mmCIF export: chain ID KeyError

[lpravda@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-03-12)
Description
mmcif file export

Log:
UCSF ChimeraX version: 0.9 (2019-03-12)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/lpravda/assembly.cif

Summary of feedback from opening /Users/lpravda/assembly.cif  
---  
warnings | Atom H1 is not in the residue template for GLN #1 in chain A  
Mismatched number of atoms (530 vs. 531)  
Mismatched number of atoms (530 vs. 531)  
Mismatched number of atoms (530 vs. 531)  
Mismatched number of atoms (530 vs. 531)  
Mismatched number of atoms (530 vs. 531)  
4 messages similar to the above omitted  
  
Chain information for assembly.cif  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A | copper (I) ion  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 813, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 576, in file_save_cb  
self.save_dialog.display(self, session)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 141, in display  
fmt.save(session, filename)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 40, in save  
return self._save(session, filename)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 66, in <lambda>  
fmt.export(ses, _add_missing_suffix(fn, fmt), fmt.name))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 203, in export  
result = self.export_func(session, path, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 61, in save_file  
return mmcif_write.write_mmcif(session, path, models=models)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 108, in write_mmcif  
save_structure(session, f, models, used_data_names)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 516, in save_structure  
asym_id, entity_id = het_asym_info[r.mmcif_chain_id]  
KeyError: 'B'  
  
KeyError: 'B'  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 516, in save_structure  
asym_id, entity_id = het_asym_info[r.mmcif_chain_id]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: assembly.cif.gz

assembly.cif.gz​

[lpravda@…]

Added by email2trac

[Greg Couch]

Needed to look at all submodels for figure the set of non-polymer entities.