![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 14 months ago
#15858 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-14.6-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00000001f1d74f40 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, chimerax.connect_structure._cs, PIL._imagingmath, chimerax.md_crds._gromacs, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 57)
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{
"uptime" : 800000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 26818,
"osVersion" : {
"train" : "macOS 14.6",
"build" : "23G80",
"releaseType" : "User"
},
"captureTime" : "2024-08-30 23:10:58.2144 +0200",
"codeSigningMonitor" : 1,
"incident" : "370F87BC-D9E4-45E1-8FE0-E858E92BA316",
"pid" : 73092,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-27 17:08:54.6358 +0200",
"procStartAbsTime" : 16718481774201,
"procExitAbsTime" : 19280440466517,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A503A440-03DC-56F9-96D9-62D053FE756F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "000F7903-988F-CB0E-5464-A86207E45B02",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 2,
"sleepWakeUUID" : "3A260D87-795C-416A-BD56-3F8B14C885BA",
"sip" : "enabled",
"vmRegionInfo" : "0x19c is not in any region. Bytes before following region: 4337991268\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102908000-10290c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x000000000000019c","rawCodes":[1,412],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000000000000019c"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":73092},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x19c is not in any region. Bytes before following region: 4337991268\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102908000-10290c000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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"base" : 6609760256,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5083136,
"uuid" : "55720ee0-d8c3-33a1-9854-8e61a6f44895",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2602"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6785867776,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2899968,
"uuid" : "4166f6cb-b599-306c-8568-823bd29a74c3",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6605623296,
"size" : 562440,
"uuid" : "015e99c9-3c3f-3e28-ac31-9c9770316250",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6608400384,
"size" : 577528,
"uuid" : "aaa5636d-6f3f-3fa7-9f4a-cf966f0308fe",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6607323136,
"size" : 249848,
"uuid" : "8a69a1ac-6d54-3b64-9860-cd0db47473ed",
"path" : "\/usr\/lib\/system\/libsystem_malloc.dylib",
"name" : "libsystem_malloc.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6605291520,
"size" : 331276,
"uuid" : "5c6386bd-f308-3370-bce9-63d1a89dab87",
"path" : "\/usr\/lib\/libobjc.A.dylib",
"name" : "libobjc.A.dylib"
}
],
"sharedCache" : {
"base" : 6604865536,
"size" : 4214308864,
"uuid" : "2652ccc8-2581-3c2f-b259-753b7522cfa5"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=11.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=11.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 1104K 58 \nColorSync 672K 31 \nCoreAnimation 2112K 125 \nCoreGraphics 64K 4 \nCoreServices 624K 2 \nCoreUI image data 5616K 61 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 10.4G 1078 \nMALLOC guard page 192K 12 \nMach message 96K 5 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.5M 33 \nStack 159.7M 33 \nVM_ALLOCATE 295.3M 260 \nVM_ALLOCATE (reserved) 192.0M 5 reserved VM address space (unallocated)\n__AUTH 2199K 404 \n__AUTH_CONST 31.8M 622 \n__CTF 824 1 \n__DATA 21.9M 769 \n__DATA_CONST 42.3M 779 \n__DATA_DIRTY 2024K 232 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 554.0M 152 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 936.1M 796 \ndyld private memory 272K 2 \nmapped file 523.7M 86 \nshared memory 3168K 26 \n=========== ======= ======= \nTOTAL 13.2G 5590 \nTOTAL, minus reserved VM space 13.1G 5590 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "8cbedfd3389350aa71673457583e225457d5d478",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5fb4245a1bbfe8005e33a1e1",
"factorPackIds" : {
},
"deploymentId" : 240000021
},
{
"rolloutId" : "64c025b28b7f0e739e4fbe58",
"factorPackIds" : {
},
"deploymentId" : 240000019
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> help help:quickstart
> open /Users/vjc493/Documents/martini_ligand_go/no_solvent_CG-eq.gro
Cannot guess atomic element from atom name in file no_solvent_CG-eq.gro.
