color byattr: min() arg is an empty sequence

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open J:\Projekty\DHS_K329A_ELF1_cryoEM_022021\J147_inverted_finalmap.mrc
> format mrc

Opened J147_inverted_finalmap.mrc as #1, grid size 256,256,256, pixel 0.86,
shown at level 0.106, step 1, values float32  

> open J:/Projekty/DHS_K329A_ELF1_cryoEM_022021/RealSpaceRefine_55/4DHS_1Elf-
> coot-1.pdb

Summary of feedback from opening
J:/Projekty/DHS_K329A_ELF1_cryoEM_022021/RealSpaceRefine_55/4DHS_1Elf-
coot-1.pdb  
---  
warning | Ignored bad PDB record found on line 12144  
END  
  
Chain information for 4DHS_1Elf-coot-1.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> surface dust #2

No surfaces specified  

> surface dust #1

> volume #1 level 0.1218

> ui tool show "Surface Color"

> ui tool show "Surface Zone"

> ui tool show "Color Zone"

> color zone #1 near #2 distance 5.16

> hide #!2 models

> volume #1 level 0.151

> hide #!1 models

> show #!2 models

> style sphere

Changed 12019 atom styles  

> style sphere

Changed 12019 atom styles  

> show cartoons

> hide surfaces

> style stick

Changed 12019 atom styles  

> style stick

Changed 12019 atom styles  

> style ball

Changed 12019 atom styles  

> style ball

Changed 12019 atom styles  

> style stick

Changed 12019 atom styles  

> show cartoons

> set bgColor white

> style sphere

Changed 12019 atom styles  

> show cartoons

> style sphere

Changed 12019 atom styles  

> lighting full

> mlp

Map values for surface "4DHS_1Elf-coot-1.pdb_A SES surface": minimum -26.08,
mean -3.93, maximum 95.9  
Map values for surface "4DHS_1Elf-coot-1.pdb_B SES surface": minimum -27.28,
mean -4.014, maximum 24.99  
Map values for surface "4DHS_1Elf-coot-1.pdb_C SES surface": minimum -26.89,
mean 5.87e+29, maximum 3.017e+32  
Map values for surface "4DHS_1Elf-coot-1.pdb_D SES surface": minimum -26.81,
mean 3.483e+31, maximum 1.68e+34  
Map values for surface "4DHS_1Elf-coot-1.pdb_E SES surface": minimum -25.44,
mean -4.38, maximum 24.57  
To also show corresponding color key, enter the above mlp command and add key
true  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/121p-consurf.aln

Summary of feedback from opening
//www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln
fetched from https  
---  
notes | Fetching 121p-consurf.aln from
https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/121p-consurf.aln  
Downloaded 121p-consurf.aln to C:\Users\Admin\Downloads\121p-consurf.aln  
Alignment identifier is 121p-consurf.aln  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 121p-consurf.aln  
  
Opened 150 sequences from 121p-consurf.aln  

> Command: color byattr seq_conservation

Unknown command: Command: color byattr seq_conservation  

> color byattribute seq_conservation

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1142, in color_by_attr  
non_none_colors = _value_colors(palette, range, non_none_attr_vals)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1263, in _value_colors  
min_val, max_val = min(values), max(values)  
ValueError: min() arg is an empty sequence  
  
ValueError: min() arg is an empty sequence  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1263, in _value_colors  
min_val, max_val = min(values), max(values)  
  
See log for complete Python traceback.  
  

> color byattribute seq_conservation palette cyanmaroon range -1.4,1.4

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 280, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1142, in color_by_attr  
non_none_colors = _value_colors(palette, range, non_none_attr_vals)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1263, in _value_colors  
min_val, max_val = min(values), max(values)  
ValueError: min() arg is an empty sequence  
  
ValueError: min() arg is an empty sequence  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\std_commands\color.py", line 1263, in _value_colors  
min_val, max_val = min(values), max(values)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 462.31
OpenGL renderer: GeForce GTX 1060 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: G5 5587
OS: Microsoft Windows 10 Home (Build 19042)
Memory: 34,129,870,848
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8750H CPU @ 2.20GHz
OSLanguage: pl-PL
Locale: ('pl_PL', 'cp1250')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
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    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
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    Jinja2: 2.11.2
    jupyter-client: 6.1.7
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    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
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    networkx: 2.5
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    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
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    python-dateutil: 2.8.1
    pytz: 2021.1
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