![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16945 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: 1.9 (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 0x00000001eaa00f40 (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, 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.surface._surface, 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, PIL._webp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 62)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,3",
"coalitionID" : 2802,
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"build" : "23G80",
"releaseType" : "User"
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"captureTime" : "2025-02-23 22:08:09.3278 -0800",
"codeSigningMonitor" : 1,
"incident" : "0A7ED491-98D0-451A-B24A-7AB39036C856",
"pid" : 38203,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-23 20:11:22.0316 -0800",
"procStartAbsTime" : 7288158022088,
"procExitAbsTime" : 7456328920571,
"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"},
"storeInfo" : {"deviceIdentifierForVendor":"00B753AC-ED12-56CA-9167-3A75EB681B87","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "53D10C58-BF9C-6FAE-A3EE-EF9DBFEF514C",
"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" : 13639,
"sleepWakeUUID" : "B17B387E-407C-417B-995C-EFA18130054D",
"sip" : "enabled",
"vmRegionInfo" : "0x38363032379f is not in any region. Bytes after previous region: 61324351649696 Bytes before following region: 43747728279649\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x333438363032379f","rawCodes":[1,3689635800111265695],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x333438363032379f -> 0x000038363032379f (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":38203},
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"faultingThread" : 0,
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=3.0G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 1264K 58 \nColorSync 656K 31 \nCoreAnimation 2880K 176 \nCoreGraphics 48K 3 \nCoreServices 624K 2 \nCoreUI image data 4704K 56 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.4G 101 \nMALLOC guard page 192K 12 \nMach message 96K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 688K 43 \nStack 217.9M 44 \nStack Guard 56.0M 1 \nVM_ALLOCATE 212.9M 231 \nVM_ALLOCATE (reserved) 128.0M 2 reserved VM address space (unallocated)\n__AUTH 3370K 569 \n__AUTH_CONST 40.9M 823 \n__CTF 824 1 \n__DATA 26.2M 979 \n__DATA_CONST 52.0M 993 \n__DATA_DIRTY 2902K 323 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 555.8M 164 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2200K 1 \n__TEXT 1.1G 1011 \ndyld private memory 592K 6 \nmapped file 536.5M 79 \nshared memory 3312K 25 \n=========== ======= ======= \nTOTAL 5.4G 5752 \nTOTAL, minus reserved VM space 5.3G 5752 \n",
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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"logWritingSignature" : "2896988f9eb829aeca244d29025cd427efd2e7d7",
"trialInfo" : {
"rollouts" : [
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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/ckayrouz/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/B8DD358B-7617-498C-83CE-C4993204C355/chimera template .cxs" format
> session
opened ChimeraX session
> select #1.1/A:259@NE2
1 atom, 1 residue, 1 model selected
> select #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> select up
4320 atoms, 4365 bonds, 281 residues, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select ~sel & ##selected
4319 atoms, 4365 bonds, 5 pseudobonds, 280 residues, 2 models selected
> select up
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> select add #1.1/A:259@NE2
1 atom, 1 residue, 1 model selected
> select add #1.1/A:301@Fe
2 atoms, 2 residues, 1 model selected
> close
> open "/Users/ckayrouz/Library/Containers/com.apple.mail/Data/Library/Mail
> Downloads/B8DD358B-7617-498C-83CE-C4993204C355/chimera template .cxs" format
> session
opened ChimeraX session
> ui mousemode right select
> select clear
> select add #1
4367 atoms, 4414 bonds, 5 pseudobonds, 283 residues, 5 models selected
> color (#1.2.1#!1.1 & sel) dark gray
> color sel byhetero
> select clear
> select add #1.2
47 atoms, 49 bonds, 2 residues, 2 models selected
> color sel #44aa99ff
> color sel byhetero
> select subtract #1.2
Nothing selected
