The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
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.
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"incident" : "B7075888-9B1B-495F-B5A2-0EEFF2B82670",
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"uuid" : "53b6853f-0bc3-33f5-be72-1aca3a188ff8"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=205.8M resident=0K(0%) swapped_out_or_unallocated=205.8M(100%)\nWritable regions: Total=2.9G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.9G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG backing stores 6400K 8 \nCG image 152K 14 \nColorSync 232K 27 \nCoreAnimation 152K 12 \nCoreGraphics 16K 3 \nCoreUI image data 3960K 27 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 1.1G 163 \nMALLOC guard page 192K 8 \nMALLOC_MEDIUM (reserved) 736.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 4 \nOpenGL GLSL 384K 4 \nRosetta Arena 4096K 2 \nRosetta Generic 1504K 373 \nRosetta IndirectBranch 2048K 1 \nRosetta JIT 128.0M 1 \nRosetta Return Stack 640K 64 \nRosetta Thread Context 640K 64 \nSTACK GUARD 28K 7 \nStack 143.6M 32 \nStack Guard 56.1M 25 \nVM_ALLOCATE 268.3M 225 \nVM_ALLOCATE (reserved) 160.1M 15 reserved VM address space (unallocated)\n__DATA 355K 45 \n__DATA_CONST 3033K 40 \n__DATA_DIRTY 79K 24 \n__LINKEDIT 192.9M 7 \n__OBJC_RO 82.7M 1 \n__OBJC_RW 3200K 2 \n__TEXT 13.0M 50 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 6.6G 948 \nshared memory 5352K 35 \nunshared pmap 11.8M 8 \n=========== ======= ======= \nTOTAL 9.9G 2257 \nTOTAL, minus reserved VM space 8.6G 2257 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60356660bbe37970735c5624",
"factorPackIds" : {
},
"deploymentId" : 240000027
},
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000015
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/rflores/Downloads/cryosparc_P117_J24_005_volume_map (2).mrc"
Opened cryosparc_P117_J24_005_volume_map (2).mrc as #1, grid size 300,300,300,
pixel 0.834, shown at level 0.208, step 2, values float32
> volume flip #1
Opened cryosparc_P117_J24_005_volume_map (2).mrc z flip as #2, grid size
300,300,300, pixel 0.834, shown at step 1, values float32
> volume #2 level 0.1736
> ui windowfill toggle
> open emdb:8697
Opened emdb 8697 as #3, grid size 256,256,256, pixel 1, shown at level 0.0268,
step 1, values float32
> select add #2
2 models selected
> ui mousemode right "translate selected models"
> show #!2 models
> select subtract #2
Nothing selected
> select add #3
2 models selected
> view matrix models #3,1,0,0,21.603,0,1,0,48.691,0,0,1,105.16
> view matrix models #3,1,0,0,-4.3285,0,1,0,49.812,0,0,1,113.67
> view matrix models
> #3,0.1257,0.98776,0.092389,-31.532,-0.53668,-0.010622,0.84372,138.13,0.83437,-0.15564,0.52877,88.516
> view matrix models
> #3,-0.37709,0.31653,0.87041,17.642,0.80801,-0.34691,0.47621,58.047,0.45269,0.88287,-0.12494,88.491
> view matrix models
> #3,-0.45989,0.39804,0.79377,27.594,0.76999,-0.26648,0.57975,39.272,0.44229,0.87781,-0.18393,98.048
> view matrix models
> #3,-0.45989,0.39804,0.79377,23.772,0.76999,-0.26648,0.57975,-15.957,0.44229,0.87781,-0.18393,-18.31
> view matrix models
> #3,-0.45989,0.39804,0.79377,22.477,0.76999,-0.26648,0.57975,-14.194,0.44229,0.87781,-0.18393,-20.769
> view matrix models
> #3,-0.45989,0.39804,0.79377,23.498,0.76999,-0.26648,0.57975,-20.231,0.44229,0.87781,-0.18393,-23.506
> view matrix models
> #3,-0.45989,0.39804,0.79377,22.566,0.76999,-0.26648,0.57975,-19.027,0.44229,0.87781,-0.18393,-25.861
> view matrix models
> #3,-0.45989,0.39804,0.79377,22.666,0.76999,-0.26648,0.57975,-18,0.44229,0.87781,-0.18393,-22.129
> view matrix models
> #3,-0.24606,0.48988,0.83634,-21.615,0.89397,-0.21871,0.39112,-15.517,0.37452,0.84391,-0.38412,16.549
> view matrix models
> #3,-0.25638,0.098565,0.96154,13.509,0.8776,-0.39316,0.2743,23.853,0.40508,0.91417,0.014299,-47.573
> view matrix models
> #3,-0.63331,-0.20262,0.7469,127.3,0.6836,-0.59888,0.41717,56.281,0.36278,0.77478,0.51779,-89.241
> view matrix models
> #3,-0.39672,0.48729,0.77792,5.3177,0.75594,-0.30732,0.57802,-10.788,0.52073,0.81738,-0.24644,-16.306
> fitmap #3 inMap #2
Fit map emdb 8697 in map cryosparc_P117_J24_005_volume_map (2).mrc z flip
using 167649 points
correlation = 0.6051, correlation about mean = 0.01272, overlap = 765.3
steps = 112, shift = 8.04, angle = 10.3 degrees
Position of emdb 8697 (#3) relative to cryosparc_P117_J24_005_volume_map
(2).mrc z flip (#2) coordinates:
Matrix rotation and translation
-0.50973133 0.37292178 0.77530853 42.03747489
0.69424845 -0.35395134 0.62668775 -3.64502823
0.50812701 0.85769913 -0.07848028 -40.66860054
Axis 0.48379686 0.55954638 0.67294016
Axis point 35.50899958 19.26350229 0.00000000
Rotation angle (degrees) 166.18732265
Shift along axis -9.06949861
> select subtract #3
Nothing selected
> volume #2 level 0.344
> volume #2 level 0.2188
> ui windowfill toggle
> transparency #2.1#3.1 50
> transparency #2.1#3.1 0
> open "/Users/rflores/Downloads/cryosparc_P117_J23_004_volume_map (1).mrc"
Opened cryosparc_P117_J23_004_volume_map (1).mrc as #4, grid size 300,300,300,
pixel 0.834, shown at level 0.203, step 2, values float32
> volume #4 level 0.1725
> volume #4 level 0.1198
> open "/Users/rflores/Downloads/cryosparc_P117_J25_004_volume_map (1).mrc"
Opened cryosparc_P117_J25_004_volume_map (1).mrc as #5, grid size 300,300,300,
pixel 0.834, shown at level 0.211, step 2, values float32
> volume #5 level 0.1709
> volume flip #5
Opened cryosparc_P117_J25_004_volume_map (1).mrc z flip as #6, grid size
300,300,300, pixel 0.834, shown at step 1, values float32
> volume #6 level 0.1247
> volume #2 level 0.1572
> volume #3 level 0.01093
===== 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
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: AppleHardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Processor Name: Unknown
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache: 16 MB
Memory: 32 GB
Software:
System Software Overview:
System Version: macOS 12.4 (21F79)
Kernel Version: Darwin 21.5.0
Time since boot: 32 days 4:04
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG UltraFine:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
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
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: 21.0
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
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
Was using 8.6GB at the time