Mutation scores: wrapped C/C++ object of type ScoresList has been deleted

[willow.coyote-maestas@…]

The following bug report has been submitted:
Platform:        macOS-15.7.3-arm64-arm-64bit
ChimeraX Version: 1.13.dev202605282311 (2026-05-28 23:11:54 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.13.dev202605282311 (2026-05-28)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/structures/AF_P05177.pdb"

AF_P05177.pdb title:  
Alphafold monomer V2.0 prediction for cytochrome P450 1A2 (P05177) [more
info...]  
  
Chain information for AF_P05177.pdb #1  
---  
Chain | Description | UniProt  
A | cytochrome P450 1A2 | CP1A2_HUMAN 1-516  
  
Computing secondary structure  

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP1A2_variant_effects.csv"

Summary of feedback from opening /Users/willowcoyote-
maestas/Library/CloudStorage/Box-Box/WCM
Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP1A2_variant_effects.csv  
---  
notes | Ignored 1446 variants: 1446 deletions p.(A2_L3del), p.(A2_S4del), p.(A2del) ...  
Associated 1 chains #1/A with mutations CYP1A2_variant_effects  
  
Opened deep mutational scan data for 10687 mutations of 515 residues with
score names effect_CYP1A2_norm, effect_CYP1A2_raw, position.  

> mutationscores scatterplot position effect_CYP1A2_norm

Plotted 10687 mutations with position on x-axis and effect_CYP1A2_norm on
y-axis  

> mutationscores define mutation_score fromScoreName effect_CYP1A2_raw combine
> mean

Defined score mutation_score having range -0.615 to 0.277 for 515 residues
using 10687 mutations  
Set attribute mutation_score for 515 residues of chain #1/A  

> color byattribute r:mutation_score #1/A palette
> -0.535,red:-0.259,white:0.0168,white:0.292,blue noValueColor white

4123 atoms, 516 residues, atom mutation_score range -0.615 to 0.277  

> set bgColor white

> lighting soft

> lighting flat

> lighting simple

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting simple

[Repeated 2 time(s)]

> lighting soft

> lighting simple

> lighting soft

> save "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/CYP1A2_structure.cxs"

> ui tool show "Render/Select by Attribute"

> color byattribute r:cyp1a2_mean target csab palette
> -0.535,red:-0.259,white:0.0168,white:0.292,blue

4123 atoms, 516 residues, atom cyp1a2_mean range -0.615 to 0.277  

> color byattribute r:cyp1a2_mean target csab palette
> -0.535,red:-0.259,white:0.0168,white:0.292,blue

4123 atoms, 516 residues, atom cyp1a2_mean range -0.615 to 0.277  

> save "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/CYP1A2_structure.cxs"

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/structures/AF_P11712.pdb"

AF_P11712.pdb title:  
Alphafold monomer V2.0 prediction for cytochrome P450 2C9 (P11712) [more
info...]  
  
Chain information for AF_P11712.pdb #2  
---  
Chain | Description | UniProt  
A | cytochrome P450 2C9 | CP2C9_HUMAN 1-490  
  
Computing secondary structure  

> close session

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/structures/AF_P11712.pdb"

AF_P11712.pdb title:  
Alphafold monomer V2.0 prediction for cytochrome P450 2C9 (P11712) [more
info...]  
  
Chain information for AF_P11712.pdb #1  
---  
Chain | Description | UniProt  
A | cytochrome P450 2C9 | CP2C9_HUMAN 1-490  
  
Computing secondary structure  

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP2C9_variant_effects.csv"

Summary of feedback from opening /Users/willowcoyote-
maestas/Library/CloudStorage/Box-Box/WCM
Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP2C9_variant_effects.csv  
---  
notes | Ignored 1353 variants: 1353 deletions p.(M1del), p.(D2_L4del), p.(D2_S3del) ...  
Associated 1 chains #1/A with mutations CYP2C9_variant_effects  
  
Opened deep mutational scan data for 10165 mutations of 489 residues with
score names effect_CYP2C9_norm, effect_CYP2C9_raw, position.  