> select add #6
17580 atoms, 17665 bonds, 21 pseudobonds, 1231 residues, 4 models selected
> color (#!6 & sel) #ee6677ff
> color sel byhetero
> select clear
> select #1.1/A
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> ui tool show "Basic Actions"
> select clear
> show #!3 models
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> lighting flat
> lighting simple
> ui tool show "Side View"
> set bgColor black
> undo
> set bgColor white
> view
> view orient
> ui tool show "Side View"
> select #1.1/A:77
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel dim gray
> select clear
> lighting shadows true
> lighting shadows false
> lighting simple
> select clear
> select #1.1/A:91
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1.1/A:90
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select #1.1/A:250
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #1.1/A:92
17 atoms, 16 bonds, 1 residue, 1 model selected
> hide sel cartoons
> transparency / A 50
> transparency / A 75
> transparency / 1.1A 75
Missing or invalid "percent" argument: Expected a number
> transparency / #1.1A 75
Missing or invalid "percent" argument: Expected a number
> transparency / #1.1/A 75
Missing or invalid "percent" argument: Expected a number
> transparency / #1.1A 75
Missing or invalid "percent" argument: Expected a number
> transparency #1/A 75
> transparency #1.1/A 75
> select #1.1/A
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> select subtract #1.1
Nothing selected
> select add #1.1
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> select add #1.2
4367 atoms, 4414 bonds, 5 pseudobonds, 283 residues, 4 models selected
> select subtract #1.2
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> transparency 75
> select clear
> transparency 100
> transparency #1.1A 100
Missing or invalid "percent" argument: Expected a number
> transparency #1.1/A 100
> transparency #1.1/A 60
> select clear
> select add #1.1
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> color (#!1.1 & sel) #bbbbbbff
> select clear
> color #1.2.1#!6#!1.1 byhetero
> select clear
> select #1.1/A:77
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel dim gray
> select clear
> view
> view orient
> view
> ui tool show "Side View"
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/overlay-alt.tif" width 936 height 767 supersample 3
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/overlay-alt.cxs"
> close #2
> close
> open "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/ind-3-menthol-wt.cxs"
opened ChimeraX session
> select add #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> select add #1.1/A:164@NE2
2 atoms, 2 residues, 1 model selected
> pbonds
Unknown command: pbonds
> pbond
Missing or invalid "atoms" argument: empty atom specifier
> pbond #1.1/A:164@NE2, #1.1/A:301@Fe
Missing or invalid "atoms" argument: only initial part "#1.1/A:164@NE2" of
atom specifier valid
> pbond #1.1/A:164@NE2 #1.1/A:301@Fe
Drag select of 4 atoms, 8 bonds, 1 pseudobonds
> pbond
Missing or invalid "atoms" argument: empty atom specifier
> select clear
> hide sel atoms
> select clear
Drag select of 3 atoms, 5 bonds, 1 pseudobonds
> select #1.1/A:302@CL
1 atom, 1 residue, 1 model selected
> style sel ball
Changed 1 atom style
> select clear
Drag select of 4 atoms, 7 bonds, 1 pseudobonds
> select clear
> select #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> select sel @ select sel @ select sel @ select clear
> select #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> select sel @ select sel @ select sel @ pbond
Missing or invalid "atoms" argument: empty atom specifier
> select clear
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> undo
> close
> open "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/ind-3-menthol-wt.cxs" format session
opened ChimeraX session
> select #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> pbond #1.1/A:301@Fe
Must specify exactly 2 atoms to form pseudobond between; you specified 1
> select #1.1/A:164@NE2
1 atom, 1 residue, 1 model selected
> select #1.1/A:164@NE2
1 atom, 1 residue, 1 model selected
> select #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> select add #1.1/A:164@NE2
2 atoms, 2 residues, 1 model selected
> select subtract #1.1/A:164@NE2
1 atom, 1 residue, 1 model selected
> select #1.1/A:164@NE2
1 atom, 1 residue, 1 model selected
