![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#17726 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000002025fcc80 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 63)
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"procRole" : "Foreground",
"version" : 2,
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"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 51312,
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"build" : "24E263",
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"captureTime" : "2025-05-19 14:13:33.0276 +0200",
"codeSigningMonitor" : 1,
"incident" : "9AE7D975-375D-482E-922E-3692F1467DF7",
"pid" : 28356,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-19 10:41:02.7318 +0200",
"procStartAbsTime" : 7361290341409,
"procExitAbsTime" : 7612062046868,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B362EAEC-D592-0B8A-05EB-D3BB388A7463",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "48E5351C-FEB6-40CC-B43C-BB7C25A7D393",
"wakeTime" : 23,
"sleepWakeUUID" : "6C517427-89E3-4FA6-8B19-36EB1F42561A",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4372758167\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104a30000-104a34000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":28356},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4372758167\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104a30000-104a34000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"base" : 13234454528,
"size" : 131072,
"uuid" : "c8b24269-c8a2-3244-b044-b85c3449800d",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/lxml\/_elementpath.cpython-311-darwin.so",
"name" : "_elementpath.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 5277892608,
"size" : 32768,
"uuid" : "8abbdcef-1901-3d4b-9e6b-a38214b79214",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
},
{
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"size" : 32768,
"uuid" : "a55a4181-c446-3fa3-8fd6-27f845527eab",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
},
{
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"arch" : "arm64",
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"size" : 16384,
"uuid" : "a516c5bc-1157-318a-a306-5c9b350e0c09",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
},
{
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"arch" : "arm64",
"base" : 5281710080,
"size" : 49152,
"uuid" : "f4191524-316f-3e56-8aa1-9a441a05fd70",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atom_search\/ast.cpython-311-darwin.so",
"name" : "ast.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 6024855552,
"size" : 65536,
"uuid" : "c6fd286f-9d33-37a1-9d00-a213039662b6",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/chem_group\/_chem_group.cpython-311-darwin.so",
"name" : "_chem_group.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 5281955840,
"size" : 16384,
"uuid" : "f07c07fb-2e38-3764-9cff-1bd00023b5ae",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/coulombic\/_esp.cpython-311-darwin.so",
"name" : "_esp.cpython-311-darwin.so"
},
{
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"arch" : "arm64e",
"base" : 6768455680,
"size" : 242444,
"uuid" : "225cb279-20a9-381d-a163-d2be263f5327",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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{
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"size" : 51784,
"uuid" : "8d27ec9a-d919-31a4-8df8-31a2fd2e593c",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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{
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"base" : 6767222784,
"size" : 529520,
"uuid" : "20ebe22e-66e2-3556-b70b-54a04e8363a8",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
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{
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"arch" : "arm64e",
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"size" : 31568,
"uuid" : "27ed40c8-6b18-3266-93a7-387fb33ca186",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
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"base" : 6832697344,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21564928,
