id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
18169	Crash changing volume level	mohammad.bahar@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.119.1.el7.x86_64-x86_64-with-glibc2.38
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f4d85f12740 (most recent call first):
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2772 in draw_elements
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1749 in draw
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 852 in _draw_geometry
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 787 in draw_self
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 780 in draw
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1567 in _draw_multiple
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1554 in draw_opaque
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1579 in draw_depth
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 1647 in use_multishadow_map
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 633 in _compute_shadowmaps
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 227 in _draw_scene
  File ""/app/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw
  File ""/app/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame
  File ""/app/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback
  File ""/app/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop
  File ""/app/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init
  File ""/app/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in 
  File """", line 88 in _run_code
  File """", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_linux, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics (total: 48)
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> camera ortho

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/mo/emdata/PV-
> mAB_31082023/PV1-mAB_31082023/cryosparc_P1039_J107_008_volume_map_sharp.mrc

Opened cryosparc_P1039_J107_008_volume_map_sharp.mrc as #1, grid size
896,896,896, pixel 0.73, shown at step 1, values float32  

> volume #1 region 0,0,0,895,895,895 step 4

> ui mousemode right zoom

> view orient

> volume #1 step 1

> volume #1 sdLevel 4

> surface dust #1 size 7.3

> volume #1 sdLevel 3

> set bgColor white

> lighting soft

> volume #1 sdLevel 2

> volume #1 sdLevel 2.5

> volume #1 sdLevel 3

> open /home/mo/emdata/PV-
> mAB_31082023/PV1-mAB_31082023/locres/cryosparc_P62_J118_map_locres.mrc

Opened cryosparc_P62_J118_map_locres.mrc as #2, grid size 896,896,896, pixel
0.73, shown at step 1, values float32  

> volume #2 region 0,0,0,895,895,895 step 4

> ui tool show ""Surface Color""

> color sample #1.2 map #1 palette #0000ff:#7f7fff:#ffffff:#ff7f7f:#ff0000

Map values for surface ""surface"": minimum 0.3181, mean 0.3182, maximum 0.3184  

> color sample #1.2 map #2 palette
> 0.3181,#0000ff:0.3182,#7f7fff:0.3182,#ffffff:0.3183,#ff7f7f:0.3184,#ff0000

Map values for surface ""surface"": minimum 0, mean 1.551, maximum 15.56  

> color sample #1.2 map #2 palette #0000ff:#7f7fff:#ffffff:#ff7f7f:#ff0000

Map values for surface ""surface"": minimum 0, mean 1.551, maximum 15.56  

> color sample #1.2 map #2 palette
> 1.7,#0000ff:2,#7f7fff:2.3,#ffffff:11.67,#ff7f7f:15.56,#ff0000

Map values for surface ""surface"": minimum 0, mean 1.551, maximum 15.56  

> color sample #1.2 map #2 palette
> 1.7,#0000ff:1.8,#7f7fff:1.9,#ffffff:2,#ff7f7f:2.1,#ff0000

Map values for surface ""surface"": minimum 0, mean 1.551, maximum 15.56  

> color single #1.2

> color sample #1.2 map #2 palette
> #0000ff:#7f7fff:#ffffff:#ff7f7f:#ff0000:#808080:#808080

Map values for surface ""surface"": minimum 0, mean 1.551, maximum 15.56  

> color sample #1.2 map #2 palette
> 1.7,#0000ff:1.75,#7f7fff:1.8,#ffffff:1.85,#ff7f7f:1.9,#ff0000:1.95,#808080:2,#808080

Map values for surface ""surface"": minimum 0, mean 1.551, maximum 15.56  

> ui tool show ""Side View""

> color sample #1.2 map #2 palette
> 1.7,#0000ff:1.72,#5555ff:1.74,#aaaaff:1.76,#ffffff:1.78,#ffa9a9:1.8,#ff5555:1.82,#ff0000

Map values for surface ""surface"": minimum 0, mean 1.551, maximum 15.56  
Map values for surface ""cap far"": minimum 1.718, mean 1.72, maximum 2.1  
Map values for surface ""cap near"": minimum 1.718, mean 1.72, maximum 1.981  

> view orient

> color single #1.2

> open /home/mo/emdata/PV-
> mAB_31082023/PV1-mAB_31082023/locres/cryosparc_P62_J113_map_locres.mrc

Opened cryosparc_P62_J113_map_locres.mrc as #3, grid size 896,896,896, pixel
0.73, shown at step 1, values float32  

> color sample #1.2 map #3 palette
> 1.7,#0000ff:1.72,#5555ff:1.74,#aaaaff:1.76,#ffffff:1.78,#ffa9a9:1.8,#ff5555:1.82,#ff0000

Map values for surface ""surface"": minimum 0, mean 1.503, maximum 18.67  

> color sample #1.2 map #3 palette
> 1.7,#0000ff:1.75,#5555ff:1.8,#aaaaff:1.85,#ffffff:1.9,#ffa9a9:1.95,#ff5555:2,#ff0000

Map values for surface ""surface"": minimum 0, mean 1.503, maximum 18.67  

> color sample #1.2 map #3 palette
> 1.7,#0fc6ce:1.75,#5fd9de:1.8,#afecee:1.85,#ffffff:1.9,#deb4c9:1.95,#be6a93:2,#9e1f5e

Map values for surface ""surface"": minimum 0, mean 1.503, maximum 18.67  

> volume #1 sdLevel 1


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

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> camera ortho

UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 470.63.01
OpenGL renderer: NVIDIA GeForce GTX 745/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome-classic
XDG_SESSION_DESKTOP=gnome-classic
XDG_CURRENT_DESKTOP=GNOME-Classic:GNOME
DISPLAY=:99.0
Manufacturer: Dell Inc.
Model: OptiPlex 9020
OS: Freedesktop SDK 23.08 Flatpak runtime
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 8 Intel(R) Core(TM) i7-4790 CPU @ 3.60GHz
Cache Size: 8192 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       1.7Gi        29Gi       163Mi       781Mi        29Gi
	Swap:           15Gi       916Mi        14Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 [GeForce GTX 745] [10de:1382] (rev a2)	
	Subsystem: NVIDIA Corporation Device [10de:1065]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    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-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    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: 1.2.4
    ChimeraX-DiffPlot: 1.0
    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: 1.1.10
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    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: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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: 3.0.15
    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: 1.16.5
    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
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    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: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
}}}
"	defect	closed	normal		Graphics		nonchimerax						all	ChimeraX