Opened 3 days ago

Closed 43 hours ago

#20454 closed defect (fixed)

Volume model not volume menu

Reported by: ndempsey@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-26.5-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/nate/Library/CloudStorage/Box-Box/Team-Nate-Laurie/Cryo-EM-
> structures-revision/cryosparc_P20_J206_006_volume_map_sharp_closed-HR.mrc

Opened cryosparc_P20_J206_006_volume_map_sharp_closed-HR.mrc as #1, grid size
256,256,256, pixel 1.05, shown at level 0.674, step 1, values float32  

> open /Users/nate/Library/CloudStorage/Box-Box/Team-Nate-Laurie/Cryo-EM-
> structures-revision/cryosparc_P20_J207_006_volume_map_sharp_open-HR.mrc

Opened cryosparc_P20_J207_006_volume_map_sharp_open-HR.mrc as #2, grid size
256,256,256, pixel 1.05, shown at level 0.65, step 1, values float32  

> open /Users/nate/Library/CloudStorage/Box-Box/Team-Nate-Laurie/Cryo-EM-
> structures-revision/cryosparc_P20_J353_map-closed-local-4.5A-lowpass.mrc

Opened cryosparc_P20_J353_map-closed-local-4.5A-lowpass.mrc as #3, grid size
256,256,256, pixel 1.05, shown at level 0.523, step 1, values float32  

> open /Users/nate/Library/CloudStorage/Box-Box/Team-Nate-Laurie/Cryo-EM-
> structures-revision/cryosparc_P20_J331_006_volume_map_sharp_open-
> local_6AngLP.mrc

Opened cryosparc_P20_J331_006_volume_map_sharp_open-local_6AngLP.mrc as #4,
grid size 256,256,256, pixel 1.05, shown at level 0.544, step 1, values
float32  

> open /Users/nate/Library/CloudStorage/Box-Box/Team-Nate-Laurie/Cryo-EM-
> structures-revision/local-resolution/cryosparc_P20_J352_map_locres-
> open-2b.mrc

Opened cryosparc_P20_J352_map_locres-open-2b.mrc as #5, grid size 256,256,256,
pixel 1.05, shown at level 9.35, step 1, values float32  

> open /Users/nate/Library/CloudStorage/Box-Box/Team-Nate-Laurie/Cryo-EM-
> structures-revision/local-resolution/cryosparc_P20_J237_map_locres-
> closed-1a.mrc

Opened cryosparc_P20_J237_map_locres-closed-1a.mrc as #6, grid size
256,256,256, pixel 1.05, shown at level 7.57, step 1, values float32  

> open /Users/nate/Library/CloudStorage/Box-Box/Team-Nate-Laurie/Cryo-EM-
> structures-revision/local-resolution/cryosparc_P20_J238_map_locres-
> open-2a.mrc

Opened cryosparc_P20_J238_map_locres-open-2a.mrc as #7, grid size 256,256,256,
pixel 1.05, shown at level 7.67, step 1, values float32  

> open /Users/nate/Library/CloudStorage/Box-Box/Team-Nate-Laurie/Cryo-EM-
> structures-revision/local-resolution/cryosparc_P20_J351_map_locres-
> closed-1b.mrc

Opened cryosparc_P20_J351_map_locres-closed-1b.mrc as #8, grid size
256,256,256, pixel 1.05, shown at level 3.29, step 1, values float32  

> hide #!5 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> volume #4 level 0.3324

> set bgColor white

> graphics silhouettes true

> lighting soft

> lighting flat

> lighting soft

> rename #4 id #9

> rename #3 id #4

> rename #9 id #3

> ui tool show "Surface Color"

> color sample #1.1 map #1 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0.6734, mean 0.6735, maximum 0.6737  

> color sample #1.1 map #6 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 5.657, maximum 32.84  

> color sample #2.1 map #7 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 5.893, maximum 32.31  

> color sample #4.1 map #8 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 1.435, maximum 40.78  

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 2.916, mean 5.839, maximum 46.42  

> tile

4 models tiled  

> volume #1 level 1.326

> volume #4 level 0.685

> volume #3 level 0.3571

> volume #5 level 11.09

> undo

> tile

5 models tiled  

> volume #1 level 1.244

> volume #2 level 1.209

> volume #3 level 0.3394

> color sample #2.1 map #7 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #2.1 map #7 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #2.1 map #7 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> tile off

