Crash computing surface cap

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.15.0-72-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 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 0x00007fc333e53680 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/surface/cap.py", line 95 in compute_cap
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/surface/cap.py", line 38 in show_surface_clip_caps
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/surface/cap.py", line 28 in update_clip_caps
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/updateloop.py", line 62 in draw_new_frame
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/updateloop.py", line 138 in _redraw_timer_callback
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py", line 293 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 866 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 1015 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.8/runpy.py", line 194 in _run_module_as_main


Log:
> mousemode shift leftMode "translate selected models"

> mousemode shift middleMode "rotate selected models"

> mousemode rightMode zoom

> mousemode control wheelMode "contour level"

> mousemode setting "contour level" speed 0.1

> mousemode shift wheelMode "rotate selected models"

> camera ortho

> set bgColor grey

> lighting soft

> functionkey F1 cofr sel

> functionkey F2 mousemode rightMode 'mark surface'

> functionkey F3 mousemode rightMode 'move markers'

> functionkey F4 markercolour 3 1

> functionkey F5 view

> functionkey F6 view sel pad 0.92 clip false

> functionkey F7 mousemode rightMode 'delete markers'

> functionkey F8 mousemode rightMode zoom

> functionkey F9 sequence chain sel

> functionkey F10 transparency sel 65

> functionkey F11 transparency sel 0

> functionkey F12 tool show 'Fit in Map'

> color name f01graublau #BADBED

Color 'f01graublau' is opaque, 72.94% red, 85.88% green, and 92.94% blue

  

> color name f02silberblau #F6FAFC

Color 'f02silberblau' is opaque, 96.47% red, 98.04% green, and 98.82% blue

  

> color name f03muschel #FFFFE5

Color 'f03muschel' is opaque, 100% red, 100% green, and 89.8% blue

  

> color name f04beige #F3F3A9

Color 'f04beige' is opaque, 95.29% red, 95.29% green, and 66.27% blue

  

> color name f05blau #00AAFF

Color 'f05blau' is opaque, 0% red, 66.67% green, and 100% blue

  

> color name f06hellgrün #7EBE7E

Color 'f06hellgrün' is opaque, 49.41% red, 74.51% green, and 49.41% blue

  

> color name f07rot #FD625E

Color 'f07rot' is opaque, 99.22% red, 38.43% green, and 36.86% blue

  

> color name f08grün #349E34

Color 'f08grün' is opaque, 20.39% red, 61.96% green, and 20.39% blue

  

> color name f09flieder #D57AD5

Color 'f09flieder' is opaque, 83.53% red, 47.84% green, and 83.53% blue

  

> color name f10rotorange #FF6A25

Color 'f10rotorange' is opaque, 100% red, 41.57% green, and 14.51% blue

  

> color name f11cyan #8CEAEA

Color 'f11cyan' is opaque, 54.9% red, 91.76% green, and 91.76% blue

  

> color name f12grau #B2B2B2

Color 'f12grau' is opaque, 69.8% red, 69.8% green, and 69.8% blue

  

> color name f13gelb #FFFF00

Color 'f13gelb' is opaque, 100% red, 100% green, and 0% blue

  

> color name f14orange #FEB172

Color 'f14orange' is opaque, 99.61% red, 69.41% green, and 44.71% blue

  

> color name f15dunkelblau #0088CC

Color 'f15dunkelblau' is opaque, 0% red, 53.33% green, and 80% blue

  

> color name f16gold #FFBF34

Color 'f16gold' is opaque, 100% red, 74.9% green, and 20.39% blue

  

> color name f17lila #5B42CD

Color 'f17lila' is opaque, 35.69% red, 25.88% green, and 80.39% blue

  

> color name f18hellgrau #DCDCDC

Color 'f18hellgrau' is opaque, 86.27% red, 86.27% green, and 86.27% blue

  

> color name f19limette #32CD32

Color 'f19limette' is opaque, 19.61% red, 80.39% green, and 19.61% blue

  

> color name f20pink #E6ADE6

Color 'f20pink' is opaque, 90.2% red, 67.84% green, and 90.2% blue

  

> color name f21altrot #FF6B6B

Color 'f21altrot' is opaque, 100% red, 41.96% green, and 41.96% blue

  

> color name f22altgrün #60D89C

Color 'f22altgrün' is opaque, 37.65% red, 84.71% green, and 61.18% blue

  

> color name f23anthrazit #323F45

Color 'f23anthrazit' is opaque, 19.61% red, 24.71% green, and 27.06% blue

  

> color name f24altorange #D5A755

Color 'f24altorange' is opaque, 83.53% red, 65.49% green, and 33.33% blue

  

> color name f25altblau #0088CC

Color 'f25altblau' is opaque, 0% red, 53.33% green, and 80% blue

  

> color name f26dunkelgrün #39815D

Color 'f26dunkelgrün' is opaque, 22.35% red, 50.59% green, and 36.47% blue

  

> alias localres color sample #$1 map #$2 offset 0.1 update true palette
> "#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"
> range $3,$4

> alias markercolour color zone #$2 near #$1 sharpEdges true distance 3; fun
> F4 'markercolour $1 $2'

> alias quickmarkercolour color zone #$2 near #$1 sharpEdges false distance 3;
> fun F4 'quickmarkercolour $1 $2'

> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3

> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3

> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow

> alias chaininfo preset custom chaininfo

> alias foto save browse format tiff width 4000 height 3000 supersample 4
> transparentBackground false

> alias durch save browse format tiff width 4000 height 3000 supersample 4
> transparentBackground true

> alias session save browse format session includeMaps true compress lz4

> alias nomapsession save browse format session includeMaps false compress lz4

UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 460.80
OpenGL renderer: GeForce GTX 1050/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Notebook
Model: N85_N87,HJ,HJ1,HK1
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            31G        5.1G         22G         75M        3.3G         25G
	Swap:          8.0G          0B        8.0G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:591b] (rev 04)	
	Subsystem: CLEVO/KAPOK Computer Device [1558:850a]	
	Kernel driver in use: i915
Locale: ('de_DE', 'UTF-8')
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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    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: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    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-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    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: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 1.0.1
    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-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    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: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    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: 5.0.9
    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: 2.0.1
    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: 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: 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

[Eric Pettersen]

Anonymous user is apparently German and has quite the extensive set of at-startup commands!

[Tom Goddard]

I am surprised to see 3 reports of this clip cap computation crash in the last 4 weeks, two on Windows, one on Linux, 3 different users, and none in the previous years. The clip cap code did not change. But in response to the first report #4630 I switched the cap border calculation to use 64 bit integer indexing. That is in the 1.3 daily build after May 13, 2021 but not in 1.2. None of the crash reports used the newer code. It seems unlikely that the border calculation overflowed the 32-bit integer indexing, but I have no other clues what might have caused the crashes. Will wait and see if the crash is reported in the daily build.