing selected
> select #5/L:388-390
23 atoms, 23 bonds, 3 residues, 1 model selected
> color sel orange
> color sel orange red
> select #5/L:388-397
71 atoms, 72 bonds, 10 residues, 1 model selected
> color sel orange
> color sel byhetero
> select #5/M:43-123
607 atoms, 624 bonds, 81 residues, 1 model selected
> color sel light steel blue
> select #5/S:43-123
651 atoms, 670 bonds, 81 residues, 1 model selected
> color sel light steel blue
> select #5/:15-30,35-52,58-387,396-477
Expected an objects specifier or a keyword
> select #5/L:15-30,35-52,58-387,396-477
2866 atoms, 2890 bonds, 18 pseudobonds, 423 residues, 2 models selected
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> select #5/L:1-400 &~15-30,35-52,58-387,396-477
Expected a keyword
> select #5/L:1-400 &~:15-30,35-52,58-387,396-477
240 atoms, 241 bonds, 30 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select clear
> hide #!5 models
> view viewH2ase
> show #!5 models
> select #2/F:1766-1776
160 atoms, 160 bonds, 11 residues, 1 model selected
> select #2/F:1766-1775
146 atoms, 146 bonds, 10 residues, 1 model selected
> hide #!2 models
> show #!2 models
> select #2/F:1766-1775,1792-1795,1814-1821
293 atoms, 293 bonds, 22 residues, 1 model selected
> color sel cyan
> color sel byhetero
> select clear
> view viewH2ase
> hide #!5 models
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
> select #2/F &protein
7149 atoms, 7242 bonds, 473 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0096ff showDist true interModel false intraMol false
> intraRes false reveal true log true
Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A
CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb
#2/A CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 DdHyd_PSI.opt.chains.pdb
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
13 hydrogen bonds found
> select #2/F &protein
7149 atoms, 7242 bonds, 473 residues, 1 model selected
> select #2 &protein
34783 atoms, 35343 bonds, 13 pseudobonds, 2238 residues, 2 models selected
> style sel stick
Changed 34783 atom styles
> select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730
161 atoms, 154 bonds, 8 residues, 1 model selected
> ui tool show "Color Actions"
> color sel deep pink
> color sel byhetero
> select #2 &H
17179 atoms, 2238 residues, 1 model selected
> hide sel atoms
> ui tool show H-Bonds
> hbonds sel color #0096ff showDist true interModel false intraMol false
> intraRes false select true log true
Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A
CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb
#2/A CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 DdHyd_PSI.opt.chains.pdb
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select #2/F &protein
7149 atoms, 7242 bonds, 473 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #0096ff showDist true interModel false intraMol false
> intraRes false select true log true
Skipping possible acceptor with bad geometry: DdHyd_PSI.opt.chains.pdb #2/A
CYF 575 SG
Wrong number of grandchild atoms for phi/psi acceptor DdHyd_PSI.opt.chains.pdb
#2/A CYF 575 SG
[Repeated 1 time(s)]
Skipped 2 atom(s) with bad connectivities; see log for details
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 DdHyd_PSI.opt.chains.pdb
13 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
DdHyd_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
13 hydrogen bonds found
> show sel atoms
> hide #2.2.1 models
> color #2/E #FFDAB9 target c
> color #2/D #DEB887 target c
> color #2/C #D2B48C target c
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
> view list
Named views: session-start, viewH2ase, zoom1, zoom2
> view session-start
> color #2/A #DDA0DD target c
> view name viewH2aseHbonds
[Repeated 1 time(s)]
> select clear
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
——— End of log from Mon Sep 15 19:12:58 2025 ———
> view name session-start
opened ChimeraX session
> view viewH2aseHbonds
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd Hbonds.png" width
> 1800 height 1358 supersample 3 transparentBackground true
> select #2/A:27/C:1491,1510/D:1665/E:1700,1706,1742,1730
161 atoms, 154 bonds, 8 residues, 1 model selected
> name frozen HbondingDdH sel
> select clear
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
——— End of log from Mon Sep 15 20:51:36 2025 ———
> view name session-start
opened ChimeraX session
> select #2/F:1766-1775,1792-1795,1814-1821 &H
139 atoms, 22 residues, 1 model selected
> select #2/F:1766-1775,1792-1795,1814-1821 &~H
154 atoms, 154 bonds, 22 residues, 1 model selected
> show sel atoms
> select #2/F:1766-1775,1792-1795,1814-1821,2151-2156 &~H
196 atoms, 196 bonds, 28 residues, 1 model selected
> select #2/F:1766-1775,1792-1795,1814-1821,2152-2156 &~H
192 atoms, 192 bonds, 27 residues, 1 model selected
> show sel atoms
> color sel byhetero
> view session-start
> select clear
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd design H-bonds.cxs"
——— End of log from Mon Sep 15 21:24:55 2025 ———
> view name session-start
opened ChimeraX session
> select #2/C-F &protein
11691 atoms, 11840 bonds, 12 pseudobonds, 762 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmp_ytc_0iz/ante.in.mol2);
atoms read (25), bonds read (24).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 102; net charge: -1`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for DdHyd_PSI.opt.chains.pdb_C SES surface #2.3: minimum,
-22.19, mean -4.05, maximum 8.43
Coulombic values for DdHyd_PSI.opt.chains.pdb_D SES surface #2.4: minimum,
-10.22, mean 2.11, maximum 15.27
Coulombic values for DdHyd_PSI.opt.chains.pdb_E SES surface #2.5: minimum,
-11.34, mean 1.57, maximum 12.31
Coulombic values for DdHyd_PSI.opt.chains.pdb_F SES surface #2.6: minimum,
-23.25, mean -3.85, maximum 11.53
To also show corresponding color key, enter the above coulombic command and
add key true
> view name coulSide
> select #2/A-B &protein
23092 atoms, 23503 bonds, 1476 residues, 1 model selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CYF (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -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
(CYF) ``
(CYF) `Welcome to antechamber 20.0: molecular input file processor.`
(CYF) ``
(CYF) `Info: Finished reading file
(/var/folders/ff/pgct52s94yngsgq2dx2fmynr0000gn/T/tmplhn52lb6/ante.in.mol2);
atoms read (22), bonds read (21).`
(CYF) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CYF) `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`
(CYF) ``
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CYF) `Info: Total number of electrons: 94; net charge: -1`
(CYF) ``
(CYF) `Running: /Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(CYF) ``
(CYF) `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`
(CYF) ``
(CYF) `Running:
/Applications/ChimeraX-1.10.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CYF) ``
Charges for residue CYF determined
Coulombic values for DdHyd_PSI.opt.chains.pdb_A SES surface #2.7: minimum,
-12.58, mean -0.47, maximum 17.74
Coulombic values for DdHyd_PSI.opt.chains.pdb_B SES surface #2.8: minimum,
-15.68, mean -0.16, maximum 13.13
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #2.6 models
> combine #5
> hide #!2 models
> select #6/L:CMO,CYN,PDT,FE2:424
23 atoms, 20 bonds, 4 pseudobonds, 8 residues, 2 models selected
> hide sel atoms
> show sel atoms
> select #6 &~/L:CMO,CYN,PDT,FE2:424
8705 atoms, 7722 bonds, 29 pseudobonds, 2164 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> show #!2 models
> align #6/L:424@FE4,S3,FE1,S2,S1,FE2,S4,FE3 toAtoms
> #2/F:2244@F4,S3,F1,S2,S1,F2,S4,F3
RMSD between 8 atom pairs is 0.065 angstroms
> select #2/F:CYF
120 atoms, 108 bonds, 12 residues, 1 model selected
> show sel atoms
> select #2/F:CYF &H
48 atoms, 12 residues, 1 model selected
> hide sel atoms
> select #2/F:SF4
24 atoms, 54 pseudobonds, 3 residues, 2 models selected
> style sel ball
Changed 24 atom styles
> select #6:SF4
8 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #2/F:SF4
24 atoms, 54 pseudobonds, 3 residues, 2 models selected
> style sel sphere
Changed 24 atom styles
> select #6
23 atoms, 20 bonds, 4 pseudobonds, 8 residues, 2 models selected
> ui tool show "Color Actions"
> color sel maroon
> color sel byhetero
> style sel sphere
Changed 23 atom styles
> show #2.6 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> show #2.3 models
> show #2.4 models
> show #2.5 models
> save "/Users/drornoy/Dropbox/2024 NSF BSF Dror iron
> sulfu/Resubmission2025/Models and structures/PSI-DdHyd design coulombic
> surfs.cxs"
> close #1
> close #4
> rename #6 "Catalytic Site"
> ui tool show Matchmaker
> close #3
> matchmaker #5/L to #2/F pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5),
sequence alignment score = 1795.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #2/F,
1hfe #5/L
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs:
2.105)
> matchmaker #5/L to #2/F pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5),
sequence alignment score = 1795.1
