Somehow model.overall_color is being saved/restored

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202509250039 (2025-09-25 00:39:44 UTC)
Description
scenes again, not sure what I did, but was trying mlp and coulombic surface coloring,  maybe when clicking scene thumbnail to try to restore that coloring

Log:
UCSF ChimeraX version: 1.11.dev202509250039 (2025-09-25)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/meng/Desktop/scenes2.cxs format session

Log from Thu Sep 25 12:44:00 2025UCSF ChimeraX version: 1.11.dev202509250039
(2025-09-25)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open scenes2.cxs

Log from Thu Sep 25 12:42:34 2025

> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start toolshed show $1

> alias whereprefs info path user unversioned config

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> http://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias segtest open 0557 from emdb; vol threshold #1 min 0; vol scale #2
> value uint8; open 6nzk

executed startup.cxc  
UCSF ChimeraX version: 1.11.dev202509250039 (2025-09-25)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1enl

Summary of feedback from opening 1enl fetched from pdb  
---  
warnings | PDB entry 1ENL has been replaced by 2ENL  
Invalid residue range for struct_conf "HELX_P1": residue in non-polymer entity
"1", on line 289  
Invalid residue range for struct_conf "HELX_P2": residue in non-polymer entity
"1", on line 290  
Invalid residue range for struct_conf "HELX_P3": residue in non-polymer entity
"1", on line 291  
Invalid residue range for struct_conf "HELX_P4": residue in non-polymer entity
"1", on line 292  
Invalid residue range for struct_conf "HELX_P5": residue in non-polymer entity
"1", on line 293  
7 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "MEA 1": residue in non-polymer
entity "1", on line 348  
Invalid sheet range for struct_sheet_range "MEA 2": residue in non-polymer
entity "1", on line 349  
Invalid sheet range for struct_sheet_range "MEA 3": residue in non-polymer
entity "1", on line 350  
Invalid sheet range for struct_sheet_range "BAR 1": residue in non-polymer
entity "1", on line 351  
Invalid sheet range for struct_sheet_range "BAR 2": residue in non-polymer
entity "1", on line 352  
7 messages similar to the above omitted  
note | Fetching compressed mmCIF 1enl from http://files.rcsb.org/download/1enl.cif  
  
1enl title:  
Crystal structure of enolase indicates that enolase and pyruvate kinase
evolved from A common ancestor [more info...]  
  
Non-standard residues in 1enl #1  
---  
ALA — alanine  
ARG — arginine  
ASN — asparagine  
ASP — aspartic acid  
CYS — cysteine  
GLN — glutamine  
GLU — glutamic acid  
GLY — glycine  
HIS — histidine  
ILE — isoleucine  
LEU — leucine  
LYS — lysine  
MET — methionine  
PHE — phenylalanine  
PRO — proline  
SER — serine  
THR — threonine  
TRP — tryptophan  
TYR — tyrosine  
VAL — valine  
  

> close

> open 4enl

4enl title:  
Crystal structure of holoenzyme refined At 1.9 angstroms resolution: trigonal-
bipyramidal geometry of the cation binding site [more info...]  
  
Chain information for 4enl #1  
---  
Chain | Description | UniProt  
A | ENOLASE | ENO1_YEAST 1-436  
  
Non-standard residues in 4enl #1  
---  
SO4 — sulfate ion  
ZN — zinc ion  
  
4enl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> scenes save 1

> ui tool show Scenes

> graphics silhouettes true

> set bgColor white

> open 2mnr

2mnr title:  
Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal
structure of mandelate racemase At 2.5 angstroms resolution: identification of
the active site and possible catalytic residues [more info...]  
  
