Opened 4 years ago

Closed 4 years ago

#4554 closed defect (fixed)

Error when no surfaces

Reported by: chimerax-bug-report@… 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:        Linux-5.4.0-47-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.3.dev202104230049 (2021-04-23 00:49:01 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3.dev202104230049 (2021-04-23)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/mpillana/KR5_SEPT_2020/011452_XmippProtMonoRes/011452/extra/import_relion_half1_class001_unfil.mrc
> format mrc

Opened import_relion_half1_class001_unfil.mrc as #1, grid size 758,758,758,
pixel 1.43, shown at step 1, values float32  

> open
> /home/mpillana/KR5_SEPT_2020/011452_XmippProtMonoRes/extra/monoresResolutionChimera.mrc
> format mrc

Opened monoresResolutionChimera.mrc as #2, grid size 758,758,758, pixel 1,
shown at step 1, values float32  

> ui tool show "Map Coordinates"

> color sample #1 map #2 key true palette
> 3.0,#000080:3.7,#0000e8:4.4,#003cff:5.11,#0098ff:5.81,#0cf4eb:6.51,#56ffa0:7.21,#a4ff53:7.91,#eeff09:8.62,#ffab00:9.32,#ff5500:10.02,#e40000

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2853, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/surface/colorvol.py", line 40, in color_sample  
_color_by_map_value(session, surfaces, map, palette = palette, range = range,
key = key,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/surface/colorvol.py", line 132, in _color_by_map_value  
return cs  
UnboundLocalError: local variable 'cs' referenced before assignment  
  
UnboundLocalError: local variable 'cs' referenced before assignment  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/surface/colorvol.py", line 132, in _color_by_map_value  
return cs  
  
See log for complete Python traceback.  
  

> color sample #1 map #2 palette
> 3.0,#000080:3.7,#0000e8:4.4,#003cff:5.11,#0098ff:5.81,#0cf4eb:6.51,#56ffa0:7.21,#a4ff53:7.91,#eeff09:8.62,#ffab00:9.32,#ff5500:10.02,#e40000

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2853, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/surface/colorvol.py", line 40, in color_sample  
_color_by_map_value(session, surfaces, map, palette = palette, range = range,
key = key,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/surface/colorvol.py", line 132, in _color_by_map_value  
return cs  
UnboundLocalError: local variable 'cs' referenced before assignment  
  
UnboundLocalError: local variable 'cs' referenced before assignment  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/surface/colorvol.py", line 132, in _color_by_map_value  
return cs  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.100
OpenGL renderer: GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP Pavilion Laptop 14-ce0xxx
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G         13G        167M        151M        1.9G        1.6G
	Swap:          2.0G        1.4G        621M

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07)	
	Subsystem: Hewlett-Packard Company UHD Graphics 620 [103c:84ba]	
	Kernel driver in use: i915
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.1.1
    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: 1.18
    ChimeraX-AtomicLibrary: 3.2
    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: 1.3
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202104230049
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.2.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.1
    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: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.3
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2
    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
    ChimeraX-ModelPanel: 1.1
    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
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.4
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    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: 1.5
    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: 1.8
    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
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    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
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

Change History (3)

comment:1 by pett, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Error when no surfaces

comment:2 by Tom Goddard, 4 years ago

Need to give a clear error message when first argument of "color sample" is not a surface. User opened very large map 758 x 758 * 758 so it displays as a single plane in image style initially, not a surface.

comment:3 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Added error message when no surfaces specified when coloring by map value (sample, electrostatic, gradient).

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