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: DdHyd_PSI.opt.chains.pdb #2/F,
1hfe #5/L
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs:
2.105)
> hide #2.3 models
> show #2.3 models
> hide #2.6 models
> hide #2.7 models
> hide #2.8 models
> show #2.8 models
> show #2.7 models
> show #!5 models
> select #2/F:1812
20 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/F:1812-1820 #5/L:51-56
164 atoms, 166 bonds, 15 residues, 2 models selected
MatchMaker Alignment [ID: 2] region chain F..chain L [51-59] RMSD: 2.042
> select #2/F:1766
21 atoms, 20 bonds, 1 residue, 1 model selected
> select #2/F:1766-1773 #5/L:3-12
213 atoms, 212 bonds, 18 residues, 2 models selected
MatchMaker Alignment [ID: 2] region chain F..chain L [3-12] RMSD: 8.370
> hide #!5 models
> show #2.6 models
> hide #2.6 models
> select clear
> select #5/L:389
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:389-391
22 atoms, 22 bonds, 3 residues, 1 model selected
> select #2/F:2149
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/F:2149-2152
28 atoms, 27 bonds, 4 residues, 1 model selected
> select #2/F:2152
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/F:2152-2153
22 atoms, 21 bonds, 2 residues, 1 model selected
> select #2/F:2152
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/F:2152-2155
50 atoms, 50 bonds, 4 residues, 1 model selected
> select #2/F:2152
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/F:2152-2156
65 atoms, 65 bonds, 5 residues, 1 model selected
> show #!5 models
> ui tool show Matchmaker
> matchmaker #5/L to #2/F pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 1hfe, chain L (#5),
sequence alignment score = 1795.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb #2/F,
1hfe #5/L
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 374 pruned atom pairs is 0.505 angstroms; (across all 390 pairs:
2.105)
> save "/Users/drornoy/OneDrive - Migal/ISF-DFG/PSI-DdHyd design.cxs"
——— End of log from Wed Sep 17 15:57:48 2025 ———
> view name session-start
opened ChimeraX session
> hide #!5 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select clear
> select #5/L:2-3
17 atoms, 16 bonds, 2 residues, 1 model selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> select #5/L:389
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/L:389-391
22 atoms, 22 bonds, 3 residues, 1 model selected
> show #!5 models
> select #2/F:2153
15 atoms, 14 bonds, 1 residue, 1 model selected
> select #2/F:2153-2158
96 atoms, 97 bonds, 6 residues, 1 model selected
> select #5/L:388-389
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/L:389-398
63 atoms, 64 bonds, 10 residues, 1 model selected
> open 3lx4
Summary of feedback from opening 3lx4 fetched from pdb
---
note | Fetching compressed mmCIF 3lx4 from http://files.rcsb.org/download/3lx4.cif
3lx4 title:
Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of
HydA(deltaEFG) [more info...]
Chain information for 3lx4 #1
---
Chain | Description | UniProt
A B | Fe-hydrogenase | Q9FYU1_CHLRE 17-457
Non-standard residues in 3lx4 #1
---
ACT — acetate ion
CL — chloride ion
SF4 — iron/sulfur cluster
3lx4 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains.pdb, chain F (#2) with 3lx4, chain B (#1),
sequence alignment score = 861.9
RMSD between 264 pruned atom pairs is 1.082 angstroms; (across all 356 pairs:
3.848)
> hide #2.8 models
> hide #2.7 models
> show #2.6 models
> hide #2.6 models
> show #2.7 models
> hide #2.7 models
> hide #2.3 models
> hide #2.4 models
> hide #2.5 models
> show #2.6 models
> hide #2.6 models
> show #2.5 models
> show #2.4 models
> show #2.3 models
> hide #2.3 models
> show #2.7 models
> show #2.8 models
> hide #!2 models
> hide #!5 models
> show #!2 models
> hide #!2 models
> select #1/A
3460 atoms, 3157 bonds, 7 pseudobonds, 774 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> show #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/S #5/T
Alignment identifier is 2
> select clear
[Repeated 1 time(s)]
> show #!5 models
> hide #!2 models
> hide #!1 models
> select clear
[Repeated 1 time(s)]
> select #5/S-T:38
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/S-T:38-45
140 atoms, 140 bonds, 16 residues, 1 model selected
> select #5/S-T:46
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #5/S-T:46-51
100 atoms, 100 bonds, 12 residues, 1 model selected
> select #5/S-T:38
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #5/S-T:38-45
140 atoms, 140 bonds, 16 residues, 1 model selected
> select #5/L:2-14
115 atoms, 116 bonds, 13 residues, 1 model selected
> select #5/L:2-14,31-34,53-57
183 atoms, 183 bonds, 22 residues, 1 model selected
> select #5/L:2-14,31-34,53-57,388-397
254 atoms, 255 bonds, 32 residues, 1 model selected
> ui tool show "Color Actions"
> color sel alice blue
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel pale turquoise
> color sel light steel blue
> color sel pale turquoise
> color sel wheat
> color sel gainsboro
> color sel powder blue
> color sel pale turquoise
> color sel byhetero
> show #!2 models
> hide #!2 models
> show #!2 models
> select #5/L:2-14,31-34,53-57,388-397/S:36-42
316 atoms, 317 bonds, 39 residues, 1 model selected
> select #5/L:2-14,31-34,53-57,388-397/S:36-41
304 atoms, 304 bonds, 38 residues, 1 model selected
> hide #!5 models
> save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking
> design.cxs"
> close #1
> rename #1 id 1
> rename #2 id 1
> rename #1 id 2
> help help:user
> rename #2#6 id #1
> rename #1 DdHyd_PSI
> rename #5 id #2
> show #!1.2 models
> combine #1 copy t
Expected a keyword
> combine #1
Associated combination chain F to chain F with 0 mismatches
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb
#1.1/F, 1hfe #2/L, combination #3/F
> hide #3.1 models
> show #3.1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> hide #3.1 models
> hide #3.2 models
> help help:user
[Repeated 1 time(s)]
> split #3 chains
Split combination (#3) into 7 models
Chain information for combination A #3.1
---
Chain | Description
A | No description available
Chain information for combination B #3.2
---
Chain | Description
B | No description available
Chain information for combination C #3.3
---
Chain | Description
C | No description available
Chain information for combination D #3.4
---
Chain | Description
D | No description available
Chain information for combination E #3.5
---
Chain | Description
E | No description available
Chain information for combination F #3.6
---
Chain | Description
F | No description available
Associated combination F (3.6) chain F to chain F with 0 mismatches
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains.pdb
#1.1/F, 1hfe #2/L, combination F #3.6/F
> hide #!3.1 models
> hide #3.2 models
> hide #!3.3 models
> hide #3.4 models
> hide #3.5 models
> show #!1 models
> select #3.1-3.3
Nothing selected
> select #3.1
11587 atoms, 11778 bonds, 18 pseudobonds, 744 residues, 2 models selected
> select #3.1#3.2
23100 atoms, 23503 bonds, 18 pseudobonds, 1477 residues, 3 models selected
> rename #3.1#3.2#3.3#3.4#3.5 id #4
> show #1.1.3 models
> hide #1.1.3 models
> select #1/F
7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected
> select #1.1/F
7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1.1/F
7173 atoms, 7242 bonds, 54 pseudobonds, 476 residues, 2 models selected
> delete atoms (#!1.1 & sel)
Chains used in RMSD evaluation for alignment 1: 1hfe #2/L, combination F
#3.6/F
> delete bonds (#!1.1 & sel)
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> show #!1.1 models
> close #1.2
> rename #1.1 id #1
> rename #1.1 id 1
> combine #1.1
> hide #!4 models
> hide #!1 models
> close #5
> show #!1 models
> hide #!1.1 models
> show #!1.1 models
> rename #1 PSI
> rename #1.1 "DdHyd_PSI.opt.chains no DdHyd"
> rename #2 id 6
> show #!4 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> show #!4.1 models
> show #4.2 models
> show #!4.3 models
> show #4.4 models
> show #4.5 models
> close #4
> show #!1 models
> rename #3.6 DdHyd_PSI.opt.chains
> rename #3.7 "Catalytic site"
> rename #3 id 2
> rename #6 id 3
> rename #2 DdHyd_PSI
> hide #!1 models
> show #!3 models
> open 9gbu 9gnk
Summary of feedback from opening 9gbu fetched from pdb
---
warnings | Atom HS2 is not in the residue template for 402 /A:505
Atom HS2 is not in the residue template for 402 /B:504
notes | Fetching compressed mmCIF 9gbu from http://files.rcsb.org/download/9gbu.cif
Fetching CCD MPD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif
Summary of feedback from opening 9gnk fetched from pdb
---
warnings | Atom HS2 is not in the residue template for 402 /A:502
Atom H3 is not in the residue template for PG4 /A:512
notes | Fetching compressed mmCIF 9gnk from http://files.rcsb.org/download/9gnk.cif
Fetching CCD EPE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/EPE/EPE.cif
Fetching CCD PG4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PG4/PG4.cif
9gbu title:
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 [more info...]