Chain information for 2mnr #2  
---  
Chain | Description | UniProt  
A | MANDELATE RACEMASE | MANR_PSEPU 3-359  
  
Non-standard residues in 2mnr #2  
---  
MN — manganese (II) ion  
SO4 — sulfate ion  
  
2mnr mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> scenes save ""

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 4enl, chain A (#1) with 2mnr, chain A (#2), sequence alignment
score = 219.9  
RMSD between 73 pruned atom pairs is 1.307 angstroms; (across all 312 pairs:
12.638)  
  

> label ligand

> label ligand height 1

> label ligand height 4

> label ligand height 2

> scenes save ""

[Repeated 1 time(s)]

> 2dlabels text "enolase and mandelate racemizing enzyme" color blue xpos .1
> ypos .9

> ui tool show "Side View"

> scenes save ""

> scenes restore 5

> scenes save 5

> save scenes.cxs

> scenes restore 1

> scenes restore 2

> scenes restore 3

> scenes restore 4

> scenes restore 5

> scenes restore 4

> scenes restore 5

> scenes restore 1

> scenes restore 2

> scenes restore 3

> scenes restore 4

> scenes restore 5

> usage scenes restore

scenes restore sceneName  
— Restore the scene named 'scene_name'.  
sceneName: a text string  

> scenes restore 5

> scenes restore 4

> scenes restore 3

> scenes restore 4

> scenes restore 3

> scenes rename 3 scene-three

> scenes rename scene-three three

> scenes rename three matched

> scenes restore 4

> scenes delete 4

> scenes restore 5

> preset cartoons/nucleotides cylinders/stubs

Using preset: Cartoons/Nucleotides / Cylinders/Stubs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> scenes restore 5

[Repeated 1 time(s)]

> scenes rename 5 title+ribbons

> scenes rename title+ribbons title

> scenes rename title titled

> scenes save ""

> scenes restore 6

> scenes rename 6 titled-tubes

> scenes restore titled-tubes

> save scenes.cxs

> scenes restore matched

> scenes restore 2

> scenes restore 1

> scenes restore 2

> scenes restore matched

> scenes restore titled

> scenes restore titled-tubes

> scenes restore titled

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> save scenes.cxs

> scenes restore titled-tubes

> scenes restore titled

> scenes restore titled-tubes

> help 2dl

> 2dlabels #3 visibility false

> scenes save ""

> scenes restore 7

> scenes rename 7 title-hidden

> scenes restore titled-tubes

> scenes restore titled

> scenes restore matched

> scenes restore title-hidden

[Repeated 1 time(s)]

> set bgColor plum

> scenes save title-hidden

> scenes restore titled-tubes

> scenes restore title-hidden

> label delete

> scenes save ""

> scenes restore 8

> scenes rename 8 lab-hidden

> set bgColor cream

Invalid "bgColor" argument: Invalid color name or specifier  

> ui tool show "Color Actions"

> set bgColor linen

> scenes save lab-hidden

> scenes save ""

> scenes restore 9

> scenes rename 9 unclip

> scenes restore titled

> scenes restore titled-tubes

> scenes restore 2

> scenes restore lab-hidden

> scenes restore title-hidden

> scenes restore titled-tubes

> scenes restore matched

> scenes restore 2

> scenes restore 1

> scenes restore titled

> scenes restore titled-tubes

> scenes restore unclip

> scenes restore lab-hidden

> scenes restore title-hidden

> scenes restore lab-hidden

> scenes restore unclip

> hide ligand

> hide solvent

> size ions vdwrad +1

Expected a keyword  

> size ions atomRadius +1

Changed 2 atom radii  

> size ions atomRadius +1

Changed 2 atom radii  

> scenes save ""

> scenes restore 10

> scenes rename 10 bigions

> scenes restore unclip

> scenes restore lab-hidden

> scenes restore title-hidden

> size atomRadius default

Changed 6558 atom radii  

> size stickRadius .5

Changed 6111 bond radii  

> hide solvent

> scenes save ""

> scenes restore 11

> scenes rename 11 fatsticks

> scenes restore unclip

> scenes restore bigions

> scenes restore fatsticks

> save scenes2.cxs

——— End of log from Thu Sep 25 12:42:34 2025 ———

> view name session-start

opened ChimeraX session  

> scenes restore 1

> scenes restore 2

> scenes restore matched

> scenes restore titled

> scenes restore titled-tubes

> scenes restore title-hidden

> scenes restore lab-hidden

> scenes restore unclip

> scenes restore bigions

> scenes restore fatsticks

> size stickRadius .2

Changed 6111 bond radii  

> save scenes2.cxs

——— End of log from Thu Sep 25 12:44:00 2025 ———

> view name session-start

opened ChimeraX session  

> style sphere

Changed 6558 atom styles  

> scenes save spheres

> scenes restore spheres

> scenes restore bigions

> scenes restore fatsticks

> scenes restore bigions

> scenes restore lab-hidden

> scenes restore title-hidden

> style stick

Changed 6558 atom styles  

> color white pseudobonds

> style ions sphere

Changed 2 atom styles  

> save scene whitepbs

Cannot determine format for 'scene'  

