Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#8629 closed defect (fixed)

Write mmCIF: 'NoneType' object has no attribute 'get'

Reported by: corbin.black@… Owned by: Greg Couch
Priority: normal Milestone: 1.6
Component: Input/Output Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.2-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Saving a combined cif. it always fails regardless of the cif!

Log:
UCSF 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/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/fap21b_1J.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/fap21b_1J.cif  
---  
warnings | Unknown polymer entity '1' near line 112  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for fap21b_1J.cif #1  
---  
Chain | Description  
1J | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/fap115_1L.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/fap115_1L.cif  
---  
warnings | Unknown polymer entity '1' near line 112  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for fap115_1L.cif #2  
---  
Chain | Description  
1L | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/fap115_2L.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/fap115_2L.cif  
---  
warnings | Unknown polymer entity '1' near line 112  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for fap115_2L.cif #3  
---  
Chain | Description  
2L | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/fap115_3L.cif"

Chain information for fap115_3L.cif #4  
---  
Chain | Description  
3L | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/fap129_4F.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/fap129_4F.cif  
---  
warnings | Unknown polymer entity '1' near line 111  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for fap129_4F.cif #5  
---  
Chain | Description  
4F | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q23JL9_0B.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q23JL9_0B.cif  
---  
warnings | Unknown polymer entity '1' near line 112  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Q23JL9_0B.cif #6  
---  
Chain | Description  
0B | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q231B6_6H.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q231B6_6H.cif  
---  
warnings | Unknown polymer entity '1' near line 110  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Q231B6_6H.cif #7  
---  
Chain | Description  
6H | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q237T1_0G.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q237T1_0G.cif  
---  
warnings | Unknown polymer entity '1' near line 110  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Q237T1_0G.cif #8  
---  
Chain | Description  
0G | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q237T1_1G.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q237T1_1G.cif  
---  
warnings | Unknown polymer entity '1' near line 110  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Q237T1_1G.cif #9  
---  
Chain | Description  
1G | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q238X3_0D.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q238X3_0D.cif  
---  
warnings | Unknown polymer entity '1' near line 111  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Q238X3_0D.cif #10  
---  
Chain | Description  
0D | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q238X3_1D.cif"

Chain information for Q238X3_1D.cif #11  
---  
Chain | Description  
1D | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/Q238X3_2D.cif"

Chain information for Q238X3_2D.cif #12  
---  
Chain | Description  
2D | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/rib43aS_0X.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/rib43aS_0X.cif  
---  
warnings | Unknown polymer entity '1' near line 112  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for rib43aS_0X.cif #13  
---  
Chain | Description  
0X | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/rib43aS_1X.cif"

Summary of feedback from opening /Users/corbin/Dropbox/8 -
Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/rib43aS_1X.cif  
---  
warnings | Unknown polymer entity '1' near line 112  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for rib43aS_1X.cif #14  
---  
Chain | Description  
1X | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/rib43aS_2X.cif"

Chain information for rib43aS_2X.cif #15  
---  
Chain | Description  
2X | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/rib43aS_3X.cif"

Chain information for rib43aS_3X.cif #16  
---  
Chain | Description  
3X | No description available  
  

> open "/Users/corbin/Dropbox/8 -
> Manuscripts/2022_OJ/Deposition/K40R/march9_mip_cif/rib43aS_4X.cif"

Chain information for rib43aS_4X.cif #17  
---  
Chain | Description  
4X | No description available  
  

> set bgColor white

> combine #1-17

> save /Users/corbin/Desktop/t.cif models #18

Not saving entity_poly_seq for non-authoritative sequences  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mmcif/__init__.py", line 90, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "src/mmcif_write.pyx", line 149, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 156, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 382, in
chimerax.mmcif.mmcif_write.save_structure  
AttributeError: 'NoneType' object has no attribute 'get'  
  
AttributeError: 'NoneType' object has no attribute 'get'  
  
File "src/mmcif_write.pyx", line 382, in
chimerax.mmcif.mmcif_write.save_structure  
  
See log for complete Python traceback.  
  

> save /Users/corbin/Desktop/t.cif models #18

Not saving entity_poly_seq for non-authoritative sequences  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 165, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider  
providers.run_provider(session, name)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 45, in run_provider  
what(session)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/providers.py", line 27, in _file_save  
show_save_file_dialog(session)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mmcif/__init__.py", line 90, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "src/mmcif_write.pyx", line 149, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 156, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 382, in
chimerax.mmcif.mmcif_write.save_structure  
AttributeError: 'NoneType' object has no attribute 'get'  
  
AttributeError: 'NoneType' object has no attribute 'get'  
  
File "src/mmcif_write.pyx", line 382, in
chimerax.mmcif.mmcif_write.save_structure  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,4
      Model Number: Z15H00109LL/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8419.80.7
      OS Loader Version: 8419.80.7

Software:

    System Software Overview:

      System Version: macOS 13.2 (22D49)
      Kernel Version: Darwin 22.3.0
      Time since boot: 49 minutes, 48 seconds

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      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


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0
File attachment: Screenshot 2023-03-10 at 12.27.09 PM.png

Screenshot 2023-03-10 at 12.27.09 PM.png​

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Screenshot 2023-03-10 at 12.27.09 PM.png​ (788.5 KB ) - added by corbin.black@… 3 years ago.
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Change History (6)

by corbin.black@…, 3 years ago

Attachment: Screenshot 2023-03-10 at 12.27.09 PM.png​ added

Added by email2trac

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Write mmCIF: 'NoneType' object has no attribute 'get'

comment:2 by Greg Couch, 3 years ago

Can you share the files or a file needed to reproduce this? I suspect that just one of the original files, eg., fap21b_1J.cif, would be sufficient to reproduce this. You can send it to me directly at gregc@… to keep it private (this bug reports are publicly visible). I can attempt a fix without it, but I'd like to be able to test the fix.

comment:3 by Greg Couch, 3 years ago

Thank you for the files. They are very helpful.

comment:4 by Greg Couch, 3 years ago

Cc: Greg Couch added
Resolution: → fixed
Status: assigned → closed

Fixed bug when writing mmCIF if authoritative sequence information is missing.

I noticed that many of the input mmCIF files are missing the sequence information (entity_poly_seq table). Hence the "Not saving entity_poly_seq for non-authoritative sequences". If there are no missing segments, then you could reasonably do "save t.cif models #18 bestGuess true" to fill out the entity_poly_seq table in the output. The bestGuess option also runs a DSSP calculation to figure out the sheet information (normally, ChimeraX only outputs strand information, because it doesn't save the sheet information).

comment:5 by Greg Couch, 3 years ago

Milestone: → 1.6
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