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#14501 closed defect (fixed)

self.vertex_colors is empty

Reported by:	chimerax-bug-report@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Surface	Version:
Keywords:		Cc:	pett
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  

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 D:/6j5t.pdb

6j5t.pdb title:  
Reconstitution and structure of A plant NLR resistosome conferring immunity
[more info...]  

Chain information for 6j5t.pdb #1  
---  
Chain | Description | UniProt  
A D I J M | probable serine/threonine-protein kinase PBL2 |  
B E H K N | protein kinase superfamily protein | Q9SVY5_ARATH 1-351  
C F G L O | disease resistance RPP13-like protein 4 | R13L4_ARATH 1-852  

Non-standard residues in 6j5t.pdb #1  
---  
DTP \u2014 2&#x27;-deoxyadenosine 5&#x27;-triphosphate  
U5P \u2014 uridine-5&#x27;-monophosphate  


> color bychain

> color byhetero

> color bypolymer

> show surfaces

> hide atoms

> hide surfaces

> show atoms

> style stick

Changed 53488 atom styles  

> style sphere

Changed 53488 atom styles  

> style ball

Changed 53488 atom styles  

> style sphere

Changed 53488 atom styles  

> hide atoms

> show cartoons

> hide cartoons

> show surfaces

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> select /I:168@CG1

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 6 bonds, 1 residue, 2 models selected  

> select up

369 atoms, 379 bonds, 46 residues, 2 models selected  

> select up

832 atoms, 851 bonds, 104 residues, 2 models selected  

> select up

935 atoms, 956 bonds, 118 residues, 2 models selected  

> select up

1199 atoms, 1228 bonds, 150 residues, 2 models selected  

> select up

1322 atoms, 1353 bonds, 165 residues, 2 models selected  

> select up

1561 atoms, 1595 bonds, 197 residues, 2 models selected  

> select up

53488 atoms, 54538 bonds, 6665 residues, 2 models selected  

> select up

53488 atoms, 54538 bonds, 25 pseudobonds, 6665 residues, 17 models selected  

> select down

53488 atoms, 54538 bonds, 6665 residues, 16 models selected  

> select down

1561 atoms, 1595 bonds, 197 residues, 16 models selected  

> surface level 5

> surface level 10

> surface resolution 10

15 Gaussian surfaces, threshold level 10.000  

> surface resolution 5

15 Gaussian surfaces, threshold level 10.000  

> show sel atoms

> show sel surfaces

> hide sel atoms

> select /C/F/G/L/O

32530 atoms, 33140 bonds, 10 pseudobonds, 4045 residues, 2 models selected  

> show sel atoms

> color sel bypolymer

> color sel bychain

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 178, in <lambda>  
lambda *args, ft=self._fill_tree, ar=always_rebuild: ft(always_rebuild=ar))  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 218, in _fill_tree  
self._get_info(model, all_selected_models, part_selected_models)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 314, in _get_info  
bg_color = self._model_color(obj)  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 345, in _model_color  
return model.model_color  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molsurf.py", line 404, in _get_model_color  
return self.color if vc is None else most_common_color(vc)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\colors.py", line 816, in most_common_color  
max_index = argmax(counts)  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\numpy\core\fromnumeric.py", line 1229, in argmax  
return _wrapfunc(a, 'argmax', axis=axis, out=out, **kwds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\numpy\core\fromnumeric.py", line 59, in _wrapfunc  
return bound(*args, **kwds)  
^^^^^^^^^^^^^^^^^^^^  
ValueError: attempt to get argmax of an empty sequence  

Error processing trigger "new frame":  
ValueError: attempt to get argmax of an empty sequence  

File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\numpy\core\fromnumeric.py", line 59, in _wrapfunc  
return bound(*args, **kwds)  
^^^^^^^^^^^^^^^^^^^^  

See log for complete Python traceback.  


> color sel bychain

> color sel byhetero

> color sel bypolymer

> open D:\6j5t.pdb format pdb

6j5t.pdb title:  
Reconstitution and structure of A plant NLR resistosome conferring immunity
[more info...]  

Chain information for 6j5t.pdb #2  
---  
Chain | Description | UniProt  
A D I J M | probable serine/threonine-protein kinase PBL2 |  
B E H K N | protein kinase superfamily protein | Q9SVY5_ARATH 1-351  
C F G L O | disease resistance RPP13-like protein 4 | R13L4_ARATH 1-852  

Non-standard residues in 6j5t.pdb #2  
---  
DTP \u2014 2&#x27;-deoxyadenosine 5&#x27;-triphosphate  
U5P \u2014 uridine-5&#x27;-monophosphate  

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 182, in <lambda>  
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 218, in _fill_tree  
self._get_info(model, all_selected_models, part_selected_models)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 314, in _get_info  
bg_color = self._model_color(obj)  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 345, in _model_color  
return model.model_color  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molsurf.py", line 404, in _get_model_color  
return self.color if vc is None else most_common_color(vc)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\colors.py", line 816, in most_common_color  
max_index = argmax(counts)  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\numpy\core\fromnumeric.py", line 1229, in argmax  
return _wrapfunc(a, 'argmax', axis=axis, out=out, **kwds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\numpy\core\fromnumeric.py", line 59, in _wrapfunc  
return bound(*args, **kwds)  
^^^^^^^^^^^^^^^^^^^^  
ValueError: attempt to get argmax of an empty sequence  

Error processing trigger "new frame":  
ValueError: attempt to get argmax of an empty sequence  

File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\numpy\core\fromnumeric.py", line 59, in _wrapfunc  
return bound(*args, **kwds)  
^^^^^^^^^^^^^^^^^^^^  

See log for complete Python traceback.  


