Opened 20 months ago

Closed 20 months ago

#14815 closed defect (limitation)

volume splitbyzone problems

Reported by: rawalswasti@… 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: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x000077fc (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\map_data\arrays.py", line 298 in zone_mask
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\surface\colorzone.py", line 358 in split_zones_by_color
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\surface\colorzone.py", line 321 in split_volume_by_color_zone
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\surface\colorzone.py", line 378 in split_volumes_by_color_zone
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2856 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\surface\colorzonegui.py", line 253 in _split_map
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/SHASHANK/OneDrive/Desktop/CryoSparc/cryosparc_P398_J236_006_volume_map_sharp.mrc

Opened cryosparc_P398_J236_006_volume_map_sharp.mrc as #1, grid size
360,360,360, pixel 0.95, shown at level 0.0772, step 2, values float32  

> open
> C:/Users/SHASHANK/OneDrive/Desktop/CryoSparc/C9CARD_H38R_final_monomer.pdb

Chain information for C9CARD_H38R_final_monomer.pdb #2  
---  
Chain | Description  
A | No description available  
  

> volume #1 level 0.1023

> volume #1 level 0.1367

> fitmap #2 inMap #1

Fit molecule C9CARD_H38R_final_monomer.pdb (#2) to map
cryosparc_P398_J236_006_volume_map_sharp.mrc (#1) using 788 atoms  
average map value = 0.241, steps = 44  
shifted from previous position = 0.0117  
rotated from previous position = 0.0728 degrees  
atoms outside contour = 296, contour level = 0.13675  
  
Position of C9CARD_H38R_final_monomer.pdb (#2) relative to
cryosparc_P398_J236_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999921 0.00024446 -0.00123593 0.16959097  
-0.00024467 0.99999996 -0.00016537 0.07530409  
0.00123589 0.00016567 0.99999922 -0.25768044  
Axis 0.13025899 -0.97262034 -0.19246366  
Axis point 208.82680243 0.00000000 137.24732747  
Rotation angle (degrees) 0.07280584  
Shift along axis -0.00155742  
  

> volume #1 step 1 level 0.13 color grey transparency 0

> set silhouettes true

> set silhouetteWidth 2

> ui tool show "Color Actions"

> sym #2 c2*h,9.129,-67.562,30,-15 coordinateSystem #3 center
> 171.0,171.0,171.0

Invalid "coordinateSystem" argument: Must specify 1 model, got 0  

> sym #2 c2*h,9.129,-67.562,30,-15 coordinateSystem #1 center
> 171.0,171.0,171.0

> ui tool show "Color Actions"

> color bychain

> color byelement

> color red

> color orange

> preset "initial styles" "space-filling (chain colors)"

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

> undo

> preset "initial styles" "space-filling (chain colors)"

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

> preset "initial styles" "space-filling (chain colors)"

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

> preset "initial styles" "space-filling (single color)"

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

> undo

> show cartoons

> style sphere

Changed 788 atom styles  

> hide atoms

> hide surfaces

> rainbow

> color zone #1 near #2 distance 5.7

Drag select of 5802 residues  

> color zone #1 near sel & #2 distance 5.7

> fitmap #2 inMap #1

Fit molecule C9CARD_H38R_final_monomer.pdb (#2) to map
cryosparc_P398_J236_006_volume_map_sharp.mrc (#1) using 788 atoms  
average map value = 0.1347, steps = 40  
shifted from previous position = 0.187  
rotated from previous position = 0.165 degrees  
atoms outside contour = 382, contour level = 0.13  
  
Position of C9CARD_H38R_final_monomer.pdb (#2) relative to
cryosparc_P398_J236_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.39499471 0.91868292 -0.00093388 -53.45444608  
-0.91868023 0.39499582 0.00222392 260.15852360  
0.00241195 -0.00002050 0.99999709 -137.21132687  
Axis -0.00122154 -0.00182099 -0.99999760  
Axis point 171.06765852 170.66190190 0.00000000  
Rotation angle (degrees) 66.73441198  
Shift along axis 136.80254713  
  

> color zone #1 near sel & #2 distance 5.7

> select clear

Drag select of 5809 residues  

> ui tool show "Color Key"

> ui mousemode right "color key"

> ui mousemode right translate

> ui tool show "Color Zone"

> color zone #1 near #2 distance 5.7

> color single #1

> color zone #1 near #2 distance 5.7

> color zone #1 near #2 distance 161.63

> color zone #1 near #2 distance 11.06

> color zone #1 near #2 distance 0.95

> color zone #1 near #2 distance 3.72

> color zone #1 near #2 distance 950

> color zone #1 near #2 distance 0.95

> volume splitbyzone #1

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\surface\colorzonegui.py", line 253, in _split_map  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\surface\colorzone.py", line 378, in
split_volumes_by_color_zone  
vlist.extend(split_volume_by_color_zone(v))  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\surface\colorzone.py", line 321, in
split_volume_by_color_zone  
grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\surface\colorzone.py", line 362, in split_zones_by_color  
g = masked_grid_data(sg, mask, m)  
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\map_data\arrays.py", line 328, in masked_grid_data  
putmask(masked, mask == mask_value, matrix)  
File "", line 5, in putmask  
ValueError: putmask: mask and data must be the same size  
  
ValueError: putmask: mask and data must be the same size  
  
File "", line 5, in putmask  
  
See log for complete Python traceback.  
  

> color zone #1 near #2 distance 710.27

> color zone #1 near #2 distance 6.67

> color single #1

Need to color zone map before it can be split  

> color zone #1 near #2 distance 950

> volume splitbyzone #1


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 516.40
OpenGL renderer: NVIDIA GeForce GTX 1660 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming A15 FA506IU_FA566IU
OS: Microsoft Windows 11 Home Single Language (Build 22631)
Memory: 16,556,470,272
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 4800H with Radeon Graphics         
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 20 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → volume splitbyzone problems

comment:2 by Tom Goddard, 20 months ago

Resolution: → limitation
Status: assigned → closed

I see "volume splitbyzone #1" crashed, probably because it ran out of memory. It appears you used rainbow coloring which colors every residue a different color and then tried to split the map into separate maps for each color, basically making as many copies of the map as there are residues. I'm not sure what you were trying to do, but you probably would run out of memory making hundreds of copies of the map.

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