Chain information for 9gbu #4
---
Chain | Description | UniProt
A B | Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit | PHFL_NITV2 1-389, PHFS_NITV2 403-480
Non-standard residues in 9gbu #4
---
402 — dicarbonyl[bis(cyanide-
kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
MPD — (4S)-2-methyl-2,4-pentanediol
SF4 — iron/sulfur cluster
9gbu mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
166 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
9gnk title:
Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits
linked by a 13 amino acid linker peptide derived from CpI of Clostridium
pasteurianum [more info...]
Chain information for 9gnk #5
---
Chain | Description | UniProt
A | Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit | PHFL_NITV2 1-390, PHFS_NITV2 404-482
Non-standard residues in 9gnk #5
---
402 — dicarbonyl[bis(cyanide-
kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
CMO — carbon monoxide
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
SF4 — iron/sulfur cluster
9gnk mmCIF Assemblies
---
1| author_defined_assembly
200 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Associated 9gbu chain A to chain L with 31 mismatches
Associated 9gbu chain B to chain L with 31 mismatches
Associated 9gnk chain A to chain L with 29 mismatches
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains #2.6/F,
1hfe #3/L, 9gbu #4/B, 9gnk #5/A
> hide #!4 models
> show #!4 models
> hide #!5 models
> select #4/B
7543 atoms, 7548 bonds, 24 pseudobonds, 577 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show #!5 models
> matchmaker #!4-5 to #2.6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 9gbu, chain A (#4),
sequence alignment score = 2182.6
RMSD between 454 pruned atom pairs is 0.553 angstroms; (across all 469 pairs:
1.405)
Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 9gnk, chain A (#5),
sequence alignment score = 2184.3
RMSD between 453 pruned atom pairs is 0.534 angstroms; (across all 470 pairs:
1.482)
Chains used in RMSD evaluation for alignment 1: DdHyd_PSI.opt.chains #2.6/F,
1hfe #3/L, 9gbu #4/A, 9gnk #5/A
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select add #3
16271 atoms, 15290 bonds, 63 pseudobonds, 2749 residues, 4 models selected
> select add #4
23871 atoms, 22854 bonds, 87 pseudobonds, 3365 residues, 4 models selected
> select subtract #4
8728 atoms, 7742 bonds, 39 pseudobonds, 2172 residues, 2 models selected
> select subtract #3
Nothing selected
> select add #5
8157 atoms, 7706 bonds, 24 pseudobonds, 1040 residues, 2 models selected
> hide #!4 models
> hide #!3 models
> hide #!2 models
> color sel sandy brown
> color sel byhetero
> show #!4 models
> show #!3 models
> show #!2 models
> color sel dark khaki
> color sel plum
> color sel byhetero
> select subtract #5
Nothing selected
> hide #!4 models
> hide #!3 models
> hide #!2 models
> select :4O2
Nothing selected
> select :402
64 atoms, 61 bonds, 4 residues, 3 models selected
> select #5:402
22 atoms, 21 bonds, 1 residue, 1 model selected
> select ::name="402"
72 atoms, 48 bonds, 33 pseudobonds, 3 residues, 4 models selected
> select :EPE,PEG,PG4,MPD
290 atoms, 278 bonds, 13 residues, 2 models selected
> hide sel & #!5 atoms
> select :EPE,PEG,PG4,MPD,HOH
2233 atoms, 278 bonds, 1956 residues, 3 models selected
> hide sel & #!5 atoms
> show #!4 models
> show #!2 models
> hide #!2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> sequence chain #4/A #4/B
Alignment identifier is 3
> select #5/A:400
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/A:388
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #5/A:388-400
209 atoms, 210 bonds, 13 residues, 1 model selected
> select #5/A:390
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #5/A:390-399
166 atoms, 166 bonds, 10 residues, 1 model selected
> select #4/A-B:402
22 atoms, 20 bonds, 2 residues, 1 model selected
> select #4/A-B:390-402
440 atoms, 442 bonds, 26 residues, 1 model selected
> select #5/A:404-405
36 atoms, 35 bonds, 2 residues, 1 model selected
> select #5/A:390-405
277 atoms, 277 bonds, 16 residues, 1 model selected
> select #5/A:390-391
32 atoms, 31 bonds, 2 residues, 1 model selected
> select #5/A:390-404
253 atoms, 253 bonds, 15 residues, 1 model selected
> select #5/A:390-404#4/A:390-402
473 atoms, 474 bonds, 28 residues, 2 models selected
> show #!2 models
> select #4/A:390-402
220 atoms, 221 bonds, 13 residues, 1 model selected
> color sel sea green
> select #5/A:390-404
253 atoms, 253 bonds, 15 residues, 1 model selected
> color sel purple
> show #!3 models
> save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking
> design.cxs"
——— End of log from Wed Oct 22 18:27:07 2025 ———
> view name session-start
opened ChimeraX session
> open "/Users/drornoy/Google
> Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_model_0.cif"
Chain information for fold_ddhyab_model_0.cif #6
---
Chain | Description
A | .
Associated fold_ddhyab_model_0.cif chain A to chain L with 27 mismatches
Computing secondary structure
> hide #!5 models
> hide #!4 models
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #6 to #2.6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with fold_ddhyab_model_0.cif,
chain A (#6), sequence alignment score = 2224.5
RMSD between 456 pruned atom pairs is 0.436 angstroms; (across all 470 pairs:
1.221)
> ui tool show "AlphaFold Error Plot"
> alphafold pae #6 file "/Users/drornoy/Google
> Drive/ISF_DFG_project/Structures/fold_ddhyab/fold_ddhyab_full_data_0.json"
> color bfactor #6 palette alphafold
3649 atoms, 474 residues, atom bfactor range 50.4 to 99
> hide #!3 models
> show #!5 models
> show #!4 models
> show #!2 models
> show #!1 models
> hide #!1 models
> save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/PSI docking
> design.cxs"
——— End of log from Wed Oct 22 19:01:49 2025 ———
> view name session-start
opened ChimeraX session
> hide #!5 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> hide #6 models
> show #!1 models
> show #!2 models
> close #6
> select add #5
8157 atoms, 7706 bonds, 24 pseudobonds, 1040 residues, 2 models selected
> select subtract #5
Nothing selected
> help help:user
> rename #5 id 9
> rename #4 id 8
> rename #3 id 7
> save "/Users/drornoy/OneDrive - Migal/ISF-DFG/Structures and
> designs/PSI_DdH2ase dock design with all single chains variants.cxs"
> open "/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"
Chain information for fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif
#3
---
Chain | Description
A | .
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to
chain L with 25 mismatches
Computing secondary structure
> hide #!1 models
> hide #!7 models
> ui tool show Matchmaker
> matchmaker #3 to #2.6 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
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
Alignment identifier is 4
Showing conservation header ("seq_conservation" residue attribute) for
alignment 4
Hiding conservation header for alignment 4
Chains 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
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 4
RMSD between 456 pruned atom pairs is 0.422 angstroms; (across all 470 pairs:
1.377)
> ui tool show "AlphaFold Error Plot"
> alphafold pae #3 file "/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"
> color bfactor #3 palette alphafold
3677 atoms, 477 residues, atom bfactor range 44.8 to 99
> select add #3
3677 atoms, 3770 bonds, 477 residues, 1 model selected
> color sel byhetero
> select subtract #3
Nothing selected
> show #!7 models
> show #!8 models
> hide #!7 models
> hide #!8 models
> open 3lx4
3lx4 title:
Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of
HydA(deltaEFG) [more info...]
Chain information for 3lx4 #4
---
Chain | Description | UniProt
A B | Fe-hydrogenase | Q9FYU1_CHLRE 17-457
Non-standard residues in 3lx4 #4
---
ACT — acetate ion
CL — chloride ion
SF4 — iron/sulfur cluster
3lx4 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
32 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select :SF4
192 atoms, 216 bonds, 108 pseudobonds, 24 residues, 9 models selected
> ui tool show Matchmaker
> matchmaker #4/A to #2.6/F pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with 3lx4, chain A (#4),
sequence alignment score = 854.7
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: DdHyd_PSI.opt.chains #2.6/F,
3lx4 #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 265 pruned atom pairs is 1.087 angstroms; (across all 356 pairs:
3.844)
> rename #4 "CrHydA1 3lx4"
> rename #7 "DdHydAHydB 1hfe"
> select #3/B
Nothing selected
> select #4/B
3507 atoms, 3157 bonds, 7 pseudobonds, 821 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> close #8
> close #9
> show #!7 models
> hide #!7 models
> rename #7 id 5
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures
> and designs/PSI_DdH2ase dock design with all single chains variants.cxs"
> open 8ru6
Summary of feedback from opening 8ru6 fetched from pdb
---
warning | Atom HS1 is not in the residue template for MHX /B:508
8ru6 title:
Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits
linked by a 4 amino acid linker peptide derived from CpI of Clostridium
pasteurianum [more info...]