> set bgColor white

> set bgColor black

> lighting simple

> lighting soft

> lighting full

> lighting soft

> set bgColor white

> select clear

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting soft

> show surfaces

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 182, in <lambda>  
lambda *args, ft=self._fill_tree: ft(always_rebuild=True))  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 218, in _fill_tree  
self._get_info(model, all_selected_models, part_selected_models)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 314, in _get_info  
bg_color = self._model_color(obj)  
^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\model_panel\tool.py", line 345, in _model_color  
return model.model_color  
^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\atomic\molsurf.py", line 404, in _get_model_color  
return self.color if vc is None else most_common_color(vc)  
^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\core\colors.py", line 816, in most_common_color  
max_index = argmax(counts)  
^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\numpy\core\fromnumeric.py", line 1229, in argmax  
return _wrapfunc(a, 'argmax', axis=axis, out=out, **kwds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\numpy\core\fromnumeric.py", line 59, in _wrapfunc  
return bound(*args, **kwds)  
^^^^^^^^^^^^^^^^^^^^  
ValueError: attempt to get argmax of an empty sequence  

Error processing trigger "new frame":  
ValueError: attempt to get argmax of an empty sequence  

File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\numpy\core\fromnumeric.py", line 59, in _wrapfunc  
return bound(*args, **kwds)  
^^^^^^^^^^^^^^^^^^^^  

See log for complete Python traceback.  