"uuid" : "1d6df541-4a74-3a0e-8a8f-15aee6f93da9",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.50.27"
},
{
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"arch" : "arm64e",
"base" : 6866669568,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 5394304,
"uuid" : "ad34bb7b-8573-3892-8ca9-78cbb7477ce0",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
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"arch" : "arm64e",
"base" : 6766919680,
"size" : 288544,
"uuid" : "3329eb0a-e722-3db0-a627-e27297282a0f",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
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{
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"size" : 5500928,
"uuid" : "39e0f63a-3ab8-39e9-97f8-333cde9a7ba4",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
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{
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"size" : 3174368,
"uuid" : "6cc82a38-f1b5-3f2b-876b-9b3d7b278490",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
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{
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"base" : 6764904448,
"size" : 633476,
"uuid" : "aca43a8d-6369-3a2c-af92-3d4c458523d6",
"path" : "\/usr\/lib\/dyld",
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{
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"uuid" : "5ab66e9b-19c0-3fe8-9793-d5156d1c7050",
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"sharedCache" : {
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=30.9G written=273.8M(1%) resident=15.9M(0%) swapped_out=257.9M(1%) unallocated=30.6G(99%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG image 97.3M 66 \nColorSync 704K 38 \nCoreAnimation 3488K 168 \nCoreGraphics 48K 3 \nCoreServices 624K 2 \nCoreUI image data 5360K 40 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 30.0G 196 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.5M 35 \nStack 190.7M 35 \nVM_ALLOCATE 504.2M 321 \nVM_ALLOCATE (reserved) 96.0M 1 reserved VM address space (unallocated)\n__AUTH 5487K 696 \n__AUTH_CONST 77.2M 943 \n__CTF 824 1 \n__DATA 34.3M 1094 \n__DATA_CONST 37.1M 1109 \n__DATA_DIRTY 2775K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 652.4M 161 \n__OBJC_RO 61.3M 1 \n__OBJC_RW 2391K 1 \n__TEXT 1.3G 1128 \n__TEXT (graphics) 32K 1 \n__TPRO_CONST 128K 2 \ndyld private memory 3872K 33 \nmapped file 639.4M 96 \npage table in kernel 15.9M 1 \nshared memory 3184K 25 \n=========== ======= ======= \nTOTAL 33.7G 6574 \nTOTAL, minus reserved VM space 33.6G 6574 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "656d6f547ef77657a87e2c88ad7e4901310b8afd",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs" format session
Opened cryosparc_P8_J16_class_03_00042_volume.mrc as #1, grid size
128,128,128, pixel 4.48, shown at level 0.481, step 1, values float32
Opened cryosparc_P8_J16_class_02_00042_volume.mrc as #2, grid size
128,128,128, pixel 4.48, shown at level 0.173, step 1, values float32
Opened cryosparc_P8_J16_class_03_00042_volume.mrc z flip as #3, grid size
128,128,128, pixel 4.48, shown at level 0.213, step 1, values float32
Opened cryosparc_P8_J16_class_00_00042_volume.mrc z flip as #5, grid size
128,128,128, pixel 4.48, shown at level 0.0367, step 1, values float32
opened ChimeraX session
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!5 models
> hide #!2 models
> hide #4 models
> hide #!5 models
> hide #!6 models
> show #!1 models
> volume #1 level 0.2009
> close #1
> show #!2 models
> show #!3 models
> volume #3 level 0.3224
> hide #!3 models
> hide #!2 models
> show #!5 models
> show #!3 models
> volume #3 level 0.2232
> volume #3 level 0.1605
> volume #3 level 0.2702
> show #4 models
> volume #5 color #b2b2ff9f
> volume #3 color #261ebf
> volume #3 color #1e1793
> volume #3 color #a41c1b
> volume #3 color #a46623
> volume #3 color #9a6021
> volume #2 level 0.1224
> show #!6 models
> select subtract #6
Nothing selected
> save "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs"
> open /Users/annguyen/Downloads/cryosparc_P5_J26_class_04_00042_volume.mrc
Opened cryosparc_P5_J26_class_04_00042_volume.mrc as #1, grid size
128,128,128, pixel 4.48, shown at level 0.939, step 1, values float32
> volume #1 level 0.6667
