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Opened 26 hours ago
#19415 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Typed in ui tool show surface
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open
> /Users/sevanstroh/Desktop/Myo9B/Structures/Work/2_full_length/Chimera/session_FL.cxs
Log from Thu Nov 20 15:12:39 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/1_cropped_1701_2157/fold_20251114_myo9b_1701_2157_model_0.cif
Chain information for fold_20251114_myo9b_1701_2157_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> close
> open
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/fold_20251114_myo9b_fl_model_0.cif
Chain information for fold_20251114_myo9b_fl_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> select #1.1000:1500
Nothing selected
> select #1:1000-1500
3850 atoms, 3916 bonds, 501 residues, 1 model selected
> select #1:1064-1500
3300 atoms, 3356 bonds, 437 residues, 1 model selected
> color sel orange
> select #1:1983-2157
1311 atoms, 1353 bonds, 175 residues, 1 model selected
> color sel orange
> ~select
Nothing selected
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/Myo9B_FL_labile.cxs
> mlp
Map values for surface "fold_20251114_myo9b_fl_model_0.cif_A SES surface":
minimum -33.52, mean -5.053, maximum 22.86
To also show corresponding color key, enter the above mlp command and add key
true
> ~surface
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/Myo9B_FL_labile.png
> width 582 height 514 supersample 3 transparentBackground true
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/Myo9B_FL_labile.png
> width 1152 height 903 supersample 3
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/Myo9B_FL_labile.png
> width 3840 height 3010 supersample 3 transparentBackground true
> mlp
Map values for surface "fold_20251114_myo9b_fl_model_0.cif_A SES surface":
minimum -33.52, mean -5.053, maximum 22.86
To also show corresponding color key, enter the above mlp command and add key
true
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/Myo9B_FL_hydro.png
> width 3840 height 3010 supersample 3 transparentBackground true
> close
> open
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/Myo9B_FL_labile.cxs
> format session
No such file/path:
/Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/Myo9B_FL_labile.cxs
> open
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/1_cropped_1701_2157/fold_20251114_myo9b_1701_2157_model_0.cif
> format mmcif
Chain information for fold_20251114_myo9b_1701_2157_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> mlp
Map values for surface "fold_20251114_myo9b_1701_2157_model_0.cif_A SES
surface": minimum -28.77, mean -4.863, maximum 22.85
To also show corresponding color key, enter the above mlp command and add key
true
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/20251114_myo9b_1701_2157/Myo9B_1701-2157_hydro.png
> width 1152 height 903 supersample 3
> ~surface
> select #1:235
6 atoms, 5 bonds, 1 residue, 1 model selected
> select stick
Expected an objects specifier or a keyword
> show sel stick
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> style sel stick
Changed 6 atom styles
> style sel stick
Changed 6 atom styles
> style sel ball
Changed 6 atom styles
> show sel atoms
> hide sel atoms
> color sel blue
> select #1:3-188
1477 atoms, 1505 bonds, 186 residues, 1 model selected
> color sel yellow
> select #1:157-246
724 atoms, 735 bonds, 90 residues, 1 model selected
> ~select
Nothing selected
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/20251114_myo9b_1701_2157/Myo9B_1701-2157_regions.png
> width 3840 height 3010 supersample 3 transparentBackground true
> ~select
Nothing selected
Drag select of 67 residues
Drag select of 14 residues
Drag select of 58 residues
> hbonds sel reveal true
70 hydrogen bonds found
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/20251114_myo9b_1701_2157/Myo9B_1701-2157_hbonds.png
> width 3840 height 3010 supersample 3
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/1_cropped_1701_2157/Myo9B_1701-2157_hbonds.png
> width 3840 height 3010 supersample 3 transparentBackground true
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/1_cropped_1701_2157/session.cxs
> close
> open
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/fold_20251114_myo9b_fl_model_0.cif
> format mmcif
Chain information for fold_20251114_myo9b_fl_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> select #1:1935
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel blue
> select #1:1703-1888
1477 atoms, 1505 bonds, 186 residues, 1 model selected
> color sel yellow
> select #1:1701-2157
3565 atoms, 3646 bonds, 457 residues, 1 model selected
> color sel green
> select #1:1703-1888
1477 atoms, 1505 bonds, 186 residues, 1 model selected
> color sel yellow
> select #1:1889-1946
469 atoms, 477 bonds, 58 residues, 1 model selected
> color sel red
> select #1:1935
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel blue
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/Chimera/2_full_length/session_FL.cxs
——— End of log from Thu Nov 20 15:12:39 2025 ———
> view name session-start
opened ChimeraX session
> surface
> ~select
Nothing selected
> ~select
Nothing selected
> color kdHydrophobicity palette viridis
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> mlp
Map values for surface "fold_20251114_myo9b_fl_model_0.cif_A SES surface":
minimum -33.52, mean -5.053, maximum 22.86
To also show corresponding color key, enter the above mlp command and add key
true
> color byattribute kdHydrophobicity
No known/registered numeric attribute kdHydrophobicity
> defattr /Applications/ChimeraX.app/share/attributes/hydrophobicity.attr
Missing or invalid "fileName" argument: File
'/Applications/ChimeraX.app/share/attributes/hydrophobicity.attr' does not
exist
> open /Users/sevanstroh/ChimeraX/Attributes/kdHydrophobicity.defattr
Summary of feedback from opening
/Users/sevanstroh/ChimeraX/Attributes/kdHydrophobicity.defattr
---
note | Assigned attribute 'kdHydrophobicity' to 2157 residues using match mode: any
> color byattribute kdHydrophobicity protein palette
> dodgerblue:white:orangered
17128 atoms, 2157 residues, 1 surfaces, atom kdHydrophobicity range -4.5 to
4.5
> save
> /Users/sevanstroh/Desktop/Myo9B/Structures/Work/2_full_length/Chimera/Myo9B_FL_hydro.png
> width 3840 height 3010 supersample 3 transparentBackground true
> sasaPerRes protein
Unknown command: measure sasaPerRes protein
> measure sasa residue True
Expected an atoms specifier or a keyword
> measure sasa residue true
Expected an atoms specifier or a keyword
> measure sasa atoms :* perResidue true
Expected a keyword
> ui tool show surface
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 248, in ui_tool_show
commas((repr(t[1]) for t in tools), 'and'))
^^^^^^
NameError: name 'commas' is not defined
NameError: name 'commas' is not defined
File
"/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/cmd.py", line 248, in ui_tool_show
commas((repr(t[1]) for t in tools), 'and'))
^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK183SM/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 35 days, 20 hours, 57 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: 3456 x 2234 Retina
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: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
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
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 1.5.1
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: 2.17.1
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: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
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: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
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