Chain information for 8ru6 #6
---
Chain | Description | UniProt
B | Periplasmic [Fe] hydrogenase large subunit,CpI,Periplasmic [Fe] hydrogenase small subunit | PHFL_DESVH 1-392, PHF1_CLOPA 393-396, PHFS_DESVH 397-481
Non-standard residues in 8ru6 #6
---
MHX — Binuclear [FeFe], di(thiomethyl)amine, carbon monoxide, cyanide cluster
(-CO form)
PG4 — tetraethylene glycol
SF4 — iron/sulfur cluster
147 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Associated 8ru6 chain B to chain L with 25 mismatches
> hide #!4 models
> hide #3 models
> hide #!2 models
> show #!2 models
> show #3 models
> show #!4 models
> ui tool show Matchmaker
> matchmaker #6/B to #3/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A
(#3) with 8ru6, chain B (#6), sequence alignment score = 2480.9
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3:
fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, 8ru6 #6/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 471 pruned atom pairs is 0.353 angstroms; (across all 475 pairs:
0.476)
> hide #!2 models
> hide #3 models
> show #!5 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!4 models
> hide #!5 models
> rename #6 "DdHydAB_L1 8ru6"
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures
> and designs/PSI_DdH2ase dock design with all single chains variants.cxs"
> open 9gnk
Summary of feedback from opening 9gnk fetched from pdb
---
warnings | Atom HS2 is not in the residue template for 402 /A:502
Atom H3 is not in the residue template for PG4 /A:512
9gnk title:
Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits
linked by a 13 amino acid linker peptide derived from CpI of Clostridium
pasteurianum [more info...]
Chain information for 9gnk #7
---
Chain | Description | UniProt
A | Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit | PHFL_NITV2 1-390, PHFS_NITV2 404-482
Non-standard residues in 9gnk #7
---
402 — dicarbonyl[bis(cyanide-
kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
CMO — carbon monoxide
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
PEG — di(hydroxyethyl)ether
PG4 — tetraethylene glycol
SF4 — iron/sulfur cluster
9gnk mmCIF Assemblies
---
1| author_defined_assembly
200 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Associated 9gnk chain A to chain L with 29 mismatches
> ui tool show Matchmaker
> matchmaker #7/A to #3/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A
(#3) with 9gnk, chain A (#7), sequence alignment score = 2461.4
Alignment identifier is 5
Showing conservation header ("seq_conservation" residue attribute) for
alignment 5
Hiding conservation header for alignment 5
Chains used in RMSD evaluation for alignment 5:
fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, 9gnk #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 5
RMSD between 469 pruned atom pairs is 0.373 angstroms; (across all 476 pairs:
0.928)
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures
> and designs/PSI_DdH2ase dock design with all single chains variants.cxs"
> open 9gbu
Summary of feedback from opening 9gbu fetched from pdb
---
warnings | Atom HS2 is not in the residue template for 402 /A:505
Atom HS2 is not in the residue template for 402 /B:504
9gbu title:
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 [more info...]
Chain information for 9gbu #8
---
Chain | Description | UniProt
A B | Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit | PHFL_NITV2 1-389, PHFS_NITV2 403-480
Non-standard residues in 9gbu #8
---
402 — dicarbonyl[bis(cyanide-
kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
MPD — (4S)-2-methyl-2,4-pentanediol
SF4 — iron/sulfur cluster
9gbu mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
166 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Associated 9gbu chain A to chain L with 31 mismatches
Associated 9gbu chain B to chain L with 31 mismatches
> matchmaker #6/B to #3/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
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
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6:
fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, DdHydAB_L1 8ru6
#6/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 471 pruned atom pairs is 0.353 angstroms; (across all 475 pairs:
0.476)
> matchmaker #8/A to #3/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif, chain A
(#3) with 9gbu, chain A (#8), sequence alignment score = 2453.1
Alignment identifier is 6
Showing conservation header ("seq_conservation" residue attribute) for
alignment 6
Hiding conservation header for alignment 6
Chains used in RMSD evaluation for alignment 6:
fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, 9gbu #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 6
RMSD between 469 pruned atom pairs is 0.356 angstroms; (across all 475 pairs:
0.810)
> select #8/B
7543 atoms, 7548 bonds, 24 pseudobonds, 577 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide #!7 models
> hide #!6 models
> hide #!8 models
> show #!8 models
> show #!7 models
> rename #7 "DdHydAB_L2 9gnk"
> rename #8 "DdHydAB_L3 9gbu"
> select :PG4
179 atoms, 172 bonds, 7 residues, 2 models selected
> hide sel & #!7 atoms
> select :MPD
132 atoms, 126 bonds, 6 residues, 1 model selected
> hide sel atoms
> select :HOH
3198 atoms, 3198 residues, 5 models selected
> hide sel & #!7-8 atoms
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures
> and designs/PSI_DdH2ase dock design with all single chains variants.cxs"
> show #!6 models
> ui tool show "Color Actions"
> select #8
15143 atoms, 15112 bonds, 48 pseudobonds, 1193 residues, 2 models selected
> show #!4 models
> color sel plum
> color sel byhetero
> color sel magenta
> color sel byhetero
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures
> and designs/PSI_DdH2ase dock design with all single chains variants.cxs"
> select :PG4
179 atoms, 172 bonds, 7 residues, 2 models selected
> hide sel atoms
> select :PG4,HOH
3377 atoms, 172 bonds, 3205 residues, 5 models selected
> hide sel & #!4,6-8 atoms
> ui tool show Matchmaker
> matchmaker #4/A to #3/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
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
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, CrHydA1 3lx4
#4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 268 pruned atom pairs is 1.062 angstroms; (across all 361 pairs:
3.707)
> matchmaker #4/A to #3/A pairing ss showAlignment true
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
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
Alignment identifier is 7
Showing conservation header ("seq_conservation" residue attribute) for
alignment 7
Hiding conservation header for alignment 7
Chains used in RMSD evaluation for alignment 7:
fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif #3/A, CrHydA1 3lx4
#4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 7
RMSD between 268 pruned atom pairs is 1.062 angstroms; (across all 361 pairs:
3.707)
> select #3/A:392
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:392-393 #4/A:391-392
30 atoms, 28 bonds, 4 residues, 2 models selected
MatchMaker Alignment [ID: 7] region chain A..chain A [451-452] RMSD: 1.147
> select clear
> help help:user
> view name All_H2ases
> select #3/A:392
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:392-393 #4/A:391-392
30 atoms, 28 bonds, 4 residues, 2 models selected
MatchMaker Alignment [ID: 2] region chain A..chain A [451-452] RMSD: 1.147
> view All_H2ases
> show #!2 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures
> and designs/PSI_DdH2ase dock design with all single chains variants.cxs"
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!4 models
> select clear
> select #2.6/F:2153-2156 #3/A:389-395
112 atoms, 112 bonds, 11 residues, 2 models selected
MatchMaker Alignment [ID: 4] region chain F..chain A [392-398] RMSD: 7.546
> show #!1 models
> show #1.1.3 models
> hide #1.1.3 models
> show #!6 models
> show #!7 models
> show #!8 models
> view name PsaC_interface
> save "/Users/drornoy/Library/CloudStorage/OneDrive-Migal/ISF-DFG/Structures
> and designs/PSI_DdH2ase dock design with all single chains variants.cxs"
——— End of log from Wed Oct 29 10:26:11 2025 ———
> view name session-start
opened ChimeraX session
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!1.1 models
> show #!1.1 models
> hide #!2 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!1 models
> open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif"
Chain information for HydAB_TD_linker_model.cif #9
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
Associated HydAB_TD_linker_model.cif chain A to chain L with 25 mismatches
Associated HydAB_TD_linker_model.cif chain A to chain A with 0 mismatches
[Repeated 4 time(s)]Computing secondary structure
> rename #9 HydAB_TD_linker_model_MSA.cif
> open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_model.cif"
Chain information for HydAB_TD_linker_model.cif #10
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
Associated HydAB_TD_linker_model.cif chain A to chain L with 25 mismatches
Associated HydAB_TD_linker_model.cif chain A to chain A with 0 mismatches
[Repeated 4 time(s)]Computing secondary structure
> rename #10 HydAB_TD_linker_model_noMSA.cif
> ui tool show AlphaFold
> ui tool show "AlphaFold Error Plot"
> alphafold pae #9 file "/Users/drornoy/Library/CloudStorage/OneDrive-
> SharedLibraries-Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json"
> color bfactor #9 palette alphafold
3720 atoms, 481 residues, atom bfactor range 41.5 to 99