> volume #1 level 0.4251
> select add #1
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.40929,-0.65604,-0.6341,536.58,0.78647,0.60599,-0.11931,-80.382,0.46253,-0.44987,0.76399,61.851
> view matrix models
> #1,-0.73119,-0.5255,0.43499,523.78,-0.63977,0.74955,-0.1699,303.51,-0.23677,-0.40252,-0.88426,717.96
> view matrix models
> #1,-0.87902,-0.38562,0.28041,570.49,0.10705,0.41349,0.90419,-121.06,-0.46462,0.82482,-0.32219,274.98
> view matrix models
> #1,0.19695,0.69453,0.69198,-162.99,0.97841,-0.094136,-0.184,81.753,-0.062652,0.71328,-0.69808,297.86
> view matrix models
> #1,-0.29704,0.79315,-0.53167,298.83,0.73184,0.54676,0.40677,-197.33,0.61333,-0.26827,-0.74287,395.06
> view matrix models
> #1,0.1497,0.17546,-0.97304,471.27,-0.71619,0.69773,0.015628,287.51,0.68166,0.69454,0.23012,-174.72
> view matrix models
> #1,0.18604,0.15582,-0.97011,465.56,-0.7458,0.66518,-0.036181,320,0.63966,0.73024,0.23996,-175.58
> view matrix models
> #1,0.23095,-0.78863,-0.56985,607.31,-0.59414,0.3495,-0.72447,561.67,0.7705,0.50588,-0.38783,28.943
> view matrix models
> #1,0.89719,0.44148,0.011772,-99.235,0.43013,-0.87955,0.20343,352.6,0.10017,-0.17746,-0.97902,583.99
> view matrix models
> #1,-0.41649,0.19223,-0.88858,605.39,0.69543,0.69691,-0.17519,-64.149,0.58558,-0.69092,-0.42394,432.53
> view matrix models
> #1,-0.22124,-0.039478,-0.97442,639.46,-0.60387,0.79012,0.1051,203.51,0.76576,0.61167,-0.19865,-53.521
> volume #1 level 0.07814
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.22124,-0.039478,-0.97442,670.85,-0.60387,0.79012,0.1051,340.1,0.76576,0.61167,-0.19865,-209.78
> view matrix models
> #1,-0.22124,-0.039478,-0.97442,654.95,-0.60387,0.79012,0.1051,326.79,0.76576,0.61167,-0.19865,-244.74
> ui tool show "Fit in Map"
> fitmap #1 inMap #3
Fit map cryosparc_P5_J26_class_04_00042_volume.mrc in map
cryosparc_P8_J16_class_03_00042_volume.mrc z flip using 65273 points
correlation = 0.9061, correlation about mean = 0.6579, overlap = 3.211e+04
steps = 156, shift = 35.6, angle = 28.9 degrees
Position of cryosparc_P5_J26_class_04_00042_volume.mrc (#1) relative to
cryosparc_P8_J16_class_03_00042_volume.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.93406661 -0.35210391 0.05951852 104.50707603
-0.35681245 -0.92693681 0.11607363 619.00643654
0.01429993 -0.12965744 -0.99145575 598.50364802
Axis -0.98331257 0.18094583 -0.01884164
Axis point 0.00000000 338.20544482 278.49701894
Rotation angle (degrees) 172.82209465
Shift along axis -2.03327796
> save "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs"
> hide #!1 models
> show #!1 models
> ui tool show "Side View"
> ui mousemode right zoom
> select add #1
3 models selected
> select subtract #1
Nothing selected
> hide #4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.5925
> ui mousemode right translate
> ui mousemode right zoom
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!1 models
> volume #2 color #ffffb2
> volume #2 level 0.2583
> volume #2 level 0.4657
> volume #2 level 0.1653
> hide #!6 models
> ui mousemode right translate
> volume #2 level 0.1975
> hide #!2 models
Enter a PDB ID in the entry field
> open 70ld fromDatabase pdb format mmcif
Fetching url http://files.rcsb.org/download/70ld.cif failed:
HTTP Error 404: Not Found
> open "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/18-05-25-scSec72-scRibo-10xbin.cxs" format session
Opened cryosparc_P8_J16_class_02_00042_volume.mrc as #2, grid size
128,128,128, pixel 4.48, shown at level 0.122, step 1, values float32
Opened cryosparc_P8_J16_class_03_00042_volume.mrc z flip as #3, grid size
128,128,128, pixel 4.48, shown at level 0.27, step 1, values float32
Opened cryosparc_P8_J16_class_00_00042_volume.mrc z flip as #5, grid size
128,128,128, pixel 4.48, shown at level 0.0367, step 1, values float32
Opened cryosparc_P5_J26_class_04_00042_volume.mrc as #1, grid size
128,128,128, pixel 4.48, shown at level 0.0781, step 1, values float32
opened ChimeraX session
> open 5L0y fromDatabase pdb format mmcif
Summary of feedback from opening 5L0y fetched from pdb
---
note | Fetching compressed mmCIF 5l0y from http://files.rcsb.org/download/5l0y.cif
5l0y title:
Crystal Structure of a Sec72-ssa1 c-terminal peptide fusion protein [more
info...]
