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Opened 4 weeks ago
Last modified 4 weeks ago
#19302 closed defect
sequence align: 'StructureSeq' object has no attribute 'atomspec' — at Version 1
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sequence | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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
[deleted to fit within ticket limits]
> 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
File attachment: log_06_11_25.html
Change History (3)
by , 4 weeks ago
| Attachment: | log_06_11_25.html added |
|---|
comment:1 by , 4 weeks ago
| Component: | Unassigned → Sequence |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → sequence align: 'StructureSeq' object has no attribute 'atomspec' |
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