> ui tool show "AlphaFold Error Plot"
> alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-
> SharedLibraries-Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json"
> color bfactor #10 palette alphafold
3720 atoms, 481 residues, atom bfactor range 13.2 to 97
> ui tool show "AlphaFold Error Plot"
> alphafold pae #9 file "/Users/drornoy/Library/CloudStorage/OneDrive-
> SharedLibraries-Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_TD_linker/HydAB_TD_linker_confidences.json"
> color bfactor #9 palette alphafold
3720 atoms, 481 residues, atom bfactor range 41.5 to 99
> color bfactor #9 palette alphafold
3720 atoms, 481 residues, atom bfactor range 41.5 to 99
> ui tool show Matchmaker
> matchmaker #!9-10 to #2.6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with
HydAB_TD_linker_model_MSA.cif, chain A (#9), sequence alignment score = 2218.3
RMSD between 458 pruned atom pairs is 0.496 angstroms; (across all 470 pairs:
1.251)
Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with
HydAB_TD_linker_model_noMSA.cif, chain A (#10), sequence alignment score =
1834.3
RMSD between 35 pruned atom pairs is 1.452 angstroms; (across all 470 pairs:
19.133)
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select add #9
3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected
> select add #10
7552 atoms, 7744 bonds, 22 pseudobonds, 973 residues, 6 models selected
> select subtract #10
3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected
> select subtract #9
112 atoms, 112 bonds, 11 residues, 2 models selected
> hide #3 models
> hide #!9 models
> select add #9
3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected
> select add #10
7552 atoms, 7744 bonds, 22 pseudobonds, 973 residues, 6 models selected
> color sel & #!10 byhetero
> show #!9 models
> color sel & #!9-10 byhetero
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!5 models
> hide #!5 models
> select subtract #9
3832 atoms, 3928 bonds, 11 pseudobonds, 492 residues, 4 models selected
> show #!9 models
> select subtract #10
112 atoms, 112 bonds, 11 residues, 2 models selected
> hide #!10 models
> show #3 models
> select add #3
3735 atoms, 3828 bonds, 481 residues, 2 models selected
> select subtract #3
58 atoms, 58 bonds, 4 residues, 1 model selected
> hide #3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #3 models
> view list
Named views: All_H2ases, PsaC_interface, coulSide, session-start, viewH2ase,
viewH2aseHbonds, zoom1, zoom2
> view zoom1
> view zoom2
> select #9:392-393
15 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 15 atom styles
> style sel stick
Changed 15 atom styles
> ui tool show "Selection Inspector"
> setattr sel r ribbon_hide_backbone false
Assigning ribbon_hide_backbone attribute to 2 items
> style sel sphere
Changed 15 atom styles
> style sel ball
Changed 15 atom styles
> style sel stick
Changed 15 atom styles
> ui tool show "Color Actions"
> color sel lime target cspf
> hide #3 models
> view name linkerZoom
> show #!6 models
> select #6/B:392
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #6/B:392-398
123 atoms, 123 bonds, 7 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime target cspf
> select #9:392-393
15 atoms, 14 bonds, 2 residues, 1 model selected
> show #!7 models
> select #7/A:391
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #7/A:391-398
134 atoms, 134 bonds, 8 residues, 1 model selected
> select #7/A:397-398
37 atoms, 36 bonds, 2 residues, 1 model selected
> select #7/A:391-398
134 atoms, 134 bonds, 8 residues, 1 model selected
> select #7/A:399-400
28 atoms, 27 bonds, 2 residues, 1 model selected
> select #7/A:391-400
162 atoms, 162 bonds, 10 residues, 1 model selected
> color sel lime target cspf
> show #!8 models
> select #8/A:390
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #8/A:390-400
194 atoms, 195 bonds, 11 residues, 1 model selected
> select #8/A:390
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402
469 atoms, 470 bonds, 43 residues, 4 models selected
MatchMaker Alignment [ID: 6] region chain A..chain A [390-402] RMSD: 30.556
> select #3/A:399 #9/A:399 #10/A:399
24 atoms, 21 bonds, 3 residues, 3 models selected
> select #3/A:399-400 #9/A:399-400 #10/A:399-400
57 atoms, 54 bonds, 6 residues, 3 models selected
MatchMaker Alignment [ID: 6] region chain A [402-403] RMSD: 34.950
> select #8/A:390
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402
469 atoms, 470 bonds, 43 residues, 4 models selected
MatchMaker Alignment [ID: 6] region chain A..chain A [390-402] RMSD: 30.556
> select #8/A:390
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #3/A:390-399 #9/A:390-399 #10/A:390-399 #8/A:390-402
469 atoms, 470 bonds, 43 residues, 4 models selected
MatchMaker Alignment [ID: 6] region chain A..chain A [390-402] RMSD: 30.556
> select #8/A:390
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #8/A:390-400
194 atoms, 195 bonds, 11 residues, 1 model selected
> select #8:390-399
344 atoms, 346 bonds, 20 residues, 1 model selected
> hide #!6 models
> hide #!7 models
> select #8:390-402
440 atoms, 442 bonds, 26 residues, 1 model selected
> color sel lime target cspf
> select #3/A:392 #9/A:392 #10/A:392
21 atoms, 18 bonds, 3 residues, 3 models selected
> select #3/A:392-393 #9/A:392-393 #10/A:392-393 #8/A:395-396
78 atoms, 74 bonds, 8 residues, 4 models selected
MatchMaker Alignment [ID: 6] region chain A..chain A [395-396] RMSD: 30.689
> select #8/A:392
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #8/A:392-396
88 atoms, 88 bonds, 5 residues, 1 model selected
> rename #10 id 11
> open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif"
Chain information for HydAB_PSI_Interface_model.cif #10
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
Associated HydAB_PSI_Interface_model.cif chain A to chain F with 0 mismatches
[Repeated 1 time(s)]Computing secondary structure
> rename #10 HydAB_PSI_Interface_model_MSA.cif
> open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_model.cif"
Chain information for HydAB_PSI_Interface_model.cif #12
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
Associated HydAB_PSI_Interface_model.cif chain A to chain F with 0 mismatches
[Repeated 1 time(s)]Computing secondary structure
> hide #!12 models
> show #!12 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-
> SharedLibraries-Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json"
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
This 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.
> alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-
> SharedLibraries-Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json"
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
This 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.
> alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-
> SharedLibraries-Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json"
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
This 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.
> alphafold pae #10 file "/Users/drornoy/Library/CloudStorage/OneDrive-
> SharedLibraries-Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_summary_confidences.json"
JSON file "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
Migal/Dror Noy Group -
General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_summary_confidences.json"
is not AlphaFold predicted aligned error data, expected a top level list
> alphafold pae #10 file "/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"
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
This 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.
> alphafold pae #12 file "/Users/drornoy/Library/CloudStorage/OneDrive-
> SharedLibraries-Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/No_MSA/HydAB_PSI_Interface/HydAB_PSI_Interface_confidences.json"
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
This 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.
> ui tool show Matchmaker
> matchmaker #!10,12 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
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
RMSD between 455 pruned atom pairs is 0.339 angstroms; (across all 470 pairs:
1.307)
Matchmaker HydAB_TD_linker_model_MSA.cif, chain A (#9) with
HydAB_PSI_Interface_model.cif, chain A (#12), sequence alignment score =
1931.8
RMSD between 100 pruned atom pairs is 0.836 angstroms; (across all 470 pairs:
23.291)
> hide #!12 models
> show #3 models
> hide #3 models
> hide #!8 models
> hide #!9 models
> select #10:cys
36 atoms, 30 bonds, 6 residues, 1 model selected
> select #10:cys,unk
84 atoms, 67 bonds, 18 residues, 1 model selected
> show sel atoms
> select #10:unk
48 atoms, 36 bonds, 12 residues, 1 model selected
> color sel orange
> color sel yellow
> save "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB
> PSI.cxs"
——— End of log from Wed Nov 5 11:09:20 2025 ———
> view name session-start
opened ChimeraX session
> hide #!10 models
> show #!9 models
> show #!8 models
> show #!4 models
> hide #!4 models
> show #!6 models
> hide #!6 models
> show #!7 models
> rename #12 id 16
> rename #11 id 15
> rename #10 id 14
> rename #9 id 11
> open 8ryh
Summary of feedback from opening 8ryh fetched from pdb
---
warning | Atom HS2 is not in the residue template for 402 /A:504
8ryh title:
Desulfovibrio desulfuricans [FeFe]-hydrogenase variant with both subunits
linked by a linker peptide derived from a group A1 type [FeFe]-hydrogenase of
Veillonella atypica [more info...]