Chain information for 5l0y #7
---
Chain | Description | UniProt
A B C D E F G H | Sec72-ssa1 c-terminal peptide fusion protein | G0SH41_CHATD 68-214
I J K L M | PRO-THR-VAL-GLU-GLU-VAL-ASP |
5l0y mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
5| author_defined_assembly
6| author_defined_assembly
7| author_defined_assembly
> open 5L0W fromDatabase pdb format mmcif
Summary of feedback from opening 5L0W fetched from pdb
---
note | Fetching compressed mmCIF 5l0w from http://files.rcsb.org/download/5l0w.cif
5l0w title:
Structure of post-translational translocation Sec71/Sec72 complex [more
info...]
Chain information for 5l0w #8
---
Chain | Description | UniProt
A | Sec71 | G0S0B5_CHATD 30-184
B | Sec72 | G0SH41_CHATD 1-214
> select add #8
2962 atoms, 3017 bonds, 371 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,8.8878,0,1,0,80.457,0,0,1,11.261
> hide #!7 models
> view matrix models #8,1,0,0,24.989,0,1,0,226.21,0,0,1,31.963
> view matrix models #8,1,0,0,380.19,0,1,0,251.27,0,0,1,36.255
> view matrix models #8,1,0,0,359.91,0,1,0,451.82,0,0,1,159.08
> view matrix models #8,1,0,0,426,0,1,0,389.42,0,0,1,158.37
> view matrix models #8,1,0,0,453.19,0,1,0,380.2,0,0,1,146.52
> view matrix models #8,1,0,0,456.94,0,1,0,375.32,0,0,1,147.52
> hide #!1 models
> hide #!3 models
> hide #4 models
> hide #!6 models
> hide #!2 models
> coulombic sel
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
5l0w #8/A LYS 184 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 5l0w_A SES surface #8.1: minimum, -15.79, mean -1.73,
maximum 8.04
Coulombic values for 5l0w_B SES surface #8.2: minimum, -16.86, mean -0.36,
maximum 12.01
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for 5l0w_A SES surface #8.1: minimum, -15.79, mean -1.73,
maximum 8.04
Coulombic values for 5l0w_B SES surface #8.2: minimum, -16.86, mean -0.36,
maximum 12.01
To also show corresponding color key, enter the above coulombic command and
add key true
> show sel cartoons
> hide #8.1 models
> hide #8.2 models
> show #8.2 models
> hide #8.2 models
> show #8.1 models
> show #8.2 models
> hide #8.1 models
> select subtract #8.1
1642 atoms, 1677 bonds, 209 residues, 3 models selected
> hide #8.2 models
> show #8.1 models
> select add #8.1
2962 atoms, 1677 bonds, 371 residues, 2 models selected
> hide #8.1 models
> show #8.2 models
> select subtract #8.1
1642 atoms, 1677 bonds, 209 residues, 3 models selected
Mismatch between Cocoa 'h' and Carbon '\x0' for virtual key 4 with
QFlags(NoModifier)
Mismatch between Cocoa 'H' and Carbon '\x0' for virtual key 4 with
QFlags(ShiftModifier)
Mismatch between Cocoa 'h' and Carbon '\x0' for virtual key 4 with
QFlags(ControlModifier)
Mismatch between Cocoa 'h' and Carbon '\x0' for virtual key 4 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\u02d9' and Carbon '\x0' for virtual key 4 with
QFlags(AltModifier)
Mismatch between Cocoa '\u00d3' and Carbon '\x0' for virtual key 4 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\u02d9' and Carbon '\x0' for virtual key 4 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\u00d3' and Carbon '\x0' for virtual key 4 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 4 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 4 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 4 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 4 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 4 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 4 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 4 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 4 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\xd' and Carbon '\x0' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #8.2
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(NoModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(AltModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(NoModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(AltModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x1d' and Carbon '\x0' for virtual key 124 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select ~sel & ##selected
1320 atoms, 1340 bonds, 162 residues, 1 model selected
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(NoModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(AltModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x8' and Carbon '\x0' for virtual key 51 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa 's' and Carbon '\x0' for virtual key 1 with
QFlags(NoModifier)
Mismatch between Cocoa 'S' and Carbon '\x0' for virtual key 1 with
QFlags(ShiftModifier)
Mismatch between Cocoa 's' and Carbon '\x0' for virtual key 1 with
QFlags(ControlModifier)
Mismatch between Cocoa 's' and Carbon '\x0' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\u00df' and Carbon '\x0' for virtual key 1 with
QFlags(AltModifier)
Mismatch between Cocoa '\u00cd' and Carbon '\x0' for virtual key 1 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\u00df' and Carbon '\x0' for virtual key 1 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\u00cd' and Carbon '\x0' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x13' and Carbon '\x0' for virtual key 1 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x13' and Carbon '\x0' for virtual key 1 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x13' and Carbon '\x0' for virtual key 1 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x13' and Carbon '\x0' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x13' and Carbon '\x0' for virtual key 1 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x13' and Carbon '\x0' for virtual key 1 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x13' and Carbon '\x0' for virtual key 1 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x13' and Carbon '\x0' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #8/A
1320 atoms, 1340 bonds, 162 residues, 1 model selected
> delete atoms (#!8 & sel)
> delete bonds (#!8 & sel)
> show #!3 models
> hide #!3 models
> show #!2 models
> volume #2 level 0.2368
> volume #2 color #ffffb2
> volume #2 level 0.2225
Cell requested for row 7 is out of bounds for table with 9 rows! Resizing
table model.