> mutationscores scatterplot effect_CYP2C9_norm position

Plotted 10165 mutations with effect_CYP2C9_norm on x-axis and position on
y-axis  

> mutationscores define mutation_score fromScoreName effect_CYP2C9_norm
> combine mean

Defined score mutation_score having range -0.432 to 1.41 for 489 residues
using 10165 mutations  
Set attribute mutation_score for 489 residues of chain #1/A  

> color byattribute r:mutation_score #1/A palette
> -0.0513,red:0.52,white:1.09,white:1.66,blue noValueColor white

3910 atoms, 490 residues, atom mutation_score range -0.432 to 1.41  

> close session

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/structures/AF_P08684.pdb"

AF_P08684.pdb title:  
Alphafold monomer V2.0 prediction for cytochrome P450 3A4 (P08684) [more
info...]  
  
Chain information for AF_P08684.pdb #1  
---  
Chain | Description | UniProt  
A | cytochrome P450 3A4 | CP3A4_HUMAN 1-503  
  
Computing secondary structure  

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP3A4_variant_effects.csv"

Error processing trigger "mutation set added":  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
mset_list.clear()  
  
See log for complete Python traceback.  
  
Summary of feedback from opening /Users/willowcoyote-
maestas/Library/CloudStorage/Box-Box/WCM
Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP3A4_variant_effects.csv  
---  
notes | Ignored 1422 variants: 1422 deletions p.(M1del), p.(A2_L3del), p.(A2del) ...  
Traceback (most recent call last):  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
  
return self._func(self._name, data)  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 82, in _mutation_set_added  
  
self._update_list()  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
  
mset_list.clear()  
  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
  
Associated 1 chains #1/A with mutations CYP3A4_variant_effects  
  
Opened deep mutational scan data for 10390 mutations of 502 residues with
score names effect_CYP3A4_norm, effect_CYP3A4_raw, position.  

> mutationscores define mutation_score fromScoreName effect_CYP3A4_norm
> combine mean

Defined score mutation_score having range 0.0865 to 1.39 for 502 residues
using 10390 mutations  
Set attribute mutation_score for 502 residues of chain #1/A  

> color byattribute r:mutation_score #1/A palette
> 0.274,red:0.672,white:1.07,white:1.47,blue noValueColor white

4034 atoms, 503 residues, atom mutation_score range 0.0865 to 1.39  

> close session

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/structures/AF_P08684.pdb" format pdb

AF_P08684.pdb title:  
Alphafold monomer V2.0 prediction for cytochrome P450 3A4 (P08684) [more
info...]  
  
Chain information for AF_P08684.pdb #1  
---  
Chain | Description | UniProt  
A | cytochrome P450 3A4 | CP3A4_HUMAN 1-503  
  
Computing secondary structure  

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP3A4_variant_effects.csv"

Error processing trigger "mutation set added":  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
mset_list.clear()  
  
See log for complete Python traceback.  
  
Summary of feedback from opening /Users/willowcoyote-
maestas/Library/CloudStorage/Box-Box/WCM
Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP3A4_variant_effects.csv  
---  
notes | Ignored 1422 variants: 1422 deletions p.(M1del), p.(A2_L3del), p.(A2del) ...  
Traceback (most recent call last):  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
  
return self._func(self._name, data)  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 82, in _mutation_set_added  
  
self._update_list()  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
  
mset_list.clear()  
  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
  
Associated 1 chains #1/A with mutations CYP3A4_variant_effects  
  
Opened deep mutational scan data for 10390 mutations of 502 residues with
score names effect_CYP3A4_norm, effect_CYP3A4_raw, position.  

> mutationscores define mutation_score fromScoreName effect_CYP3A4_norm
> combine mean

Defined score mutation_score having range 0.0865 to 1.39 for 502 residues
using 10390 mutations  
Set attribute mutation_score for 502 residues of chain #1/A  

> color byattribute r:mutation_score #1/A palette
> 0.274,red:0.672,white:1.07,white:1.47,blue noValueColor white

4034 atoms, 503 residues, atom mutation_score range 0.0865 to 1.39  

> save "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/CYP3A4_structure.cxs"

> close session

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/structures/AF_P11712.pdb" format pdb

AF_P11712.pdb title:  
Alphafold monomer V2.0 prediction for cytochrome P450 2C9 (P11712) [more
info...]  
  
Chain information for AF_P11712.pdb #1  
---  
Chain | Description | UniProt  
A | cytochrome P450 2C9 | CP2C9_HUMAN 1-490  
  
Computing secondary structure  

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP2C9_variant_effects.csv"

Error processing trigger "mutation set added":  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
mset_list.clear()  
  
See log for complete Python traceback.  
  