Chain information for 8ryh #9
---
Chain | Description | UniProt
A | Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit | PHFL_DESVH 1-389, PHFS_DESVH 403-480
Non-standard residues in 8ryh #9
---
402 — dicarbonyl[bis(cyanide-
kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
SF4 — iron/sulfur cluster
41 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Associated 8ryh chain A to chain L with 30 mismatches
Associated 8ryh chain A to chain A with 7 mismatches
> rename #9 "DdHydAB_L4 8ryh"
> ui tool show Matchmaker
> matchmaker #!9 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHydAB_L3 9gbu, chain A (#8) with DdHydAB_L4 8ryh, chain A (#9),
sequence alignment score = 2520.8
RMSD between 468 pruned atom pairs is 0.433 angstroms; (across all 469 pairs:
0.443)
> open "/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"
Chain information for hHydAB_L4_linker_PDB_8ryh_model.cif #10
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to chain L with 30
mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to chain A with 7
mismatches
Computing secondary structure
> ui tool show "AlphaFold Error Plot"
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> rename #3 id 13
> rename #11 id 3
> rename #3 id 11
> rename #5 id #3
> show #!2 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> show #!14 models
> hide #!2.7 models
> hide #2.6.1 models
> show #2.6.1 models
> rename #2 DdHyd_PSI_interface_opt
> rename #4 id #5
> rename #11 id #4
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> hide #!14 models
> select #2:2152-2156
65 atoms, 65 bonds, 5 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lime target cspf
> show #!5 models
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> select add #5
7032 atoms, 6379 bonds, 14 pseudobonds, 1600 residues, 5 models selected
> color sel light salmon
> color sel gainsboro
> color sel plum
> color sel & #!5 byhetero
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!3 models
> show #!4 models
> select #5:391-392
30 atoms, 28 bonds, 4 residues, 1 model selected
> color sel lime
> show sel atoms
> color sel plum target aspf
> color sel byhetero
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!2 models
> hide #!2 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> show #!9 models
> alphafold pae #10 file "/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"
> color bfactor #10 palette alphafold
3825 atoms, 494 residues, atom bfactor range 17.3 to 99
> ui tool show Matchmaker
> matchmaker #!10 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHydAB_L4 8ryh, chain A (#9) with
hHydAB_L4_linker_PDB_8ryh_model.cif, chain A (#10), sequence alignment score =
2532.7
RMSD between 468 pruned atom pairs is 0.400 angstroms; (across all 469 pairs:
0.426)
> select add #10
3855 atoms, 3954 bonds, 11 pseudobonds, 498 residues, 3 models selected
> color sel & #!10 byhetero
> select subtract #10
30 atoms, 28 bonds, 4 residues, 1 model selected
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> hide #!4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A #10/A
Alignment identifier is 1
> select #9/A:402 #10/A:402
15 atoms, 13 bonds, 2 residues, 2 models selected
> select #9/A:386-402 #10/A:386-402
270 atoms, 270 bonds, 1 pseudobond, 27 residues, 3 models selected
Periplasmic [Fe] Hydrogenase Large subunit,Periplasmic [Fe] Hydrogenase Small
Subunit [ID: 1] region 2 chains [386-402] RMSD: 1.363
> select #9/A:390 #10/A:390
35 atoms, 33 bonds, 2 residues, 2 models selected
> select #9/A:390-402 #10/A:390-402
201 atoms, 199 bonds, 1 pseudobond, 19 residues, 3 models selected
Periplasmic [Fe] Hydrogenase Large subunit,Periplasmic [Fe] Hydrogenase Small
Subunit [ID: 1] region 2 chains [390-402] RMSD: 1.756
> color sel lime target cspf
> show #!10 models
> select #10:390-402
102 atoms, 102 bonds, 13 residues, 1 model selected
> select clear
> hide #!9 models
> show #!16 models
> hide #!16 models
> show #!14 models
> hide #!10 models
> show #!10 models
> show #!4 models
> hide #!10 models
> show #!10 models
> show #!8 models
> hide #!14 models
> show #!7 models
> show #!6 models
> show #!5 models
> hide #!5 models
> save "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB
> PSI.cxs"
> toolshed show
Alignment identifier is 1.1/A
Alignment identifier is 1.1/B
Alignment identifier is 1.1/C
Alignment identifier is 1.1/D
Alignment identifier is 1.1/E
Alignment identifier is 2.6/F
Alignment identifier is 6/B
Alignment identifier is 7/A
Alignment identifier is 3
Alignment identifier is 5
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Alignment identifier is 11
> help help:user
> sequence align 16,4,5,6,7,8,9
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align #16/A,#4-9/A
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align /A
Alignment identifier is 1
Associated DdHyd_PSI.opt.chains no DdHyd (1.1) chain A to #1.1/A with 0
mismatches
Associated DdHyd_PSI.opt.chains (2.6) chain F to #16/A with 12 mismatches
Associated DdHydAB_L2 9gnk chain A to #7/A with 0 mismatches
Associated DdHydAB_L3 9gbu chain A to #8/A with 0 mismatches
Associated DdHydAB_L3 9gbu chain B to #8/A with 0 mismatches
Associated HydAB_PSI_Interface_model.cif chain A to #16/A with 0 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to #15/A with 0 mismatches
Associated HydAB_PSI_Interface_model_MSA.cif chain A to #16/A with 0
mismatches
Associated DdHydAB_L4 8ryh chain A to #10/A with 0 mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to #10/A with 0
mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to
#15/A with 0 mismatches
Associated DdHydAHydB 1hfe chain L to #4/A with 25 mismatches
Associated DdHydAHydB 1hfe chain M to #4/A with 25 mismatches
Associated CrHydA1 3lx4 chain A to #5/A with 0 mismatches
Associated CrHydA1 3lx4 chain B to #5/A with 0 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to #4/A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Webservices job id: NZ6M9RRWIFCG5ZGZ
Webservices job finished: NZ6M9RRWIFCG5ZGZ
Populating font family aliases took 225 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> help help:user
> select add #4
3720 atoms, 3816 bonds, 11 pseudobonds, 481 residues, 2 models selected
> select add #6
11777 atoms, 11489 bonds, 36 pseudobonds, 1453 residues, 4 models selected
> select add #7
19934 atoms, 19195 bonds, 60 pseudobonds, 2493 residues, 6 models selected
> select add #8
35077 atoms, 34307 bonds, 108 pseudobonds, 3686 residues, 8 models selected
> select add #10
38902 atoms, 38233 bonds, 119 pseudobonds, 4180 residues, 10 models selected
Alignment identifier is 6/B
Alignment identifier is 7/A
Alignment identifier is 1
Alignment identifier is 10/A
Alignment identifier is 4/A
> sequence chain #4/A
Alignment identifier is 4/A
> select #4/D:1@FE3
1 atom, 1 residue, 1 model selected
> cofr sel
> select clear
> sequence chain #4/A
Destroying pre-existing alignment with identifier 4/A
Alignment identifier is 4/A
> sequence chain #4-5/A
Chains must have same sequence
> sequence chain #4/A#5/A
Chains must have same sequence
> sequence chain #4/A #5/A
Chains must have same sequence
> sequence chain #4/A
Alignment identifier is 4/A
> sequence chain #6/A
Chains must have same sequence
> sequence chain #6/B
Alignment identifier is 6/B
> sequence chain #7/A
Alignment identifier is 7/A
> sequence chain #8/A
Alignment identifier is 8/A
> sequence chain #10/A
Alignment identifier is 10/A
> sequence chain #16/A
Alignment identifier is 16/A
> sequence align id:4/A,id:6/b,id:7/A,id:8/A,id:10/A,id:16/A
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align id:4/A id:6/b id:7/A id:8/A id:10/A id:16/A
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align ID:4/A ID:6/B ID:7/A ID:8/A ID:10/A ID:16/A
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align ID:4
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align 4
Must specify 2 or more protein sequences
> sequence align 4,6
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align 4 6
Expected a keyword
> sequence align 4,6
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align ID:4,ID:6
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align [ID:4],[ID:6]
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align [ID:4/A],[ID:6/B]
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align [ID: 4/A],[ID: 6/B]
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align ID: 4/A,ID: 6/B
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align ID: 4, ID: 6
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align ID:4, ID:6
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> open /Users/drornoy/Downloads/rcsb_pdb_8RYH.fasta
Summary of feedback from opening /Users/drornoy/Downloads/rcsb_pdb_8RYH.fasta
---
notes | Alignment identifier is rcsb_pdb_8RYH.fasta
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
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
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
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
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
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
Opened 1 sequence from rcsb_pdb_8RYH.fasta
> sequence align 4/A,6/B
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align 4,6
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align 4/A , 6/A
Expected a keyword
> sequence align 4/A 6/A
Expected a keyword
> sequence align 4/A
Must specify 2 or more protein sequences
> sequence align 4/A,6/B
Missing or invalid "seqSource" argument: Expected alignment-id or sequences
> sequence align 4/A:1,6/B:1
Alignment identifier is 1
Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to chain A with 0
mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to
chain A with 0 mismatches
Associated DdHydAHydB 1hfe chain L to chain A with 25 mismatches
Associated DdHydAHydB 1hfe chain M to chain A with 25 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to chain A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Webservices job id: EQFV5H4VRVP51OI6
Webservices job finished: EQFV5H4VRVP51OI6
> sequence align 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
input_sequences = ensure_unique_seq_names(input_sequences,
structure_name_limit=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
See log for complete Python traceback.
