id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14815	volume splitbyzone problems	rawalswasti@…	Tom Goddard	"{{{
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

}}}
"	defect	closed	normal		Volume Data		limitation						all	ChimeraX