> select add #8
1642 atoms, 1677 bonds, 209 residues, 1 model selected
> view matrix models #8,1,0,0,508.64,0,1,0,354.81,0,0,1,149.48
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.52489,-0.59443,-0.60921,509.78,-0.7158,-0.69555,0.061943,374.1,-0.46056,0.40356,-0.79058,129.06
> view matrix models
> #8,0.82532,0.53171,-0.1901,487.34,0.48954,-0.84153,-0.22845,428.8,-0.28144,0.095486,-0.95482,146.07
> show #8.2 models
> view matrix models
> #8,-0.36643,0.92604,0.09049,425.45,0.92417,0.37351,-0.080012,409.01,-0.10789,0.05431,-0.99268,154.58
> view matrix models
> #8,-0.97227,-0.23175,-0.031404,436.4,-0.23385,0.96203,0.14075,342.92,-0.0024057,0.14419,-0.98955,156.14
> view matrix models
> #8,-0.62158,-0.77284,-0.12791,467.54,-0.78206,0.60284,0.15802,331.37,-0.04501,0.19825,-0.97912,152.72
> hide #8.2 models
> view matrix models
> #8,-0.88679,-0.053295,0.45909,432.89,0.018106,0.98856,0.14973,352.81,-0.46182,0.14109,-0.87568,136.87
> view matrix models
> #8,0.073448,-0.21905,0.97294,473.79,0.22612,0.95383,0.19768,361.99,-0.97133,0.20548,0.11959,108.87
> view matrix models
> #8,0.96693,-0.096625,-0.23605,513.19,-0.032113,0.87198,-0.48849,357.63,0.25303,0.47991,0.84004,146.72
> show #8.2 models
> hide #8.2 models
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.96693,-0.096625,-0.23605,487.6,-0.032113,0.87198,-0.48849,391.91,0.25303,0.47991,0.84004,159.53
> show #8.2 models
> hide #8.2 models
> volume #2 level 0.2297
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.50461,0.81571,-0.2828,442.9,-0.8042,0.56326,0.18971,365.71,0.31404,0.1317,0.94023,171.45
> view matrix models
> #8,0.43057,0.80417,-0.40977,440.93,-0.83087,0.53049,0.16803,365.69,0.3525,0.26812,0.89658,169.33
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.43057,0.80417,-0.40977,418.05,-0.83087,0.53049,0.16803,359.04,0.3525,0.26812,0.89658,173.98
> view matrix models
> #8,0.43057,0.80417,-0.40977,429.86,-0.83087,0.53049,0.16803,342.22,0.3525,0.26812,0.89658,195.79
> view matrix models
> #8,0.43057,0.80417,-0.40977,428.37,-0.83087,0.53049,0.16803,344.89,0.3525,0.26812,0.89658,188.97
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.98068,-0.12547,-0.15007,475.95,-0.064025,0.51902,-0.85236,381.95,0.18483,0.8455,0.50096,167.77
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.98068,-0.12547,-0.15007,462.9,-0.064025,0.51902,-0.85236,397.9,0.18483,0.8455,0.50096,146.53
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.068544,0.93284,-0.3537,391.06,-0.86332,-0.23314,-0.44757,384.82,-0.49997,0.27468,0.82133,133.37
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.068544,0.93284,-0.3537,396.51,-0.86332,-0.23314,-0.44757,398.37,-0.49997,0.27468,0.82133,144.53
> volume #2 level 0.2618
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.14642,0.98479,-0.093578,402.31,-0.96867,0.16192,0.1883,379.26,0.20059,0.063075,0.97764,178.17
> view matrix models
> #8,-0.059699,0.93474,-0.35029,396.8,-0.95817,0.044742,0.28269,382.53,0.27992,0.35251,0.89296,173.55
> view matrix models
> #8,-0.15522,0.94401,-0.2911,392.33,-0.94941,-0.061128,0.30802,385.78,0.27298,0.32419,0.90575,174.01
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.15522,0.94401,-0.2911,391.08,-0.94941,-0.061128,0.30802,382.08,0.27298,0.32419,0.90575,170.69
