The following bug report has been submitted:
Platform: Windows-10-10.0.22000
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.
Windows fatal exception: code 0x8001010d
Current thread 0x00001d58 (most recent call first):
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 "D:/downloads new/80S_analysis/Z_flipped_refinement.mrc"
Opened Z_flipped_refinement.mrc as #1, grid size 420,420,420, pixel 1.07,
shown at level 1.33, step 2, values float32
> volume #1 level 0.7
> ui tool show "Hide Dust"
> surface dust #1 size 30
> volume #1 color #00aaff
> set bgColor white
> volume #1 color #ffaa7f
> volume #1 color #ffff7f
> volume #1 color yellow
> volume #1 color #ffaa7f
> lighting soft
> center #1
Unknown command: center #1
> centre #1
Unknown command: centre #1
> save C:\ProgramData\ChimeraX\image4.png supersample 3
> open "D:/downloads
> new/80S_analysis/80S_figure/cryosparc_P12_J368_class_00_final_volume.mrc"
Opened cryosparc_P12_J368_class_00_final_volume.mrc as #2, grid size
192,192,192, pixel 2.34, shown at level 1.45, step 1, values float32
> open "D:/downloads
> new/80S_analysis/80S_figure/cryosparc_P12_J368_class_02_final_volume.mrc"
Opened cryosparc_P12_J368_class_02_final_volume.mrc as #3, grid size
192,192,192, pixel 2.34, shown at level 1.4, step 1, values float32
> volume #2 level 0.7
> select #2
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,5.672,0,1,0,7.5791,0,0,1,-9.5446
> view matrix models
> #2,0.6202,0.68374,-0.38452,20.107,-0.19254,0.60786,0.77034,-27.861,0.76045,-0.40373,0.50864,17.422
> view matrix models
> #2,0.65825,0.69524,0.2887,-136.7,-0.73131,0.49959,0.46432,183.3,0.17858,-0.51677,0.83729,101.94
> view matrix models
> #2,0.97095,-0.06197,-0.23111,76.13,0.15824,0.89079,0.42597,-95.466,0.17947,-0.45017,0.87472,78.655
> view matrix models
> #2,0.97095,-0.06197,-0.23111,181.57,0.15824,0.89079,0.42597,8.8159,0.17947,-0.45017,0.87472,100.58
> view matrix models
> #2,0.85184,0.44409,0.27776,-15.729,-0.51391,0.8111,0.2793,208.91,-0.10126,-0.38066,0.91915,138.16
> view matrix models
> #2,0.41238,0.23157,0.88109,-0.16187,0.24885,0.90174,-0.35347,154.77,-0.87636,0.36503,0.31423,274.83
> view matrix models
> #2,-0.51698,-0.49203,0.70045,409.67,-0.85246,0.37019,-0.36914,524.19,-0.077671,-0.78795,-0.61082,555.62
> view matrix models
> #2,0.69061,-0.6731,0.26458,274.48,-0.52714,-0.21801,0.82134,326.02,-0.49516,-0.70669,-0.50538,607.95
> view matrix models
> #2,0.75831,0.49851,-0.42005,143.99,-0.59672,0.79025,-0.1394,322.75,0.26245,0.35637,0.89673,-104.16
> close #2-3
> open "D:/downloads new/80S_analysis/Z_flipped_ab_initio0.mrc"
Opened Z_flipped_ab_initio0.mrc as #2, grid size 192,192,192, pixel 2.34,
shown at level 1.45, step 1, values float32
> volume #2 level 0.7
> hide #!1 models
> surface dust #2 size 14.04
> save C:\ProgramData\ChimeraX\image5.png supersample 3
> open "D:/downloads new/80S_analysis/Z_flipped_ab_initio2.mrc"
Opened Z_flipped_ab_initio2.mrc as #3, grid size 192,192,192, pixel 2.34,
shown at level 1.4, step 1, values float32
> hide #!2 models
> volume #3 level 0.7
> show #!2 models
> surface dust #3 size 30
> select #3
2 models selected
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,76.41,0,1,0,75.877,0,0,1,86.217
> view matrix models
> #3,0.17082,0.94668,-0.27316,105.32,-0.82999,0.28765,0.47789,318.45,0.53098,0.14508,0.83487,-28.992
> view matrix models
> #3,0.47411,0.86433,0.16782,-41.756,-0.5509,0.14252,0.82231,212.69,0.68682,-0.48232,0.54373,144.98
> view matrix models
> #3,0.22508,0.9594,-0.16997,67.301,-0.77655,0.282,0.56343,288.76,0.58849,0.0051694,0.80849,-3.8636
> view matrix models
> #3,0.14822,0.9352,-0.3216,123.8,-0.85303,0.28543,0.43688,333.24,0.50036,0.20958,0.84007,-38.105
> view matrix models
> #3,0.16621,0.94469,-0.28273,108.94,-0.83464,0.28746,0.46983,321.33,0.52511,0.15789,0.83626,-30.927
> view matrix models
> #3,0.16621,0.94469,-0.28273,28.242,-0.83464,0.28746,0.46983,242.95,0.52511,0.15789,0.83626,-107.2
> ui tool show "Fit in Map"