OpenGL version: 3.3.0 NVIDIA 512.78
OpenGL renderer: NVIDIA GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Strix G513IH_G513IH
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,558,260,224
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 4800H with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
   alabaster: 0.7.16
   appdirs: 1.4.4
   asttokens: 2.4.1
   Babel: 2.14.0
   backcall: 0.2.0
   beautifulsoup4: 4.11.2
   blockdiag: 3.0.0
   blosc2: 2.0.0
   build: 0.10.0
   certifi: 2023.11.17
   cftime: 1.6.3
   charset-normalizer: 3.3.2
   ChimeraX-AddCharge: 1.5.13
   ChimeraX-AddH: 2.2.5
   ChimeraX-AlignmentAlgorithms: 2.0.1
   ChimeraX-AlignmentHdrs: 3.4.1
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.12.2
   ChimeraX-AlphaFold: 1.0
   ChimeraX-AltlocExplorer: 1.1.1
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.49.1
   ChimeraX-AtomicLibrary: 12.1.5
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.3.2
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 2.1.2
   ChimeraX-BondRot: 2.0.4
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.10.5
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.2.2
   ChimeraX-ButtonPanel: 1.0.1
   ChimeraX-CageBuilder: 1.0.1
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.3.2
   ChimeraX-ChangeChains: 1.1
   ChimeraX-CheckWaters: 1.3.2
   ChimeraX-ChemGroup: 2.0.1
   ChimeraX-Clashes: 2.2.4
   ChimeraX-ColorActions: 1.0.3
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.5
   ChimeraX-CommandLine: 1.2.5
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.7.1
   ChimeraX-CoreFormats: 1.2
   ChimeraX-coulombic: 1.4.2
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.3
   ChimeraX-Dicom: 1.2
   ChimeraX-DistMonitor: 1.4
   ChimeraX-DockPrep: 1.1.3
   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
   ChimeraX-Hbonds: 2.4
   ChimeraX-Help: 1.2.2
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.1
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-IUPAC: 1.0
   ChimeraX-Label: 1.1.8
   ChimeraX-ListInfo: 1.2.2
   ChimeraX-Log: 1.1.6
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.9.1
   ChimeraX-Map: 1.1.4
   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: 2.1.2
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.6.1
   ChimeraX-MedicalToolbar: 1.0.2
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.12.1
   ChimeraX-MMTF: 2.2
   ChimeraX-Modeller: 1.5.14
   ChimeraX-ModelPanel: 1.4
   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
   ChimeraX-Neuron: 1.0
   ChimeraX-Nifti: 1.1
   ChimeraX-NRRD: 1.1
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.13.1
   ChimeraX-PDB: 2.7.3
   ChimeraX-PDBBio: 1.0.1
   ChimeraX-PDBLibrary: 1.0.4
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0.1
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.1
   ChimeraX-PubChem: 2.1
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.1
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.2
   ChimeraX-RNALayout: 1.0
   ChimeraX-RotamerLibMgr: 4.0
   ChimeraX-RotamerLibsDunbrack: 2.0
   ChimeraX-RotamerLibsDynameomics: 2.0
   ChimeraX-RotamerLibsRichardson: 2.0
   ChimeraX-SaveCommand: 1.5.1
   ChimeraX-SchemeMgr: 1.0
   ChimeraX-SDF: 2.0.2
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0.1
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.11
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.1.1
   ChimeraX-ShowSequences: 1.0.2
   ChimeraX-SideView: 1.0.1
   ChimeraX-Smiles: 2.1.2
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.12.4
   ChimeraX-STL: 1.0.1
   ChimeraX-Storm: 1.0
   ChimeraX-StructMeasure: 1.1.2
   ChimeraX-Struts: 1.0.1
   ChimeraX-Surface: 1.0.1
   ChimeraX-SwapAA: 2.0.1
   ChimeraX-SwapRes: 2.2.2
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-TaskManager: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.1.2
   ChimeraX-ToolshedUtils: 1.2.4
   ChimeraX-Topography: 1.0
   ChimeraX-ToQuest: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.33.3
   ChimeraX-uniprot: 2.3
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.3.2
   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: 1.1.3
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.2.1
   comtypes: 1.1.14
   contourpy: 1.2.0
   cxservices: 1.2.2
   cycler: 0.12.1
   Cython: 0.29.33
   debugpy: 1.8.0
   decorator: 5.1.1
   docutils: 0.19
   executing: 2.0.1
   filelock: 3.9.0
   fonttools: 4.47.2
   funcparserlib: 2.0.0a0
   glfw: 2.6.4
   grako: 3.16.5
   h5py: 3.10.0
   html2text: 2020.1.16
   idna: 3.6
   ihm: 0.38
   imagecodecs: 2023.9.18
   imagesize: 1.4.1
   ipykernel: 6.23.2
   ipython: 8.14.0
   ipython-genutils: 0.2.0
   ipywidgets: 8.1.1
   jedi: 0.18.2
   Jinja2: 3.1.2
   jupyter-client: 8.2.0
   jupyter-core: 5.7.1
   jupyterlab-widgets: 3.0.9
   kiwisolver: 1.4.5
   line-profiler: 4.0.2
   lxml: 4.9.2
   lz4: 4.3.2
   MarkupSafe: 2.1.4
   matplotlib: 3.7.2
   matplotlib-inline: 0.1.6
   msgpack: 1.0.4
   nest-asyncio: 1.6.0
   netCDF4: 1.6.2
   networkx: 3.1
   nibabel: 5.0.1
   nptyping: 2.5.0
   numexpr: 2.8.8
   numpy: 1.25.1
   openvr: 1.23.701
   packaging: 23.2
   ParmEd: 3.4.3
   parso: 0.8.3
   pep517: 0.13.0
   pickleshare: 0.7.5
   pillow: 10.2.0
   pip: 23.0
   pkginfo: 1.9.6
   platformdirs: 4.1.0
   prompt-toolkit: 3.0.43
   psutil: 5.9.5
   pure-eval: 0.2.2
   py-cpuinfo: 9.0.0
   pycollada: 0.7.2
   pydicom: 2.3.0
   Pygments: 2.16.1
   pynrrd: 1.0.0
   PyOpenGL: 3.1.7
   PyOpenGL-accelerate: 3.1.7
   pyopenxr: 1.0.2801
   pyparsing: 3.0.9
   pyproject-hooks: 1.0.0
   PyQt6-commercial: 6.3.1
   PyQt6-Qt6: 6.3.2
   PyQt6-sip: 13.4.0
   PyQt6-WebEngine-commercial: 6.3.1
   PyQt6-WebEngine-Qt6: 6.3.2
   python-dateutil: 2.8.2
   pytz: 2023.3.post1
   pywin32: 305
   pyzmq: 25.1.2
   qtconsole: 5.4.3
   QtPy: 2.4.1
   RandomWords: 0.4.0
   requests: 2.31.0
   scipy: 1.11.1
   setuptools: 67.4.0
   sfftk-rw: 0.7.3
   six: 1.16.0
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.5
   sphinx: 6.1.3
   sphinx-autodoc-typehints: 1.22
   sphinxcontrib-applehelp: 1.0.8
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 1.0.6
   sphinxcontrib-htmlhelp: 2.0.5
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 1.0.7
   sphinxcontrib-serializinghtml: 1.1.10
   stack-data: 0.6.3
   superqt: 0.5.0
   tables: 3.8.0
   tcia-utils: 1.5.1
   tifffile: 2023.7.18
   tinyarray: 1.2.4
   tomli: 2.0.1
   tornado: 6.4
   traitlets: 5.9.0
   typing-extensions: 4.9.0
   tzdata: 2023.4
   urllib3: 2.1.0
   wcwidth: 0.2.13
   webcolors: 1.12
   wheel: 0.38.4
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.9
   WMI: 1.5.1

Change History (2)

comment:1 by pett, 21 months ago

Cc:	pett added
Component:	Unassigned → Surface
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → self.vertex_colors is empty

comment:2 by Tom Goddard, 21 months ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

An empty molecular surface was created (using the obscure "surface level 10" by mistake). Then Model Panel wanted to know the most common color and the 0 length list of colors caused the error. Made code check that there is at least one color.

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