Line: 8946BENZ R1 9165 2.522 9.564 1.971
> open /Users/vjc493/Documents/martini_ligand_go/no_solvent_CG-
> eq_for_chimera.gro
> size all 10
Expected a keyword
> size all atomRadius 10
Changed 574 atom radii
> size all atomRadius 50
Changed 574 atom radii
> style ball
Changed 574 atom styles
> size all atomRadius 10
Changed 574 atom radii
> show surfaces
> hide surfaces
> ui mousemode right translate
> open
> /Users/vjc493/Documents/martini_ligand_go/big_run_no_water/20/trajfitted_20_no_w.xtc
Replaced existing frames of Generated with MDTraj #1 with 310520 new frames
> movie record
> movie encode /Users/vjc493/Desktop/movie1.mp4 framerate 25.0
Movie saved to /Users/vjc493/Desktop/movie1.mp4
> hide atoms NA
Expected ',' or a keyword
> hide atomtype NA
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> set bgColor white
> show target m
> hide #1.1 models
> show #1.1 models
> hide #!1 models
> show #!1 models
> view #1 clip false
> show #!1 target m
> log metadata #1
No models had metadata
> log chains #1
> log metadata #1
No models had metadata
> log chains #1
> hide CL
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide atoms CL
Expected ',' or a keyword
> hide atoms CL
Expected ',' or a keyword
> hide residue CL
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide atoms CL1
Expected ',' or a keyword
> hide atoms C
Expected ',' or a keyword
> hide atoms C
Expected ',' or a keyword
> hide atoms
> show atoms
> atom list
Unknown command: atom list
> atoms
Unknown command: atoms
> select atoms CL
Expected an objects specifier or a keyword
> select atomtype CL
Expected an objects specifier or a keyword
> select element CL
Expected an objects specifier or a keyword
> select Cl
Nothing selected
> select element CL
Expected an objects specifier or a keyword
> select element CL-
Expected an objects specifier or a keyword
> select element CL
Expected an objects specifier or a keyword
> select element CL hide
Expected an objects specifier or a keyword
> select element CL bead
Expected an objects specifier or a keyword
> select element CL spehere
Expected an objects specifier or a keyword
> select element CL sphere
Expected an objects specifier or a keyword
> select element CL ball-stick
Expected an objects specifier or a keyword
> hide target a
> show atoms
> hide #* target a
> show target ab
> select Cl
Nothing selected
> hide atoms CL
Expected ',' or a keyword
> hide atoms CL sphere
Expected ',' or a keyword
> select ::name="ION"
190 atoms, 190 residues, 1 model selected
> hide sel surfaces
> select :ION
190 atoms, 190 residues, 1 model selected
> hide select :ION
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select :ION
190 atoms, 190 residues, 1 model selected
> hide selection
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide :ION
> set framerate 30
Expected a keyword
> select protein
Nothing selected
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="BENZ"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="ION"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
574 atoms, 4 bonds, 353 residues, 1 model selected
> color: BENZ red
Unknown command: color: BENZ red
> color:BENZ red
Unknown command: color:BENZ red
> color: BENZ red
Unknown command: color: BENZ red
> color :BENZ red
> opacity all 0.5
Unknown command: opacity all 0.5
> opacity atoms 0.5
Unknown command: opacity atoms 0.5
> transparency atoms 0.5
Missing or invalid "percent" argument: Expected a number
> transparency :atoms 0.5
> transparency :atoms 50
> transparency atoms 50
Missing or invalid "percent" argument: Expected a number
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> transparency 50 atoms
> transparency atoms 50
Missing or invalid "percent" argument: Expected a number
> transparency :atoms 50
> transparency 50 atoms
> transparency 0 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color :BENZ red
> transparency 1 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 -l :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 -l:BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 l:BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 labels :BENZ
Expected ',' or a keyword
> transparency 0, :BENZ
Missing or invalid "percent" argument: Expected a number
> transparency 100, :BENZ
Missing or invalid "percent" argument: Expected a number
> transparency 0.1, :BENZ
Missing or invalid "percent" argument: Expected a number
> transparency 0.1,l :BENZ
Missing or invalid "percent" argument: Expected a number
> transparency 50 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color :atoms grey
> color atoms grey
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color atoms gray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color atoms red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color :atoms red
> color aqua grey
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color gray a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color gray atoms
> color :BENZ red
> transparency 50 atoms
> transparency 99 atoms
> transparency 10 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color :BENZ red
> transparency :BENZ 0.1
> transparency :BENZ 1
> transparency :BENZ 10
