mmCIF write: citation_author is None

[tetterst@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-54-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-08-07)
Description
Tried to save chains in mmcif format, because pdb names multiple chains the same way, e.g. /T and /TA will both be called /T after saving in pdb

Log:
UCSF ChimeraX version: 0.91 (2019-08-07)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/hilvertg/Desktop/RSR41_QRST_andSurroundings.pdb

Chain information for RSR41_QRST_andSurroundings.pdb #1  
---  
Chain | Description  
A | No description available  
B D J Q S X | No description available  
E R | No description available  
F | No description available  
G | No description available  
H V | No description available  
I | No description available  
M | No description available  
T | No description available  
U | No description available  
  

> save help

Missing filename suffix help  

> close

> open
/home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.cif

Summary of feedback from opening
/home/hilvertg/tetterst/NCL12_phenix_2/RealSpaceRefine_41/NCL12_smallermap_apply_ncs_40_real_space_refined.cif  
---  
warnings | skipping chem_comp category: Missing column 'type' near line 3469  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for secondary structure "4" near line 335  
Bad residue range for secondary structure "8" near line 339  
Bad residue range for secondary structure "12" near line 343  
Bad residue range for secondary structure "16" near line 347  
Bad residue range for secondary structure "20" near line 351  
235 messages similar to the above omitted  
Invalid sheet range for strand "1 1" near line 2253  
Invalid sheet range for strand "1 3" near line 2255  
Invalid sheet range for strand "2 1" near line 2256  
Invalid sheet range for strand "2 3" near line 2258  
Invalid sheet range for strand "3 1" near line 2259  
475 messages similar to the above omitted  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for NCL12_smallermap_apply_ncs_40_real_space_refined.cif #1  
---  
Chain | Description  
A BA BB BC BD BE BF BG BH BI C DA DB DC DD DE DF DG DH DI E FA FB FC FD FE FF
FG FH FI G HA HB HC HD HE HF HG HH I JA JB JC JD JE JF JG JH K LA LB LC LD LE
LF LG LH M NA NB NC ND NE NF NG NH O PA PB PC PD PE PF PG PH Q RA RB RC RD RE
RF RG RH S TA TB TC TD TE TF TG TH V VA VB VC VD VE VF VG VH X XA XB XC XD XE
XF XG XH Z ZA ZB ZC ZD ZE ZF ZG ZH | No description available  
AA AC AE AG AI B CB CD CF CH EA EC EE EG EI F GB GD GF GH IA IC IE IG J KB KD
KF KH MA MC ME MG N OB OD OF OH QA QC QE QG R SB SD SF SH UA UC UE UG W WB WD
WF WH YA YC YE YG | No description available  
AB AD AF AH CA CC CE CG CI D EB ED EF EH GA GC GE GG GI H IB ID IF IH KA KC KE
KG L MB MD MF MH OA OC OE OG P QB QD QF QH SA SC SE SG T UB UD UF UH WA WC WE
WG Y YB YD YF YH | No description available  
  

> select zone /Q,R,S,T 15

Selected 6950 atoms  

> select up

7748 atoms, 7801 bonds, 1 model selected  

> select up

21478 atoms, 21847 bonds, 1 model selected  

> select up

286320 atoms, 291240 bonds, 1 model selected  

> select down

21478 atoms, 21847 bonds, 1 model selected  

> select add /Q,R,S,T

26250 atoms, 26701 bonds, 1 model selected  

> save /home/hilvertg/Desktop/RSR41_QRST_andSurroundings.cif selectedOnly true
format mmcif

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2655, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/io.py", line 213, in export  
result = self.export_func(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 62, 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 "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 325, in save_structure  
citation_author.extend(ChimeraX_authors)  
AttributeError: 'NoneType' object has no attribute 'extend'  
  
AttributeError: 'NoneType' object has no attribute 'extend'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 325, in save_structure  
citation_author.extend(ChimeraX_authors)  
  
See log for complete Python traceback.  
  

> save /home/hilvertg/Desktop/RSR41_QRST_andSurroundings.cif selectedOnly true

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2655, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/io.py", line 213, in export  
result = self.export_func(session, path, **kw)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 62, 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 "/usr/lib/ucsf-chimerax-daily/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 "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 325, in save_structure  
citation_author.extend(ChimeraX_authors)  
AttributeError: 'NoneType' object has no attribute 'extend'  
  
AttributeError: 'NoneType' object has no attribute 'extend'  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif_write.py", line 325, in save_structure  
citation_author.extend(ChimeraX_authors)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 396.54
OpenGL renderer: GeForce GTX 1060 6GB/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[pett]

Reported by Stephan Tetter

[Greg Couch]

Fixed in the next daily build.

Very curious about the original CIF file, NCL12_smallermap_apply_ncs_40_real_space_refined.cif. There are lots of errors found when it is read in. I'd like to see it to figure if the errors are actually in ChimeraX. Please send it to me, either as an attachment to this ticket, or directly to me at gregc@….