Saving mmCIF: citation is None

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005121634 (2020-05-12 16:34:48 UTC)
Description
Saving a few selected RNA residues of 7bv2 with selectedOnly true.

Log:
UCSF ChimeraX version: 1.0rc202005121634 (2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7bv2 format mmcif fromDatabase pdb

7bv2 title:  
The nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate
form of Remdesivir(RTP) [more info...]  
  
Chain information for 7bv2 #1  
---  
Chain | Description  
A | SARS-CoV-2 Nsp12  
B | SARS-CoV-2 nsp8  
C | SARS-CoV-2 nsp7  
P | Primer  
T | Templete  
  
Non-standard residues in 7bv2 #1  
---  
F86 —
[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanylpyrrolo[2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl
dihydrogen phosphate  
MG — magnesium ion  
POP — pyrophosphate 2-  
ZN — zinc ion  
  

> style stick

Changed 8555 atom styles  

> style ball

Changed 8555 atom styles  

> surface /a-c

> color byhetero

> surface close

> hide /a-c

> surface /a-c

> open A.cif

Chain information for A.cif #2  
---  
Chain | Description  
T | Templete  
  

> hide #!1 models

Drag select of 22 atoms, 24 bonds  

> show #!1 models

> ui mousemode right "translate selected models"

> style sel ball

Changed 22 atom styles  

> open U.cif

Chain information for U.cif #3  
---  
Chain | Description  
T | Templete  
  

> ~select #2

Nothing selected  

> select #3

20 atoms, 21 bonds, 1 model selected  

> style sel ball

Changed 20 atom styles  

>

Unknown command: sequence #1/T  

> usage seq

sequence associate chains [target]  
— associate chain(s) with sequence  
target: alignment-id or [alignment-id:]sequence-name-or-number

sequence chain chains  
— show structure chain sequence

sequence disassociate chains [alignment]  
— disassociate chain(s) from alignment  
alignment: alignment-id

sequence dissociate [optional]  
— alias of "sequence disassociate $*"  
optional: the rest of line  

sequence viewer [alignmentS] subcommandText  
— send subcommand to viewer 'viewer'  
alignmentS: alignment-id, some alignment-id, or nothing  
subcommandText: the rest of line  

> select #1/T

290 atoms, 322 bonds, 1 model selected  
Alignment identifier is 1.T  

> sequence chain #1/T

Destroying pre-existing alignment with identifier 1.T  
Alignment identifier is 1.T  

> hide /a-c surfaces

> sequence chain #/P

Missing or invalid "chains" argument: invalid chains specifier  

> sequence chain #1/P

Alignment identifier is 1.P  

> help save

> save auaac.cif selectedOnly true

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.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/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2849, in run  
result = ci.function(session, **kw_args)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 124, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File
"/Users/goddard/ucsf/cx-1.0/ChimeraX.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/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/Users/goddard/ucsf/cx-1.0/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 5 days 23:58

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Greg Couch]

This might be a duplicate of #3204 that was fixed a couple of days ago. Where A.cif and/or U.cif originally written by ChimeraX?

[goddard@…]

Yes A.cif and U.cif were written by ChimeraX.  I believe I tried installing bundles/mmCIF from latest source before reporting this problem, but not totally sure about that.

[Greg Couch]

I'm 99.99% sure this a duplicate and has been fixed. Please update the mmcif bundle and try again.

[goddard@…]

I do not know the steps to reproduce the problem.  Seems very simple, some variable citation was None.  I tried opening a cif and saving did not get an error with current code.  But it also worked some of the time yesterday and only some time failed and I do not know the step that made it fail.

[Greg Couch]

That is consistent. The bug was happened when a mmCIF model was read from a file that had been written by ChimeraX, and then written again. That code path is no more.