> sequence align 16/A:1,4/A:1,6/B:1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
input_sequences = ensure_unique_seq_names(input_sequences,
structure_name_limit=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
See log for complete Python traceback.
> sequence align 16/A:1,4/A:1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
input_sequences = ensure_unique_seq_names(input_sequences,
structure_name_limit=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
See log for complete Python traceback.
> sequence align 4/A:1,6/B:1,7/A:1,8/A:1,10/A:1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
input_sequences = ensure_unique_seq_names(input_sequences,
structure_name_limit=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
See log for complete Python traceback.
> sequence align 4/A:1,6/B:1
Alignment identifier is 1
Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to chain A with 0
mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to
chain A with 0 mismatches
Associated DdHydAHydB 1hfe chain L to chain A with 25 mismatches
Associated DdHydAHydB 1hfe chain M to chain A with 25 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to chain A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Webservices job id: 2Z7P362WBNIJOMWR
Webservices job finished: 2Z7P362WBNIJOMWR
> sequence align 7/A:1,8/A:1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
input_sequences = ensure_unique_seq_names(input_sequences,
structure_name_limit=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
See log for complete Python traceback.
> align4/A:1,8/A:1
Unknown command: sequence align4/A:1,8/A:1
> sequence align 4/A:1,8/A:1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
input_sequences = ensure_unique_seq_names(input_sequences,
structure_name_limit=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
See log for complete Python traceback.
> sequence align 4/A:1,7/A:1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
input_sequences = ensure_unique_seq_names(input_sequences,
structure_name_limit=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
See log for complete Python traceback.
> sequence align 4/A:1,7/A:1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
input_sequences = ensure_unique_seq_names(input_sequences,
structure_name_limit=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
See log for complete Python traceback.
> sequence align 6/B:1,7/A:1
Alignment identifier is 1
Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches
Associated DdHydAB_L2 9gnk chain A to chain A with 0 mismatches
Associated DdHydAHydB 1hfe chain L to chain B with 25 mismatches
Associated DdHydAHydB 1hfe chain M to chain B with 25 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Webservices job id: 8ZTRX39PHNG45CRR
Webservices job finished: 8ZTRX39PHNG45CRR
> sequence align 6/B:1,8/A:1
Alignment identifier is 3
Associated DdHydAB_L1 8ru6 chain B to chain B with 0 mismatches
Associated DdHydAB_L3 9gbu chain A to chain A with 0 mismatches
Associated DdHydAB_L3 9gbu chain B to chain A with 0 mismatches
Associated DdHydAB_L4 8ryh chain A to chain A with 7 mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to chain A with 7
mismatches
Associated DdHydAHydB 1hfe chain L to chain B with 25 mismatches
Associated DdHydAHydB 1hfe chain M to chain B with 25 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Webservices job id: 8ICR98YVWHUEM7RR
Webservices job finished: 8ICR98YVWHUEM7RR
> sequence align 7/A:1,8/A:1
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/cmd.py", line 500, in seqalign_align
input_sequences = ensure_unique_seq_names(input_sequences,
structure_name_limit=10)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
AttributeError: 'StructureSeq' object has no attribute 'atomspec'
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
renamed_seq.name = f"{struct} {seq.name}" if include_struct_name else
f"{seq.atomspec}"
^^^^^^^^^^^^
See log for complete Python traceback.
> sequence rename "6/B:chain B" DdHydAB_L1
> sequence rename "4/A:chain A" DdHydAB_TD
> sequence rename "7/A:chain A" DdHydAB_L2
> sequence rename "10/A:chain A" DdHydAB_L3
> sequence rename 10/A:DdHydAB_L3 DdHydAB_L4
> sequence rename "8/A:chain A" DdHydAB_L3
> sequence rename "16/A:chain A" DdHydAB_PSI_Interface
> sequence align 16/A:1,4/A:1,6/B:1,7/A:1,8/A:1,10/A:1
Alignment identifier is 1
Associated DdHyd_PSI.opt.chains (2.6) chain F to DdHydAB_PSI_Interface with 12
mismatches
Associated DdHydAB_L1 8ru6 chain B to DdHydAB_L1 with 0 mismatches
Associated DdHydAB_L2 9gnk chain A to DdHydAB_L2 with 0 mismatches
Associated DdHydAB_L3 9gbu chain A to DdHydAB_L3 with 0 mismatches
Associated DdHydAB_L3 9gbu chain B to DdHydAB_L3 with 0 mismatches
Associated HydAB_PSI_Interface_model.cif chain A to DdHydAB_PSI_Interface with
0 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to DdHydAB_TD with 0
mismatches
Associated HydAB_PSI_Interface_model_MSA.cif chain A to DdHydAB_PSI_Interface
with 0 mismatches
Associated DdHydAB_L4 8ryh chain A to DdHydAB_L4 with 0 mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to DdHydAB_L4 with 0
mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to
DdHydAB_TD with 0 mismatches
Associated DdHydAHydB 1hfe chain L to DdHydAB_TD with 25 mismatches
Associated DdHydAHydB 1hfe chain M to DdHydAB_TD with 25 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to DdHydAB_TD with 0
mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Webservices job id: F9UBN2MFBD72KX6R
Webservices job finished: F9UBN2MFBD72KX6R
> save "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsla structures DdHAB
> PSI.cxs"
> ui tool show "Model Panel"
> show #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!8 models
> show #!10 models
> open 4xdc
4xdc title:
Active semisynthetic [FeFe]-hydrogenase CpI with aza-dithiolato-bridged [2Fe]
cofactor [more info...]
Chain information for 4xdc #11
---
Chain | Description | UniProt
A B | Iron hydrogenase 1 | PHF1_CLOPA 1-574
Non-standard residues in 4xdc #11
---
402 — dicarbonyl[bis(cyanide-
kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
FES — FE2/S2 (inorganic) cluster
MG — magnesium ion
SF4 — iron/sulfur cluster
4xdc mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
63 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> rename #11 id 12
> rename #10 id 11
> rename #9 id 10
> rename #8 id 9
> rename #7 id 8
> rename #6 id 7
> rename #12 id 6
> ui tool show Matchmaker
> matchmaker #6/A to #5/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker CrHydA1 3lx4, chain A (#5) with 4xdc, chain A (#6), sequence
alignment score = 892.2
RMSD between 262 pruned atom pairs is 1.077 angstroms; (across all 362 pairs:
3.983)
> select #6/B
9582 atoms, 9080 bonds, 40 pseudobonds, 1170 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> hide #!6 models
> show #!6 models
> select #6/A:139-207
1016 atoms, 1019 bonds, 69 residues, 1 model selected
> hide #!9 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!4 models
> hide #!11 models
> ui tool show "Color Actions"
> color sel light steel blue
> color sel steel blue
> color sel slate gray
> color sel light slate gray
> color sel sky blue
> color sel light sky blue
[Repeated 1 time(s)]
> color sel sky blue
> color sel light blue
[Repeated 1 time(s)]
> select #6/A:1-138
2183 atoms, 2194 bonds, 138 residues, 1 model selected
> color sel light gray
> color sel silver
> color sel powder blue
> color sel silver
> select #6/A
9693 atoms, 9132 bonds, 49 pseudobonds, 1233 residues, 2 models selected
> color sel byhetero
> select clear
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #1.1.4 models
> hide #1.1.5 models
> show #!4 models
> hide #!4 models
> show #!2 models
> hide #!1 models
> select #2:SF4
32 atoms, 12 bonds, 54 pseudobonds, 4 residues, 3 models selected
> style sel & #!2.6 stick
Changed 24 atom styles
> style sel & #!2.6 ball
Changed 24 atom styles
> style sel & #!2.6 sphere
Changed 24 atom styles
> style sel & #!2.6 ball
Changed 24 atom styles
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!6 models
> show #!1 models
> hide #!1 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1 models
> hide #!2 models
> show #!5 models
> show #!4 models
> hide #!5 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> select #6/A:19-26 :<4.5 & #6/A:513-520
51 atoms, 50 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 51 atom styles
> select #6/A:513-520 :<4.5 & #6/A:19-26
46 atoms, 44 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 46 atom styles
> save "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsal structures DdHAB
> PSI.cxs"
> open "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_model.cif"
Chain information for hydab_psi_interface_model.cif #12
---
Chain | Description
A | .