> scenes save whitepbs

> scenes restore spheres

> scenes delete spheres

> scenes restore fatsticks

> scenes delete fatsticks

> scenes restore bigions

> scenes delete bigions

> scenes restore unclip

> scenes restore whitepbs

> color lime N atoms

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color #1 & C lime atoms

> scenes save greenC

> scenes restore whitepbs

> scenes restore unclip

> scenes restore greenC

> scenes restore lab-hidden

> scenes restore greenC

> hide atoms

> scenes save hideatoms

> scenes restore greenC

> scenes restore hideatoms

> scenes restore greenC

> hide pseudobonds

> scenes save hidepb

> scenes restore whitepbs

> scenes restore hidepb

> save scenes2.cxs

> 2dlabels delete

> scenes restore titled

> scenes restore titled-tubes

> scenes save dorky

> surface #1

> hide #2

Unknown command: modelcif hide #2  

> hide #2 models

> hide solvent

> clip off

> coulombic #1

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 4enl_A SES surface #1.2: minimum, -29.61, mean -2.71,
maximum 20.74  

> scenes save dorky

> mlp #1

Map values for surface "4enl_A SES surface": minimum -28.81, mean -5.645,
maximum 21.6  

> scenes save ""

> scenes restore dorky

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.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
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/tool.py", line 130, in scene_selected_cb  
run(self.session, f'scene restore {StringArg.unparse(scene_name)}')  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/cmd.py", line 61, in restore_scene  
session.scenes.restore_scene(scene_name)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/manager.py", line 100, in restore_scene  
self.get_scene(scene_name).restore_scene()  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/scene.py", line 201, in restore_scene  
Model.restore_scene(model, scene_data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 452, in restore_scene  
setattr(self, attr, val)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 278, in _set_overall_color  
self.color = color  
^^^^^^^^^^  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 595, in set_color  
c[:, :] = rgba  
~^^^^^^  
TypeError: int() argument must be a string, a bytes-like object or a real
number, not 'NoneType'  
  
Error processing trigger "scene selected":  
TypeError: int() argument must be a string, a bytes-like object or a real
number, not 'NoneType'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 595, in set_color  
c[:, :] = rgba  
~^^^^^^  
  
See log for complete Python traceback.  
  

> scenes restore dorky

Traceback (most recent call last):  
File
"/Users/chimera/Applications/ChimeraX_Daily.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
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/tool.py", line 130, in scene_selected_cb  
run(self.session, f'scene restore {StringArg.unparse(scene_name)}')  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/cmd.py", line 61, in restore_scene  
session.scenes.restore_scene(scene_name)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/manager.py", line 100, in restore_scene  
self.get_scene(scene_name).restore_scene()  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/scenes/scene.py", line 201, in restore_scene  
Model.restore_scene(model, scene_data)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 452, in restore_scene  
setattr(self, attr, val)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 278, in _set_overall_color  
self.color = color  
^^^^^^^^^^  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 595, in set_color  
c[:, :] = rgba  
~^^^^^^  
TypeError: int() argument must be a string, a bytes-like object or a real
number, not 'NoneType'  
  
Error processing trigger "scene selected":  
TypeError: int() argument must be a string, a bytes-like object or a real
number, not 'NoneType'  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 595, in set_color  
c[:, :] = rgba  
~^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: Mac15,4
      Model Number: Z19700021LL/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 35 days, 2 hours, 41 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.8.0
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.17
    ChimeraX-AtomicLibrary: 14.2
    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
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202509250039
    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-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.7.1
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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: 0.2.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    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-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.48.3
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.4.2
    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
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.10.7
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.17
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.60.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2025.4.15
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    msgpack: 1.1.1
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.13.0
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    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: 4.4.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    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
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 8.4.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.5
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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
    stack-data: 0.6.3
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14