Save mmCIF: citation is None

[dirk.fahrenkamp@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 1.0rc202005130635 (2020-05-13 06:35:59 UTC)
Description
when saving models as .cif files

AttributeError: 'NoneType' object has no attribute 'print'

File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure
citation.print(file, fixed_width=True)

See log for complete Python traceback.

appears no matter what model.

Log:
UCSF ChimeraX version: 1.0rc202005130635 (2020-05-13)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/DirkF/Desktop/EA_apo2_new_Met_Belt.cif

Summary of feedback from opening
C:/Users/DirkF/Desktop/EA_apo2_new_Met_Belt.cif  
---  
warnings | Unknown polymer entity '1' near line 228  
Unknown polymer entity '2' near line 3430  
Unknown polymer entity '3' near line 6629  
Unknown polymer entity '4' near line 9731  
Unknown polymer entity '5' near line 12789  
20 messages similar to the above omitted  
Atom H1 is not in the residue template for GLY /A:2  
Atom H21 is not in the residue template for DD9 /A:401  
Atom H1 is not in the residue template for GLY /B:2  
Atom H1 is not in the residue template for GLY /C:2  
Atom H1 is not in the residue template for ASN /D:3  
Atom H1 is not in the residue template for GLY /E:2  
Atom H1 is not in the residue template for MET /F:1  
5 messages similar to the above omitted  
Atom H21 is not in the residue template for DD9 /K:301  
Atom H1 is not in the residue template for LEU /L:29  
Atom H1 is not in the residue template for LEU /M:29  
Atom H1 is not in the residue template for LEU /N:29  
Atom H1 is not in the residue template for SER /O:28  
Atom H1 is not in the residue template for ASP /P:25  
Atom H2 is not in the residue template for PRO /Q:4  
Atom H2 is not in the residue template for PRO /R:4  
Atom H2 is not in the residue template for PRO /S:4  
Atom H2 is not in the residue template for PRO /T:4  
Atom H1 is not in the residue template for SER /U:6  
Atom H1 is not in the residue template for SER /V:6  
Atom H1 is not in the residue template for SER /W:6  
Atom H1 is not in the residue template for SER /X:6  
Atom H2 is not in the residue template for PRO /Y:4  
Atom H1 is not in the residue template for LEU /f:9  
Atom H1 is not in the residue template for ASN /g:22  
Atom H1 is not in the residue template for VAL /h:20  
Atom H1 is not in the residue template for ASN /i:22  
Atom H1 is not in the residue template for ASP /j:21  
1 messages similar to the above omitted  
Atom H2 is not in the residue template for PRO /l:4  
Atom H2 is not in the residue template for PRO /m:4  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for EA_apo2_new_Met_Belt.cif #1  
---  
Chain | Description  
A | ?  
B | ?  
C | ?  
D | ?  
E | ?  
F | ?  
G H | ?  
I | ?  
J | ?  
K L M N | ?  
O | ?  
P | ?  
Q | ?  
R | ?  
S | ?  
T | ?  
U | ?  
V W X | ?  
Y | ?  
f | ?  
g i | ?  
h | ?  
j k | ?  
l | ?  
m | ?  
  

> save C:/Users/DirkF/Desktop/test.cif

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\ui\gui.py", line 1544, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 106, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 117, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\atomic\mmcif\\__init__.py", line 124, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\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 "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
AttributeError: 'NoneType' object has no attribute 'print'  
  
AttributeError: 'NoneType' object has no attribute 'print'  
  
File "C:\Program Files\ChimeraX 1.0rc202005130635\bin\lib\site-
packages\chimerax\atomic\mmcif\mmcif_write.py", line 303, in save_structure  
citation.print(file, fixed_width=True)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 425.31
OpenGL renderer: GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GL75 9SE
OS: Microsoft Windows 10 Home (Build 17763)
Memory: 17,016,807,424
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-9750H CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Greg Couch]

Reproduced by saving a model that was previous written by Chimerax. Does not happen the first time.

[Greg Couch]

Fixed. Thanks for report this.