KeyError writing Mol2 file

[egg08832@…]

The following bug report has been submitted:
Platform:        macOS-11.3.1-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202308092202 (2023-08-09 22:02:17 UTC)
Description
Running save format mol2 brought up this error:

Traceback (most recent call last):   File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319, in execute     cmd.run(cmd_text)   File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897, in run     result = ci.function(session, **kw_args)              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 75, in cmd_save     Command(session, registry=registry).run(provider_cmd_text, log=log)   File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897, in run     result = ci.function(session, **kw_args)              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^   File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 90, in provider_save     saver_info.save(session, path, **provider_kw)   File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mol2/__init__.py", line 27, in save     write_mol2(session, path, status=session.logger.status, **kw)   File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mol2/io.py", line 497, in write_mol2     print("%5d" % atom_indices[chain_atom], end=" ", file=f)                   ~~~~~~~~~~~~^^^^^^^^^^^^ KeyError: <chimerax.atomic.molobject.Atom object at 0x1367fcc10> KeyError:

File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mol2/io.py", line 497, in write_mol2
print("%5d" % atom_indices[chain_atom], end=" ", file=f)

Log:
UCSF ChimeraX version: 1.7.dev202308092202 (2023-08-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/elizagazaway/OneDrive - University of
> Georgia/ASN_coreglycan/EPO_TIP5P/EPO_TIP5P.pdb"

Chain information for EPO_TIP5P.pdb #1  
---  
Chain | Description  
? | No description available  
  

> open "/Users/elizagazaway/OneDrive - University of
> Georgia/ASN_coreglycan/EPO_TIP5P/snapshots_asn_TIP5P/asn_TIP5P.1.pdb"

asn_TIP5P.1.pdb title:  
TIP5P1 [more info...]  
  
Chain information for asn_TIP5P.1.pdb #2  
---  
Chain | Description  
? | No description available  
  
Non-standard residues in asn_TIP5P.1.pdb #2  
---  
0MB — (0MB)  
4YB — (4YB)  
ACE — (ACE)  
NLN — (NLN)  
NME — (NME)  
  

> show #1:24

> torsion #1:24@N,CA,CB,CG 187.928

> torsion #1:24@CA,CB,CG,ND2 224.8163

> align #2:2@N,CA,CB,CG,ND2 toAtoms #1:24@N,CA,CB,CG,ND2

RMSD between 5 atom pairs is 0.068 angstroms  

> save /Users/elizagazaway/Documents/coord_trial1.mol2 format mol2
> combineModels true skipAtoms #2:1-3

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mol2/__init__.py", line 27, in save  
write_mol2(session, path, status=session.logger.status, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mol2/io.py", line 497, in write_mol2  
print("%5d" % atom_indices[chain_atom], end=" ", file=f)  
~~~~~~~~~~~~^^^^^^^^^^^^  
KeyError: <chimerax.atomic.molobject.Atom object at 0x1367fcc10>  
  
KeyError:  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mol2/io.py", line 497, in write_mol2  
print("%5d" % atom_indices[chain_atom], end=" ", file=f)  
~~~~~~~~~~~~^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.2.16
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,4
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 1.4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.3.1 (20E241)
      Kernel Version: Darwin 20.4.0
      Time since boot: 9 days 18:52

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        LG HDR WQHD:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 100.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 306MXSK3K334
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/DisplayPort


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    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
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    ChimeraX-Atomic: 1.46.1
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202308092202
    ChimeraX-CoreFormats: 1.1
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    ChimeraX-FunctionKey: 1.0.1
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    ChimeraX-gltf: 1.0
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    widgetsnbextension: 4.0.8

[Eric Pettersen]

Reported by Eliza Gazaway

[Eric Pettersen]

Hi Eliza,

Thanks for reporting yet another error with the Mol2 writer. Sorry about that. The fix will be in tomorrow's daily build (dated August 10th or later).

--Eric