Opened 17 months ago

Closed 17 months ago

#15374 closed defect (fixed)

Color zone: name 'atom' is not defined

Reported by: Tony Schaefer Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
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: 1.8.dev202403271703 (2024-03-27 17:03:08 UTC)
Description
I tried coloring an electon density by zone. Apologies if this has been fixed already, it takes us a while to update software on work PCs. 

Log:
> cd C:\Users\ajs99778/Desktop

Current working directory is: C:\Users\ajs99778\Desktop  

> graphics selection width 4

UCSF ChimeraX version: 1.8.dev202403271703 (2024-03-27)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/ajs99778/Desktop/test_65735301.xyz

opened test_65735301.xyz as an XYZ coordinate file movie  

> close

> open opt-freq-3.log

Summary of feedback from opening opt-freq-3.log  
---  
notes | opt-freq-3.log has 1 imaginary harmonic vibrational mode  
816.41i  
  
  
Opened opt-freq-3.log as a Gaussian output file  

> preset seqcrow "index labels"

Using preset: SEQCROW / Index Labels  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select

67 atoms, 60 bonds, 12 pseudobonds, 1 residue, 4 models selected  

> ui tool show "File Info"

> close

> open C:/Users/ajs99778/Desktop/traj-50000_65788528.xyz

opened traj-50000_65788528.xyz as an XYZ coordinate file movie  

> ui mousemode right "select similar fragments"

> hide select_rings.py

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

> hide sel

> ui autostart false CliX

> close

> open C:/Users/ajs99778/Desktop/test_65779103.xyz

opened test_65779103.xyz as an XYZ coordinate file movie  

> close

> open "C:\Users\ajs99778\SEQCROW_SCRATCH\test cube 3 Thu Jan 18 14.14.24
> 2024\density.cube" format cube

Opened density.cube as #1, grid size 31,31,31, pixel 0.318, shown at level
-0.145,0.145, step 1, values float32  

> volume #1 level -0.1452 level 0.1452

> volume #1 level -0.1452 color white

> volume #1 level 0.06028

> volume #1 level 0.002

> open "C:\Users\ajs99778\SEQCROW_SCRATCH\test cube 3 Thu Jan 18 14.14.24
> 2024\test_cube_3.out" format out

Opened test_cube_3.out as an ORCA output file  

> help color

> color zone #1 near C

> color zone #1 near C distance 1.7

> color zone #1 near C distance 2

> color zone #1 near C

> close

> open smiles:O

Translated SMILES to 3D structure via NCI web service (SMILES: O)  

> preset seqcrow ball-stick-endcap

Using preset: SEQCROW / Ball-Stick-Endcap  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> ui tool show "Build QM Input"

job started: local ORCA job "water orbitals"  
job finished: local ORCA job "water orbitals"  

> open "C:\Users\ajs99778\SEQCROW_SCRATCH\water orbitals Tue Jun 4 16.01.45
> 2024\water_orbitals.out" format out

Summary of feedback from opening C:\Users\ajs99778\SEQCROW_SCRATCH\water
orbitals Tue Jun 4 16.01.45 2024\water_orbitals.out  
---  
errors | could not open water_orbitals.out  
LookupError('Could not find atom: [] on\nwater_orbitals.out\n0')  
  
SEQCROW failed to open water_orbitals.out  

> ui tool show "Orbital Viewer"

> ui tool show "Job Queue"

job started: local ORCA job "water orbitals"  
job finished: local ORCA job "water orbitals"  

> open "C:\Users\ajs99778\SEQCROW_SCRATCH\water orbitals Tue Jun 4 16.03.30
> 2024\water_orbitals.out" format out

Opened water_orbitals.out as an ORCA output file  

> ui tool show "Orbital Viewer"

Opened electron density as #2.1, grid size 36,26,20, pixel 0.1,0.104,0.105,
shown at level 0.002,-0.002, step 1, values float64  

> close #2.1

> close #1

Opened electron density as #2.1, grid size 76,66,60, pixel 0.1,0.101,0.102,
shown at level 0.002,-0.002, step 1, values float64  

> show #2.1

> volume #2.1 level 0.0200 level -0.0200 color #ffffff80 color #e666b380

> color zone #2.1 near O

[Repeated 1 time(s)]