Fit map Z_flipped_ab_initio2.mrc in map Z_flipped_ab_initio0.mrc using 198256
points
correlation = 0.9628, correlation about mean = 0.7526, overlap = 3.485e+05
steps = 240, shift = 12.8, angle = 35.9 degrees
Position of Z_flipped_ab_initio2.mrc (#3) relative to Z_flipped_ab_initio0.mrc
(#2) coordinates:
Matrix rotation and translation
-0.37282710 0.82106572 -0.43226270 218.05361140
-0.66122185 0.09173940 0.74455997 179.36552512
0.65098819 0.56341367 0.50870366 -143.71845228
Axis -0.09819096 -0.58717978 -0.80347896
Axis point 189.34604036 52.35999378 0.00000000
Rotation angle (degrees) 112.71776209
Shift along axis -11.25595146
> hide #!2 models
> show #!2 models
> hide #!2 models
> ~select #3
Nothing selected
> show #!2 models
> select #2
2 models selected
> lighting soft
> ~select #2
Nothing selected
> select #3
2 models selected
> lighting soft
> ~select #3
Nothing selected
> select #2
2 models selected
> ~select #2
Nothing selected
> hide #!2 models
> save C:\ProgramData\ChimeraX\image6.png supersample 3
> open "D:/downloads
> new/80S_analysis/80S_figure/cryosparc_P12_J368_class_01_final_volume.mrc"
Opened cryosparc_P12_J368_class_01_final_volume.mrc as #4, grid size
192,192,192, pixel 2.34, shown at level 1.14, step 1, values float32
> hide #!3 models
> volume #1 level 0.7
> hide #!4 models
> show #!4 models
> hide #!1 models
> close #1
> volume #4 level 0.8455
> surface dust #4 size 30
> volume #4 level 0.6166
> lighting soft
> color #4 #55aa00 models transparency 0
> color #4 #55aa7f models transparency 0
> save C:\ProgramData\ChimeraX\image7.png supersample 3
> close #4
> open "D:/downloads
> new/80S_analysis/80S_figure/cryosparc_P12_J368_class_03_final_volume.mrc"
Opened cryosparc_P12_J368_class_03_final_volume.mrc as #1, grid size
192,192,192, pixel 2.34, shown at level 0.848, step 1, values float32
> volume #1 level 0.668
> surface dust #1 size 14.04
> volume #1 level 0.753
> volume #1 level 0.9042
> surface dust #1 size 3
> surface dust #1 size 30
> save C:\ProgramData\ChimeraX\image8.png supersample 3
> volume #1 color cyan
> save C:\ProgramData\ChimeraX\image9.png supersample 3
> close #1
> open "D:/downloads
> new/80S_analysis/80S_figure/cryosparc_P12_J368_class_04_final_volume.mrc"
Opened cryosparc_P12_J368_class_04_final_volume.mrc as #1, grid size
192,192,192, pixel 2.34, shown at level 0.846, step 1, values float32
> volume #1 color #ffff7f
> volume #1 level 0.7395
> surface dust #1 size 30
> volume #1 level 0.8821
> save C:\ProgramData\ChimeraX\image10.png supersample 3
> close #1
> open "D:/downloads
> new/80S_analysis/80S_figure/cryosparc_P12_J368_class_01_final_volume.mrc"
Opened cryosparc_P12_J368_class_01_final_volume.mrc as #1, grid size
192,192,192, pixel 2.34, shown at level 1.14, step 1, values float32
> volume #1 level 0.7387
===== 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
> open "D:/downloads new/40S_body_final_flipped_map_beyond_2p8.mrc"
Opened 40S_body_final_flipped_map_beyond_2p8.mrc as #1, grid size 420,420,420,
pixel 1.07, shown at level 0.175, step 2, values float32
> open "D:/downloads new/40S_molmap_3JAM_resampled_map.mrc"
Opened 40S_molmap_3JAM_resampled_map.mrc as #2, grid size 420,420,420, pixel
1.07, shown at level 0.233, step 2, values float32
> open "D:/downloads new/60S_focused_refinement_resampled.mrc"
Opened 60S_focused_refinement_resampled.mrc as #3, grid size 420,420,420,
pixel 1.07, shown at level 0.171, step 2, values float32
OpenGL version: 3.3.0 NVIDIA 457.49
OpenGL renderer: GeForce GTX 1650/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82B5
OS: Microsoft Windows 11 Home Single Language (Build 22000)
Memory: 8,452,902,912
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 4600H with Radeon Graphics
OSLanguage: en-US
Locale: ('en_IN', '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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Possibly a graphics driver crash. Had just opened 420 by 420 by 420 map, not especially large.