id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4758	Crash computing surface cap	chimerax-bug-report@…	Tom Goddard	"{{{
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

}}}
"	defect	closed	normal		Surface		duplicate						all	ChimeraX