Chain KeyError opening Phenix CIF file

[henry.nguyen@…]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
I just tried to open the attached mmCIF file. I converted my pdb to cif using phenix.pdb_as_cif, and then prepared the cif for deposition using mmtbx.prepare_pdb_deposition. The first cif file can be opened and displayed properly.

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/hcnguyen/Documents/Frost_Lab/qcrg/spike/mNb6/full_mNb6_rsr24-coot-5.deposit_000.cif

Summary of feedback from opening
/Users/hcnguyen/Documents/Frost_Lab/qcrg/spike/mNb6/full_mNb6_rsr24-coot-5.deposit_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 76  
Missing entity information. Treating each chain as a separate entity.  
Atom H1 is not in the residue template for VAL /B:2  
Atom H1 is not in the residue template for VAL /D:2  
Atom H1 is not in the residue template for VAL /F:2  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 54884  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 382, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/__init__.py", line 38, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 88, in open_mmcif  
for p in pointers]  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 88, in <listcomp>  
for p in pointers]  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1146, in __init__  
self._set_chain_descriptions(self.session)  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1349, in _set_chain_descriptions  
entity_to_description[mmcif_chain_to_entity[mmcif_cid]], False)  
KeyError: 'A'  
  
KeyError: 'A'  
  
File
"/Applications/ChimeraX-1.0.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1349, in _set_chain_descriptions  
entity_to_description[mmcif_chain_to_entity[mmcif_cid]], False)  
  
See log for complete Python traceback.  
  

> open
> /Users/hcnguyen/Documents/Frost_Lab/qcrg/spike/mNb6/full_mNb6_rsr24-coot-5.cif

Summary of feedback from opening
/Users/hcnguyen/Documents/Frost_Lab/qcrg/spike/mNb6/full_mNb6_rsr24-coot-5.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 76  
Missing entity information. Treating each chain as a separate entity.  
Atom H1 is not in the residue template for VAL /B:2  
Atom H1 is not in the residue template for VAL /D:2  
Atom H1 is not in the residue template for VAL /F:2  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 53480  
  
Chain information for full_mNb6_rsr24-coot-5.cif #1  
---  
Chain | Description  
A C E | No description available  
B D F | No description available  
  

> hide atoms

> show cartoons




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GT 650M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro10,1
      Processor Name: Intel Core i7
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 16 GB
      Boot ROM Version: 261.0.0.0.0
      SMC Version (system): 2.3f36

Software:

    System Software Overview:

      System Version: macOS 10.13.6 (17G13035)
      Kernel Version: Darwin 17.7.0
      Time since boot: 16 days 16:11

Graphics/Displays:

    Intel HD Graphics 4000:

      Chipset Model: Intel HD Graphics 4000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0166
      Revision ID: 0x0009
      Automatic Graphics Switching: Supported
      gMux Version: 3.2.19 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily1 v3

    NVIDIA GeForce GT 650M:

      Chipset Model: NVIDIA GeForce GT 650M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Dynamic, Max): 1024 MB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x0fd5
      Revision ID: 0x00a2
      ROM Revision: 3688
      Automatic Graphics Switching: Supported
      gMux Version: 3.2.19 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily1 v3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
        2217:
          Resolution: 1680 x 1050 (Widescreen Super eXtended Graphics Array Plus)
          UI Looks like: 1680 x 1050 @ 60 Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: P148CHA003927
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Apple Mini DisplayPort To VGA Adapter
          Automatically Adjust Brightness: No
          Adapter Firmware Version: 1.03

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: full_mNb6_rsr24-coot-5.deposit_000.cif

full_mNb6_rsr24-coot-5.deposit_000.cif​

[henry.nguyen@…]

Added by email2trac

[Eric Pettersen]

Hi Henry,

I believe this problem is fixed in the daily build (your file works there), so if you get that you should be good to go. Sorry for the inconvenience.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Henry.Nguyen@…]

Thanks! All good.

Henry
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, July 13, 2020 3:38 PM
Cc: Couch, Gregory <gregc@cgl.ucsf.edu>; Nguyen, Henry <Henry.Nguyen@ucsf.edu>; PETTERSEN, ERIC <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #3509: Chain KeyError opening Phenix CIF file

#3509: Chain KeyError opening Phenix CIF file
-------------------------------------+------------------------
          Reporter:  henry.nguyen@…  |      Owner:  Greg Couch
              Type:  defect          |     Status:  closed
          Priority:  normal          |  Milestone:
         Component:  Input/Output    |    Version:
        Resolution:  fixed           |   Keywords:
        Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
           Project:  ChimeraX        |
-------------------------------------+------------------------
Changes (by Eric Pettersen):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 Hi Henry,
         I believe this problem is fixed in the daily build (your file
 works there), so if you get that you should be good to go.  Sorry for the
 inconvenience.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3509#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
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