> show #2.1

> volume #2.1 level 0.0020 level -0.0020 color #ffffff80 color #e666b380

> color zone #2.1 near O

> color zone #2.1 near O distance 1.8

> color zone #2.1 near O distance 1.9

> color zone #2.1 near O distance 1.7

> color zone #2.1 near O distance 1.8

> color zone #2.1 near O distance 1.8 sharpEdges true bondPointSpacing 0.1

> select #2.1

3 models selected  

> color zone #2.1 near O distance 1.8 sharpEdges true bondPointSpacing 0.1
> trans 0.5

Expected a keyword  

> transparency 0.5

> transparency 0.1

> transparency 0.1 target s

> help trans

> select clear

> select #2.1

3 models selected  

> hide #2.1.2 models

> hide #2.1.1 models

> show #2.1.2 models

> show #2.1.1 models

> volume splitbyzone #2.1

Volume electron density #2.1 does not have zone coloring  

> color zone #2.1 near O distance 1.8 sharpEdges true bondPointSpacing 0.1

> close #2.1.2

> hide #2.1.1 models

> show #2.1.1 models

> close #2.1.1

> hide #2.1 models

> show #2.1 models

> color zone #2.1 near O distance 1.8 sharpEdges true bondPointSpacing 0.1

color zone: No surfaces specified.  

> close #2.1

Opened electron density as #2.1, grid size 76,66,60, pixel 0.1,0.101,0.102,
shown at level 0.002,-0.002, step 1, values float64  

> color zone #2.1 near O distance 1.8 sharpEdges true bondPointSpacing 0.1

> volume splitbyzone #2.1

Opened electron density 0 as #1.1, grid size 76,66,60, pixel 0.1,0.101,0.102,
shown at level 0.002,-0.002, step 1, values float64  
Opened electron density 1 as #1.2, grid size 76,66,60, pixel 0.1,0.101,0.102,
shown at level 0.002,-0.002, step 1, values float64  

> close #1

> color zone #2.1 distance 1.8 sharpEdges true bondPointSpacing 0.1

Missing required "near" argument  

> close #2.1

Opened electron density as #2.1, grid size 76,66,60, pixel 0.1,0.101,0.102,
shown at level 0.002,-0.002, step 1, values float64  

> color zone #2.1 near #2 distance 1.8 sharpEdges true bondPointSpacing 0.1

Traceback (most recent call last):  
File "C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 2904, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-
packages\chimerax\std_commands\color.py", line 1372, in color_zone  
points, colors = points_and_colors(atoms, bonds, bond_point_spacing)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-
packages\chimerax\surface\colorzone.py", line 56, in points_and_colors  
bpoints, bcolors = bond_points_and_colors(bonds, bond_point_spacing)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-
packages\chimerax\surface\bondzone.py", line 6, in bond_points_and_colors  
bcolors = bond_point_colors(bonds, bond_point_spacing)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-
packages\chimerax\surface\bondzone.py", line 43, in bond_point_colors  
rgba1, rgba2 = [atom.color for a in b.atoms]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-
packages\chimerax\surface\bondzone.py", line 43, in <listcomp>  
rgba1, rgba2 = [atom.color for a in b.atoms]  
^^^^  
NameError: name 'atom' is not defined  
  
NameError: name 'atom' is not defined  
  
File "C:\Users\ajs99778\ChimeraX-032924\bin\Lib\site-
packages\chimerax\surface\bondzone.py", line 43, in  
rgba1, rgba2 = [atom.color for a in b.atoms]  
^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4953
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7000
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 16,853,479,424
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    argcomplete: 3.3.0
    asttokens: 2.4.1
    attrs: 23.2.0
    Babel: 2.14.0
    basis-set-exchange: 0.10
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.5.1
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    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: 2.12.1
    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: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-clix: 0.1.5
    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: 1.8.dev202403271703
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.9
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    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-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    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-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.37.1
    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: 0.2.2
    comtypes: 1.3.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
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    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
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    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
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    Jinja2: 3.1.3
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    jsonschema-specifications: 2023.12.1
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    PyQt6-commercial: 6.6.1
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    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    referencing: 0.35.1
    regex: 2024.5.10
    requests: 2.31.0
    rpds-py: 0.18.1
    scipy: 1.12.0
    Send2Trash: 1.8.2
    SEQCROW: 1.8.9a2
    setuptools: 69.2.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
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    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.9.2
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
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    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 17 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Color zone: name 'atom' is not defined

Pretty clearly 'atom' should be 'a'

comment:2 by Tom Goddard, 17 months ago

Resolution: → fixed
Status: assigned → closed

Fixed in 1.8 and daily builds.

This error was caused by the bondPointSpacing option of the color zone command. Apparently no one has used in 6 years since this bug has been present that long. I hate adding features like this that no one uses. But working now.

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