> transparency :BENZ 0
> color :BENZ red
> transparency 70 atoms
> transparency 70 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency :BENZ 70
> transparency :BENZ 10
> transparency :BENZ 99
> transparency :BENZ 0
> save
> /Users/vjc493/Documents/martini_ligand_go/big_run_no_water/20/no_water_20.cxs
> record movie
Unknown command: record movie
> Record movie
Unknown command: Record movie
> Record movie
Unknown command: Record movie
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting simple
> lighting full
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/vjc493/Desktop/movie2.mp4
Movie saved to /Users/vjc493/Desktop/movie2.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/vjc493/Desktop/movie3.mp4
Movie saved to /Users/vjc493/Desktop/movie3.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/vjc493/Desktop/movie4.mp4
Movie saved to /Users/vjc493/Desktop/movie4.mp4
> save /Users/vjc493/Desktop/image1.png supersample 3
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> volume region all imageMode "full region"
No volumes specified
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> volume showOutlineBox true
No volumes specified
> show box
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> movie record
> movie encode /Users/vjc493/Desktop/movie5.mp4 framerate 25.0
Movie saved to /Users/vjc493/Desktop/movie5.mp4
> movie record
> movie encode /Users/vjc493/Desktop/movie6.mp4 framerate 25.0
Movie saved to /Users/vjc493/Desktop/movie6.mp4
> movie record
> movie encode /Users/vjc493/Desktop/movie7.mp4 framerate 25.0
Movie saved to /Users/vjc493/Desktop/movie7.mp4
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> color :BENZ red
> transparency :BENZ 0
> transparency :BENZ 1
> transparency :BENZ 99
> transparency :BENZ 0
> transparency :BENZ 100
> select ::name="BENZ"
3 atoms, 1 residue, 1 model selected
> transparency :BENZ 100
> transparency :BENZ 0
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> transparency :BENZ 100
> transparency atoms 100
Missing or invalid "percent" argument: Expected a number
> transparency 100
> transparency 100 atoms
> transparency 100 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 1
> transparency 0
> transparency 0 atoms
> transparency 050 atoms
> transparency 1 selection
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50 :BNZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50,a :BENZ
Missing or invalid "percent" argument: Expected a number
> transparency 50,a:BENZ
Missing or invalid "percent" argument: Expected a number
> transparency 50,a :BENZ
Missing or invalid "percent" argument: Expected a number
> transparency a :BENZ 50
Missing or invalid "percent" argument: Expected a number
> select :BENZ
3 atoms, 1 residue, 1 model selected
> transparency 100 ,A
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 .A
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 A
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 45
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 45.A
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 50,a :BENZ
Missing or invalid "percent" argument: Expected a number
> transparency ,a :BENZ 50
Missing or invalid "percent" argument: Expected a number
> transparency 50,a :BENZ 50
Missing or invalid "percent" argument: Expected a number
> transparency :BENZ
Missing or invalid "percent" argument: Expected a number
> transparency :BENZ 50
> transparency :BENZ 100
> transparency aa:BENZ 100
Missing or invalid "percent" argument: Expected a number
> transparency a:BENZ 100
Missing or invalid "percent" argument: Expected a number
> transparency :BENZ.A 100
Missing or invalid "percent" argument: Expected a number
> transparency :BENZ.a 100
Missing or invalid "percent" argument: Expected a number
> transparency :BENZ,a 100
> transparency :BENZ,a 0
> transparency :BENZ,a 1
> transparency :BENZ ,a 1
> transparency :BENZ 1
> transparency 100 :BENZ 1
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency 100 :BENZ
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> transparency /:BENZ 100
Missing or invalid "percent" argument: Expected a number
> transparency :BENZ 100
> select :BENZ
3 atoms, 1 residue, 1 model selected
> transparency sel 0 target ac
> undo
> show sel surfaces
> ui tool show "Side View"
> movie record
> movie encode /Users/vjc493/Desktop/movie8.mp4 framerate 25.0
Movie saved to /Users/vjc493/Desktop/movie8.mp4
> show sel surfaces
> hide sel surfaces
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/vjc493/Desktop/movie9.mp4
Movie saved to /Users/vjc493/Desktop/movie9.mp4
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: Z17G000ZKDK/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6 (23G80)
Kernel Version: Darwin 23.6.0
Time since boot: 24 days, 9 hours
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
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
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 14 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 , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Mac Qt bug, crashing in _NSViewHierarchyDidChangeBackingProperties, on connecting or disconnecting external display or waking from sleep.