save mmCIF after opening PDB gives AttributeError: 'NoneType' object has no attribute 'field_has'

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-22)
Description
AttributeError: 'NoneType' object has no attribute 'field_has' from saving mmCIF after opening from PDB

open 1www format pdb
save something.cif


Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start toolshed show $1

> alias whereprefs info path user unversioned config

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> http://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias segtest open 0557 from emdb; vol threshold #1 min 0; vol scale #2
> value uint8; open 6nzk

executed startup.cxc  
UCSF ChimeraX version: 0.94.dev202004220145 (2020-04-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1www

1www title:  
NGF In complex with domain 5 of the TRKA receptor [more info...]  
  
Chain information for 1www #1  
---  
Chain | Description  
V W | protein (nerve growth factor)  
X Y | protein (TRKA receptor)  
  
  

> close

> open 1www format PDB

Summary of feedback from opening 1www fetched from pdb  
---  
note | Fetching compressed PDB 1www from
http://files.rcsb.org/download/1www.pdb  
  
1www title:  
NGF In complex with domain 5 of the TRKA receptor [more info...]  
  
Chain information for 1www #1  
---  
Chain | Description  
V W | β-NGF  
X Y | TRKA receptor  
  
  

> save nerf.cif

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 229, in export  
result = self.export_func(session, path, **kw)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 63, in save_file  
return mmcif_write.write_mmcif(session, path, models=models,
rel_model=rel_model, selected_only=selected_only,
displayed_only=displayed_only)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 139, in write_mmcif  
save_structure(session, f, [m], [xforms[m]], used_data_names, selected_only,
displayed_only)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 299, in save_structure  
ChimeraX_authors, metadata=best_metadata)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 555, in _add_citation  
if citation.field_has('id', citation_id):  
AttributeError: 'NoneType' object has no attribute 'field_has'  
  
AttributeError: 'NoneType' object has no attribute 'field_has'  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 555, in _add_citation  
if citation.field_has('id', citation_id):  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.17
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Greg Couch]

Duplicate of #3047. Fixed earlier today.