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.24465,0.89174,-0.38071,389.45,-0.91232,-0.078745,0.40183,383.57,0.32835,0.44564,0.83282,169.85
> ui mousemode right "translate selected models"
> view matrix models
> #8,-0.24465,0.89174,-0.38071,386.27,-0.91232,-0.078745,0.40183,387.74,0.32835,0.44564,0.83282,165.37
Mismatch between Cocoa 'f' and Carbon '\x0' for virtual key 3 with
QFlags(NoModifier)
Mismatch between Cocoa 'F' and Carbon '\x0' for virtual key 3 with
QFlags(ShiftModifier)
Mismatch between Cocoa 'f' and Carbon '\x0' for virtual key 3 with
QFlags(ControlModifier)
Mismatch between Cocoa 'f' and Carbon '\x0' for virtual key 3 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\u0192' and Carbon '\x0' for virtual key 3 with
QFlags(AltModifier)
Mismatch between Cocoa '\u00cf' and Carbon '\x0' for virtual key 3 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\u0192' and Carbon '\x0' for virtual key 3 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\u00cf' and Carbon '\x0' for virtual key 3 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x6' and Carbon '\x0' for virtual key 3 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x6' and Carbon '\x0' for virtual key 3 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x6' and Carbon '\x0' for virtual key 3 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x6' and Carbon '\x0' for virtual key 3 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x6' and Carbon '\x0' for virtual key 3 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x6' and Carbon '\x0' for virtual key 3 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x6' and Carbon '\x0' for virtual key 3 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x6' and Carbon '\x0' for virtual key 3 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> fitmap #8/A:65-156 inMap #2
No atoms or maps for #8/A:65-156
> show #8.2 models
> fitmap #8/B:65-156 inMap #2
Fit molecule 5l0w (#8) to map cryosparc_P8_J16_class_02_00042_volume.mrc (#2)
using 728 atoms
average map value = 0.2088, steps = 64
shifted from previous position = 3.92
rotated from previous position = 16.7 degrees
atoms outside contour = 522, contour level = 0.26184
Position of 5l0w (#8) relative to cryosparc_P8_J16_class_02_00042_volume.mrc
(#2) coordinates:
Matrix rotation and translation
0.14643252 -0.98415702 -0.09996237 220.69198225
-0.52686132 -0.16311773 0.83415212 307.08970311
-0.83724230 -0.06948069 -0.54240000 195.05549134
Axis -0.72134905 0.58855341 0.36504852
Axis point 0.00000000 282.90404614 91.76724512
Rotation angle (degrees) 141.21871574
Shift along axis 92.74745988
> select clear
> hide #8.2 models
> color #2 #ffffb2d4 models
> volume #2 level 0.2082
> volume #2 level 0.2797
> color #2 #000000d4 models
> color #2 #fffdbfd4 models
> color #2 #fffdbfff models
> volume #2 level 0.2368
> show #8.2 models
> ui mousemode right zoom
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,7
Model Number: Z16U000NJD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 7 days, 17 hours, 36 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P3223QE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.1
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
finufft: 2.3.1
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 5 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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