> color sample #2.1 map #7 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 3.274, maximum 26.45  

> color sample #4.1 map #8 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 2.629, maximum 24.58  

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> hide #!2 models

> hide #!3 models

> hide #!1 models

> show #!1 models

> show #!2 models

> show #!3 models

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> hide #!1 models

> hide #!2 models

> hide #!4 models

> show #!2 models

> show #!1 models

> show #!4 models

> hide #!2 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> hide #!1 models

> show #!3 models

> color sample #3.1 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #3 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> color sample #3 map #5 palette
> 2,#0000ff:4,#00ffff:6,#00ff00:8,#ffff00:10,#ff0000 outsideColor #808080

Map values for surface "surface": minimum 0, mean 0, maximum 0  

> close #5

> open /Users/nate/Library/CloudStorage/Box-Box/Team-Nate-Laurie/Cryo-EM-
> structures-revision/local-resolution/cryosparc_P20_J352_map_locres-
> open-2b.mrc

Opened cryosparc_P20_J352_map_locres-open-2b.mrc as #5, grid size 256,256,256,
pixel 1.05, shown at level 9.35, step 1, values float32  

> ui tool show "Surface Color"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 571, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1400, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/__init__.py", line 110, in start_tool  
ti = surfcolorgui.show_surface_color_panel(session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/surfcolorgui.py", line 701, in
show_surface_color_panel  
return surface_color_panel(session, create = True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/surfcolorgui.py", line 696, in surface_color_panel  
return SurfaceColorGUI.get_singleton(session, create=create)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/surfcolorgui.py", line 76, in get_singleton  
return tools.get_singleton(session, SurfaceColorGUI, 'Surface Color',  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/tools.py", line 216, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/surfcolorgui.py", line 64, in __init__  
self._surface_chosen()  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/surfcolorgui.py", line 377, in _surface_chosen  
self._map.value = sc.volume  
^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/composite.py", line 405, in _set_value  
self._menu.value = value  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 363, in value  
self.set_value(val)  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 385, in set_value  
self.setText(self.value_map[val])  
~~~~~~~~~~~~~~^^^^^  
KeyError: <chimerax.map.volume.Volume object at 0x142f92a50>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1939, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.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
"/Applications/ChimeraX-1.11.1.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
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
return bi.start_tool(session, name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Surface
Color in bundle ChimeraX-Surface:  
<chimerax.map.volume.Volume object at 0x142f92a50>  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Surface
Color in bundle ChimeraX-Surface:  
  
  
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 578, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
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: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 8 (6 Performance and 2 Efficiency)
      Memory: 16 GB
      System Firmware Version: 18000.120.36
      OS Loader Version: 18000.120.36

Software:

    System Software Overview:

      System Version: macOS 26.5 (25F71)
      Kernel Version: Darwin 25.5.0
      Time since boot: 3 days, 15 hours, 45 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        LU28R55:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    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: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    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: 1.11.1
    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: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    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-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    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: 1.4.2
    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: 1.3.3
    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: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    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: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    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: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    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: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    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: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    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: 3.3.2
    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: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    roman-numerals-py: 4.1.0
    rpds-py: 0.30.0
    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: 2.8.3
    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
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.3.2
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0

Change History (4)

comment:1 by Eric Pettersen, 45 hours ago

Cc: Eric Pettersen added
Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Volume model not volume menu

comment:2 by Eric Pettersen, 45 hours ago

Status: assigned → feedback

Hi Nate,

Thanks for reporting this problem. Do you remember what you were doing in the Surface Color tool when this error happened? Had you changed any of the menus from their default values?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by ndempsey@…, 44 hours ago 

Hi Eric,

I was using surface color to make a local resolution map. I had changed the scale to 5 color rainbow and had modified the bins to 2,4,6,8,10 angstroms. I believe the error occured after had tiled multiple maps then done tile off.

-Nate

-------------------
Nate Dempsey
PhD Candidate @ Park Lab

comment:4 by Tom Goddard, 43 hours ago

Resolution: → fixed
Status: feedback → closed

Fixed.

The Surface Color GUI was trying to set the map used in color by map value to the previously used value but that map had been closed. Made the code test that the map has not been closed. Fixed in daily build and release candidate dated June 5, 2026 or newer.

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