ISOLDE: cannot access local variable 'o' where it is not associated with a value

[sethh@…]

The following bug report has been submitted:
Platform:        macOS-13.6.9-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Centering on an object loaded. Used isolde commands "st #3" to move to object #3, which it did but then had this error. I think a similar error flashed before and the whole program crashed. This time stayed up but had the error.

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/sethh/0projects/egfr/structures/em_20241030_egfr_76_1770_1807/cryosparc_P96_J481_map_sharp.mrc
> format mrc

Opened cryosparc_P96_J481_map_sharp.mrc as #1, grid size 450,450,450, pixel
0.731, shown at level 0.000148, step 2, values float32  

> close #1

> open
> /Users/sethh/0projects/c3c/structures/em_G03691964_20241029/c3c_model_fit.pdb

Summary of feedback from opening
/Users/sethh/0projects/c3c/structures/em_G03691964_20241029/c3c_model_fit.pdb  
---  
warning | Ignored bad PDB record found on line 1  
HEADER STR7568 version_2 2023.09.19  
  
c3c_model_fit.pdb title:  
Structure of C3c bound to G03550495.22-1 at 2.6 A resolution. [more info...]  
  
Chain information for c3c_model_fit.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  
Non-standard residues in c3c_model_fit.pdb #1  
---  
MG — (MG)  
NAG — (NAG)  
XXX — (XXX)  
  

> open
> /Users/sethh/0projects/c3c/structures/em_G03691964_20241029/maps/cryosparc_P13_J264_003_volume_map_sharp.mrc

Opened cryosparc_P13_J264_003_volume_map_sharp.mrc as #2, grid size
420,420,420, pixel 0.731, shown at level 0.0305, step 2, values float32  

> volume #2 level 0.04922

> volume #2 step 1

> volume #2 color #bf9eb180

> volume #2 level 0.06652

> volume #2 level 0.09592

> open
> /Users/sethh/0projects/c3c/structures/em_G03691964_20241029/G03691964_grade1.pdb

> st #3

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2929, in run  
result = ci.function(session, *args, optional=optional,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3468, in __call__  
return self.cmd.run(text, _used_aliases=_used_aliases, log=log)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sethh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/cmd/cmd.py", line 294, in isolde_step  
rs.step_to(residue)  
File "/Users/sethh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/navigate.py", line 143, in step_to  
self._new_camera_position(residue)  
File "/Users/sethh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/navigate.py", line 232, in _new_camera_position  
interpolate_camera(session, 0, frames=1)  
File "/Users/sethh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/navigate.py", line 217, in interpolate_camera  
ncp, fcp = _get_clip_points(session, dist)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/sethh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/navigate.py", line 360, in _get_clip_points  
return (o+vd*dist*0.5, o+vd*dist*1.5)  
^  
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value  
  
UnboundLocalError: cannot access local variable 'o' where it is not associated
with a value  
  
File "/Users/sethh/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/isolde/navigate.py", line 360, in _get_clip_points  
return (o+vd*dist*0.5, o+vd*dist*1.5)  
^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.2
Locale: en_US.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: Mac14,9
      Model Number: Z17H001PGLL/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 8422.141.2.700.1

Software:

    System Software Overview:

      System Version: macOS 13.6.9 (22G830)
      Kernel Version: Darwin 22.6.0
      Time since boot: 71 days, 20 hours, 41 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        C34J79x:
          Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
          UI Looks like: 3440 x 1440 @ 100.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


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    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
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    ChimeraX-AlignmentMatrices: 2.1
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    ChimeraX-AlphaFold: 1.0
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    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
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    ChimeraX-AtomSearch: 2.0.1
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    ChimeraX-BondRot: 2.0.4
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    ChimeraX-CellPack: 1.0
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    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
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    ChimeraX-ConnectStructure: 2.0.1
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    ChimeraX-Crosslinks: 1.0
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    ChimeraX-DistMonitor: 1.4
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    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
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    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
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[Eric Pettersen]

Reported by Seth Harris