Summary of feedback from opening /Users/willowcoyote-
maestas/Library/CloudStorage/Box-Box/WCM
Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP2C9_variant_effects.csv  
---  
notes | Ignored 1353 variants: 1353 deletions p.(M1del), p.(D2_L4del), p.(D2_S3del) ...  
Traceback (most recent call last):  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
  
return self._func(self._name, data)  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 82, in _mutation_set_added  
  
self._update_list()  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
  
mset_list.clear()  
  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
  
Associated 1 chains #1/A with mutations CYP2C9_variant_effects  
  
Opened deep mutational scan data for 10165 mutations of 489 residues with
score names effect_CYP2C9_norm, effect_CYP2C9_raw, position.  

> mutationscores define mutation_score fromScoreName effect_CYP2C9_norm
> combine mean

Defined score mutation_score having range -0.432 to 1.41 for 489 residues
using 10165 mutations  
Set attribute mutation_score for 489 residues of chain #1/A  

> color byattribute r:mutation_score #1/A palette
> -0.0513,red:0.52,white:1.09,white:1.66,blue noValueColor white

3910 atoms, 490 residues, atom mutation_score range -0.432 to 1.41  

> save "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/CYP2C9_structure.cxs"

> close session

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/structures/AF_P10635.pdb"

AF_P10635.pdb title:  
Alphafold monomer V2.0 prediction for cytochrome P450 2D6 (P10635) [more
info...]  
  
Chain information for AF_P10635.pdb #1  
---  
Chain | Description | UniProt  
A | cytochrome P450 2D6 | CP2D6_HUMAN 1-497  
  
Computing secondary structure  

> open "/Users/willowcoyote-maestas/Library/CloudStorage/Box-Box/WCM
> Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP2D6_variant_effects.csv"

Error processing trigger "mutation set added":  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
mset_list.clear()  
  
See log for complete Python traceback.  
  
[Repeated 4 time(s)]  Summary of feedback from opening /Users/willowcoyote-
maestas/Library/CloudStorage/Box-Box/WCM
Lab/Willow/ArpaH/061926/analysis/output/chimerax/CYP2D6_variant_effects.csv  
---  
notes | Ignored 1397 variants: 1397 deletions p.(M1del), p.(G2_E4del), p.(G2_L3del) ...  
Traceback (most recent call last):  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
  
return self._func(self._name, data)  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 82, in _mutation_set_added  
  
self._update_list()  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
  
mset_list.clear()  
  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
  
Traceback (most recent call last):  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
  
return self._func(self._name, data)  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 82, in _mutation_set_added  
  
self._update_list()  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
  
mset_list.clear()  
  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
  
Traceback (most recent call last):  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
  
return self._func(self._name, data)  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 82, in _mutation_set_added  
  
self._update_list()  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
  
mset_list.clear()  
  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
  
Traceback (most recent call last):  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
  
return self._func(self._name, data)  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 82, in _mutation_set_added  
  
self._update_list()  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
  
mset_list.clear()  
  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
  
Traceback (most recent call last):  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
  
return self._func(self._name, data)  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 82, in _mutation_set_added  
  
self._update_list()  
  
File "/Applications/ChimeraX_Daily
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mutation_scores/ms_list.py", line 93, in _update_list  
  
mset_list.clear()  
  
RuntimeError: wrapped C/C++ object of type ScoresList has been deleted  
  
  
Associated 1 chains #1/A with mutations CYP2D6_variant_effects  
  
Opened deep mutational scan data for 10284 mutations of 496 residues with
score names effect_CYP2D6_norm, effect_CYP2D6_raw, position.  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 13822.61.10
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.7.3 (24G419)
      Kernel Version: Darwin 24.6.0
      Time since boot: 7 hours, 42 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.3.3
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.69.1
    ChimeraX-AtomicLibrary: 14.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.13.dev202605282311
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.1
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.3
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.4.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.17
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.16.1
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.8
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.19
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.20
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.51.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.17
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.29
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.0
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.4.4
    stack-data: 0.6.3
    starlette: 1.2.0
    superqt: 0.7.6
    tables: 3.10.2
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.6
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.7.0
    uvicorn: 0.48.0
    wcwidth: 0.7.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.24.2

[Tom Goddard]

Fixed.

This error happens after opening mutation scores (.csv), then closing the session (command close session), then opening more mutation scores. The Mutation Scores List window was deleted but later gets called when a new set of scores is opened and produces an error. I had code to detect that the window was closed, but it was wrong.