No chain in structure corresponds to chain ID given in local score info (chain
'B')
Associated hydab_psi_interface_model.cif chain A to chain F with 12 mismatches
Associated hydab_psi_interface_model.cif chain A to DdHydAB_PSI_Interface with
12 mismatches
Computing secondary structure
> hide #!12 models
> show #!12 models
> show #!16 models
> hide #!16 models
> ui tool show Log
> ui tool show Matchmaker
> matchmaker #12/A to #2.6/F pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DdHyd_PSI.opt.chains, chain F (#2.6) with
hydab_psi_interface_model.cif, chain A (#12), sequence alignment score =
2357.4
RMSD between 459 pruned atom pairs is 0.458 angstroms; (across all 473 pairs:
1.168)
> show #!2 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> hide #!10 models
> ui tool show "AlphaFold Error Plot"
> alphafold pae #12 file "/Users/drornoy/Library/CloudStorage/OneDrive-
> SharedLibraries-Migal/Dror Noy Group -
> General/Yigal/Hydrogenase_AF3/MSA/HydAB_PSI_Interface/hydab_psi_interface_confidences.json"
> color bfactor #12 palette alphafold
3658 atoms, 477 residues, atom bfactor range 24.2 to 99
> close #16
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> sequence align 12/A:1,1:2,1:3,1:4,1:5,1:6
Alignment identifier is 3
Associated DdHyd_PSI.opt.chains (2.6) chain F to chain A with 12 mismatches
Associated HydAB_TD_linker_model_noMSA.cif chain A to DdHydAB_TD with 0
mismatches
Associated HydAB_PSI_Interface_model_MSA.cif chain A to chain A with 0
mismatches
Associated fold_ddh2ase_single_chain_chlamy_tdk_linker_model_0.cif chain A to
DdHydAB_TD with 0 mismatches
Associated DdHydAHydB 1hfe chain L to DdHydAB_TD with 25 mismatches
Associated DdHydAHydB 1hfe chain M to DdHydAB_TD with 25 mismatches
Associated HydAB_TD_linker_model_MSA.cif chain A to DdHydAB_TD with 0
mismatches
Associated hHydAB_L4_linker_PDB_8ryh_model.cif chain A to DdHydAB_L4 with 0
mismatches
Associated DdHydAB_L4 8ryh chain A to DdHydAB_L4 with 0 mismatches
Associated DdHydAB_L3 9gbu chain A to DdHydAB_L3 with 0 mismatches
Associated DdHydAB_L3 9gbu chain B to DdHydAB_L3 with 0 mismatches
Associated DdHydAB_L2 9gnk chain A to DdHydAB_L2 with 0 mismatches
Associated DdHydAB_L1 8ru6 chain B to DdHydAB_L1 with 0 mismatches
Associated hydab_psi_interface_model.cif chain A to chain A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Webservices job id: 6XMP5FXUI3IT234Y
Webservices job finished: 6XMP5FXUI3IT234Y
> select #2.6/F:1796 #14/A:31 #12/A:31
20 atoms, 17 bonds, 3 residues, 3 models selected
> select #2.6/F:1796 #14/A:31 #12/A:31
20 atoms, 17 bonds, 3 residues, 3 models selected
Clustal Omega Alignment [ID: 3] region chain A [35] RMSD: 0.945
> sequence rename "3:chain A" DdHydAB_PSI_interface
> sequence disassociate #3/L 3
Disassociated DdHydAHydB 1hfe chain L from DdHydAB_TD
> sequence disassociate #3/M 3
Disassociated DdHydAHydB 1hfe chain M from DdHydAB_TD
> sequence disassociate #2.6/F 3
Disassociated DdHyd_PSI.opt.chains (2.6) chain F from DdHydAB_PSI_interface
> sequence associate #2.6/F 3
Associated DdHyd_PSI.opt.chains (2.6) chain F to DdHydAB_PSI_interface with 12
mismatches
> sequence disassociate #2.6/F 3
Disassociated DdHyd_PSI.opt.chains (2.6) chain F from DdHydAB_PSI_interface
> 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
120 atoms, 96 bonds, 24 residues, 2 models selected
> select #12
3658 atoms, 3754 bonds, 11 pseudobonds, 477 residues, 2 models selected
> color sel byhetero
> select clear
> hide #!12 models
> hide #!2 models
> show #!12 models
> show #!2 models
> select #14/A:392 #12/A:392
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #14/A:390-392 #12/A:390-392
66 atoms, 68 bonds, 6 residues, 2 models selected
Clustal Omega Alignment [ID: 3] region DdHydAB_PSI_interface [402-404] RMSD:
0.896
> select #14/A:390 #12/A:390
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #14/A:390-391 #12/A:390-391
42 atoms, 42 bonds, 4 residues, 2 models selected
Clustal Omega Alignment [ID: 3] region DdHydAB_PSI_interface [402-403] RMSD:
1.024
> select #14/A:387 #12/A:387
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #14/A:387-391 #12/A:387-391
76 atoms, 76 bonds, 10 residues, 2 models selected
Clustal Omega Alignment [ID: 3] region DdHydAB_PSI_interface [391-403] RMSD:
2.113
> hide #!4 models
> hide #!12 models
> show #!12 models
> hide #!2 models
> close #14
> close #15
> close #13
> hide #!12 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> select add #12
3658 atoms, 3754 bonds, 11 pseudobonds, 477 residues, 2 models selected
> select subtract #12
Nothing selected
> hide #!10 models
> show #!11 models
> view name linkers_zoom
[Repeated 1 time(s)]
> view linkers_zoom
[Repeated 2 time(s)]
> save "/Users/drornoy/Library/CloudStorage/OneDrive-SharedLibraries-
> Migal/Dror Noy Group - General/Yigal/Compare AF3 Crytsal structures DdHAB
> PSI.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1058, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 284, in discovery
if hasattr(sm, "include_state") and not sm.include_state(value):
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2683, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in <listcomp>
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 50, in <lambda>
filt = lambda x: (not x.structure) or open_structure(x.structure)
^^^^^^^^^^^
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
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
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
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1058, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 284, in discovery
if hasattr(sm, "include_state") and not sm.include_state(value):
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2683, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in <listcomp>
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 50, in <lambda>
filt = lambda x: (not x.structure) or open_structure(x.structure)
^^^^^^^^^^^
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
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
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
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> save "/Users/drornoy/Google Drive/ISF_DFG_project/Structures/Compare DdHydAB
> variants CrHydA1 CpI.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1058, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 284, in discovery
if hasattr(sm, "include_state") and not sm.include_state(value):
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2683, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in <listcomp>
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 50, in <lambda>
filt = lambda x: (not x.structure) or open_structure(x.structure)
^^^^^^^^^^^
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
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
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
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1058, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 284, in discovery
if hasattr(sm, "include_state") and not sm.include_state(value):
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2683, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in <listcomp>
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 50, in <lambda>
filt = lambda x: (not x.structure) or open_structure(x.structure)
^^^^^^^^^^^
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
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
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
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
> save "/Users/drornoy/Desktop/DdHydAB compare.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1058, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 284, in discovery
if hasattr(sm, "include_state") and not sm.include_state(value):
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2683, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in <listcomp>
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 50, in <lambda>
filt = lambda x: (not x.structure) or open_structure(x.structure)
^^^^^^^^^^^
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
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
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
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog
_dlg.display(session, **kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display
run(session, cmd)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 1058, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 741, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 284, in discovery
if hasattr(sm, "include_state") and not sm.include_state(value):
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in include_state
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/attributes.py", line 295, in <listcomp>
self._python_instances = [[inst for inst in inst_func(self.session)
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2683, in <lambda>
register_class(reg_class, lambda *args, cls=reg_class:
python_instances_of_class(cls),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in python_instances_of_class
return [x for x in instances if filt(x)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 61, in <listcomp>
return [x for x in instances if filt(x)]
^^^^^^^
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/molobject.py", line 50, in <lambda>
filt = lambda x: (not x.structure) or open_structure(x.structure)
^^^^^^^^^^^
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
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
TypeError: Cannot instantiate Python class corresponding to C++
30QGraphicsSimpleTextItemPrivate
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
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: Z15J002LTHB/A
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6 (24G84)
Kernel Version: Darwin 24.6.0
Time since boot: 1 day, 1 hour, 39 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E243:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.5.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.18
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.3
ChimeraX-ProfileGrids: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.9.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.4
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
MolecularDynamicsViewer: 1.6
msgpack: 1.1.0
narwhals: 1.47.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 2.2.6
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
plotly: 6.0.1
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
Pygments: 2.18.0
pyKVFinder: 0.8.1
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tomlkit: 0.13.2
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.0
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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