The following bug report has been submitted:
Platform: Linux-3.10.0-957.21.3.el7.x86_64-x86_64-with-glibc2.17
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: Segmentation fault
Current thread 0x00007fcfc013b740 (most recent call first):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1753 in masked_elements
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1730 in update_element_buffer
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 904 in _update_buffers
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 783 in _draw_geometry
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 759 in draw_self
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 752 in draw
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1512 in _draw_multiple
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1499 in draw_opaque
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/view.py", line 235 in _draw_scene
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/graphics/view.py", line 165 in draw
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 158 in update_graphics_now
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2226 in moved_marker_cb
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/map/histogram.py", line 414 in move_marker_cb
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2152 in _drag
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2148 in mouseMoveEvent
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> set selectionWidth 4
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 /home/rodolpho/Projects/isolde/AlphaFold_P39109.pdb
Chain information for AlphaFold_P39109.pdb #1
---
Chain | Description
A | No description available
> open "/home/rodolpho/Desktop/Paper
> Figures/cryosparc_P5_J665_006_volume_map.mrc"
Opened cryosparc_P5_J665_006_volume_map.mrc as #2, grid size 440,440,440,
pixel 0.822, shown at level 0.0378, step 2, values float32
> select #1
12061 atoms, 12312 bonds, 1515 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,183.5,0,1,0,73.132,0,0,1,237.03
> view matrix models #1,1,0,0,217.05,0,1,0,191.21,0,0,1,170.07
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.19693,0.77378,0.60206,209.82,0.00027236,0.61413,-0.7892,189.51,-0.98042,-0.15525,-0.12115,160.68
> fitmap #1 inMap #2
Fit molecule AlphaFold_P39109.pdb (#1) to map
cryosparc_P5_J665_006_volume_map.mrc (#2) using 12061 atoms
average map value = 0.1228, steps = 380
shifted from previous position = 28.9
rotated from previous position = 30.4 degrees
atoms outside contour = 2933, contour level = 0.037814
Position of AlphaFold_P39109.pdb (#1) relative to
cryosparc_P5_J665_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.30227880 0.66673664 0.68124135 181.96163295
-0.08291210 0.73035600 -0.67801600 190.42963641
-0.94960682 0.14846671 0.27605167 167.81254966
Axis 0.41825316 0.82531358 -0.37937025
Axis point 207.05220600 0.00000000 49.08948743
Rotation angle (degrees) 81.12129216
Shift along axis 169.60710361
> ui tool show ISOLDE
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 222 residues in model #1 to IUPAC-IUB
standards.
Chain information for AlphaFold_P39109.pdb
---
Chain | Description
1.2/A | No description available
Done loading forcefield
Opened cryosparc_P5_J665_006_volume_map.mrc as #1.1.1.1, grid size
440,440,440, pixel 0.822, shown at step 1, values float32
> select #1
12061 atoms, 12312 bonds, 1515 residues, 12 models selected
> hide sel atoms
> isolde restrain distances #2:1-856
No residues specified to restrain!
> isolde restrain distances #1:1-856
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> isolde restrain distances #2:936-1515
No residues specified to restrain!
> isolde restrain distances #1:936-1515
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> addh
Summary of feedback from adding hydrogens to AlphaFold_P39109.pdb #1.2
---
notes | No usable SEQRES records for AlphaFold_P39109.pdb (#1.2) chain A;
guessing termini instead
Chain-initial residues that are actual N termini: /A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASN 1515
Chain-final residues that are not actual C termini:
1528 hydrogen bonds
12266 hydrogens added
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error launching CUDA compiler: 256
nvcc fatal : Value 'sm_75' is not defined for option 'gpu-architecture'
ISOLDE: started sim
> select #1
24327 atoms, 24578 bonds, 1515 residues, 18 models selected
> show sel cartoons
> select clear
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 52 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> open /home/rodolpho/Desktop/Maps/cryosparc_P5_J566_006_volume_map.mrc
Opened cryosparc_P5_J566_006_volume_map.mrc as #2, grid size 440,440,440,
pixel 0.822, shown at level 0.0386, step 2, values float32
> volume #2 step 1
Opened cryosparc_P5_J566_006_volume_map.mrc as #1.1.1.2, grid size
440,440,440, pixel 0.822, shown at step 1, values float32
> volume #1.1.1.2 level 0.1122
> volume #1.1.1.2 level 0.07255
> volume #1.1.1.2 level 0.06122
> volume #1.1.1.2 color #00fff022
> volume #1.1.1.2 color cyan
> volume #1.1.1.2 level 0.05414
> volume #1.1.1.2 level 0.03289
> select #1:857-901
661 atoms, 663 bonds, 45 residues, 1 model selected
> open "/home/rodolpho/Desktop/Paper Figures/ycf1_pka_valid.pdb"
Chain information for ycf1_pka_valid.pdb #2
---
Chain | Description
A | No description available
> select clear
> select #1:1490-1515
386 atoms, 388 bonds, 26 residues, 1 model selected
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error launching CUDA compiler: 256
nvcc fatal : Value 'sm_75' is not defined for option 'gpu-architecture'
ISOLDE: started sim
> show sel cartoons
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1:857-901
661 atoms, 663 bonds, 45 residues, 1 model selected
> select #1:1490-1515
386 atoms, 388 bonds, 26 residues, 1 model selected
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error launching CUDA compiler: 256
nvcc fatal : Value 'sm_75' is not defined for option 'gpu-architecture'
ISOLDE: started sim
> show sel cartoons
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1:1490-1515
386 atoms, 388 bonds, 26 residues, 1 model selected
> select up
24327 atoms, 24578 bonds, 1515 residues, 1 model selected
> select #1:857-901
661 atoms, 663 bonds, 45 residues, 1 model selected
> isolde restrain distances #1:882-891 templateResidues #2:882-891
Expected ',' or a keyword
> isolde restrain distances #1:882-891 templateAtoms #2:882-891
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 68 residues in model #2 to IUPAC-IUB
standards.
> isolde restrain torsions #1:882-891 templateResidues #2:882-891
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
> select #1:857-901
661 atoms, 663 bonds, 45 residues, 1 model selected
> volume #1.1.1.2 level 0.09216
> select #1
24327 atoms, 24578 bonds, 1515 residues, 21 models selected
> volume #1.1.1.2 level 0.05674
> volume #1.1.1.2 level 0.04116
> volume #1.1.1.2 level 0.03691
> volume #1.1.1.2 level 0.03124
> hide #!2 models
> select #1:857-901
661 atoms, 663 bonds, 45 residues, 1 model selected
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
Error launching CUDA compiler: 256
nvcc fatal : Value 'sm_75' is not defined for option 'gpu-architecture'
ISOLDE: started sim
> show sel cartoons
> volume #1.1.1.2 style image
> volume #1.1.1.2 style surface
> volume #1.1.1.2 color #00ffff44
> open /home/rodolpho/Projects/ycf1_pka_tom_1stmodel.pdb
ycf1_pka_tom_1stmodel.pdb title:
Alphafold V2.0 prediction for metal resistance protein YCF1 (P39109) [more
info...]
Chain information for ycf1_pka_tom_1stmodel.pdb #3
---
Chain | Description | UniProt
A | metal resistance protein YCF1 | YCFI_YEAST
Non-standard residues in ycf1_pka_tom_1stmodel.pdb #3
---
SEP — (SEP)
TPO — (TPO)
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select clear
> volume #1.1.1.2 level 0.04632
> select #1
24327 atoms, 24578 bonds, 1515 residues, 22 models selected
Traceback (most recent call last):
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke
return self._func(self._name, data)
File "/home/rodolpho/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/delayed_reaction.py", line 52, in callback
self.ff(*self.ff_args)
File "/home/rodolpho/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/map_handler_base.py", line 164, in
_use_fast_thread_result
self._set_surface(va, na, ta, hidden_edges)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/map/volume.py", line 2245, in _set_surface
self.set_geometry(va, na, ta, edge_mask = hidden_edges)
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 689, in set_geometry
art()
File "/home/rodolpho/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/mask_handler.py", line 287, in __call__
self.set_surface_mask()
File "/home/rodolpho/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/mask_handler.py", line 311, in set_surface_mask
tmask = numpy.logical_and(mask[t[:,0]], mask[t[:,1]])
IndexError: index 1077207 is out of bounds for axis 0 with size 461985
Error processing trigger "new frame":
IndexError: index 1077207 is out of bounds for axis 0 with size 461985
File "/home/rodolpho/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/mask_handler.py", line 311, in set_surface_mask
tmask = numpy.logical_and(mask[t[:,0]], mask[t[:,1]])
See log for complete Python traceback.
> volume #1.1.1.2 level 0.05464
> volume #1.1.1.2 level 0.1073
> volume #1.1.1.1 level 0.1221
===== Log before crash end =====
Log:
> set selectionWidth 4
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 430.34
OpenGL renderer: GeForce RTX 2080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7B09
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 AMD Ryzen Threadripper 2950X 16-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125G 18G 27G 334M 79G 105G
Swap: 4.0G 1.4G 2.6G
Graphics:
0a:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104 [GeForce RTX 2080 Rev. A] [10de:1e87] (rev a1)
Subsystem: eVga.com. Corp. Device [3842:2183]
Kernel driver in use: nvidia
Locale: ('en_US', '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: 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-Clipper: 0.17.0
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-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
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
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
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
line-profiler: 3.3.0
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
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
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
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Duplicate of #10330.
This one has a Python traceback before the crash that indicates the cause of the problem. A mask array in Clipper is smaller than the number of vertices which is causing index out of bounds errors. This is probably a bug in old Clipper (in ChimeraX 1.3). Having a mask array that is not the right size will cause indexing out of bounds and crashing when it hits our C++ graphics code.
File "/home/rodolpho/.local/share/ChimeraX/1.3/site-
packages/chimerax/clipper/maps/mask_handler.py", line 311, in set_surface_mask
tmask = numpy.logical_and(mask[t[:,0]], mask[t[:,1]])
IndexError: index 1077207 is out of bounds for axis 0 with size 461985