> select #1.1/A:164
17 atoms, 17 bonds, 1 residue, 1 model selected
> select clear
> select #1.1/A:164@NE2
1 atom, 1 residue, 1 model selected
> select #1.1/A:303@O2
1 atom, 1 residue, 1 model selected
> select add #1.1/A:301@Fe
2 atoms, 2 residues, 1 model selected
> pbond
Missing or invalid "atoms" argument: empty atom specifier
> pbond
Missing or invalid "atoms" argument: empty atom specifier
> select clear
> select #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> select #1.1/A:164@NE2
1 atom, 1 residue, 1 model selected
> select add #1.1/A:301@Fe
2 atoms, 2 residues, 1 model selected
> pbond
Missing or invalid "atoms" argument: empty atom specifier
> select clear
> close
> open "/Users/ckayrouz/Desktop/Hartwig Lab Research New/Paper-wt-menthol-
> new.mae"
Chain information for Paper-wt-menthol-new.mae
---
Chain | Description
1.1/A | No description available
Opened Paper-wt-menthol-new.mae containing 2 structures (4367 atoms, 4419
bonds)
> viewdockx #1.1-2
> select #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> pbond
Missing or invalid "atoms" argument: empty atom specifier
> select add #1.1/A:259@NE2
2 atoms, 2 residues, 1 model selected
> pbond
Missing or invalid "atoms" argument: empty atom specifier
> select #1.1/A:302@CL
1 atom, 1 residue, 1 model selected
> pbond
Missing or invalid "atoms" argument: empty atom specifier
Drag select of 2 atoms, 1 residues, 3 bonds
Drag select of 1 atoms, 1 bonds
Drag select of 2 atoms, 2 bonds
> pbond
Missing or invalid "atoms" argument: empty atom specifier
> select #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> pbond [#1.1/A:301@Fe | #1.1/A:302@CL]
Missing or invalid "atoms" argument: invalid atoms specifier
> pbond [#1.1/A:301@Fe #1.1/A:302@CL]
Missing or invalid "atoms" argument: invalid atoms specifier
> pbond #1.1/A:301 #1.1/A:302
> style sel sphere
Changed 1 atom style
> style sel ball
Changed 1 atom style
Drag select of 46 atoms, 9 residues, 44 bonds, 1 pseudobonds
> style sel ball
Changed 158 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue + (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/vw/b9r5l0_x6r5cgg6kjcjfmp4h0000gn/T/tmpl1vqibey/ante.in.mol2 -fi
mol2 -o
/var/folders/vw/b9r5l0_x6r5cgg6kjcjfmp4h0000gn/T/tmpl1vqibey/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(+) ``
(+) `Welcome to antechamber 20.0: molecular input file processor.`
(+) ``
(+) `Info: Finished reading file
(/var/folders/vw/b9r5l0_x6r5cgg6kjcjfmp4h0000gn/T/tmpl1vqibey/ante.in.mol2);
atoms read (47), bonds read (49).`
(+) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(+) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(+) ``
(+) ``
(+) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(+) `Info: Total number of electrons: 162; net charge: 0`
(+) ``
(+) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`
(+) ``
(+) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/am1bcc
-i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(+) ``
(+) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(+) ``
Charges for residue + determined
Coulombic values for Paper-wt-menthol-new.mae_A SES surface #1.1.2: minimum,
-15.61, mean -1.91, maximum 12.67
Coulombic values for Paper-wt-menthol-new.mae_ SES surface #1.2.1.1: minimum,
0.85, mean 1.52, maximum 1.96
To also show corresponding color key, enter the above coulombic command and
add key true
> close #1.1.1#1#1.1-2#1.2.1
> open "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/overlay-alt.cxs" format session
opened ChimeraX session
> select #1.1/A:302@CL
1 atom, 1 residue, 1 model selected
> select #1.1/A:301@Fe
1 atom, 1 residue, 1 model selected
> close
> open "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/overlay-alt.cxs"
opened ChimeraX session
> ui favorite true "Model Panel"
> ui tool show "Model Panel"
> help help:user/tools/modelpanel.html
> close #2
> hide #!3 target m
> hide #!4 target m
> hide #!3 target m
> close #3.1#3-6#3.2
> select #1.1/A:77
20 atoms, 20 bonds, 1 residue, 1 model selected
> color sel #ee6699ff
> color sel #bbbbbbff
> hide sel atoms
> select clear
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/wt-pbond-model.cxs"
> select #1.1/A:89
19 atoms, 18 bonds, 1 residue, 1 model selected
Drag select of 16 residues
> show sel cartoons
> select clear
> select #1.1/A
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> show sel cartoons
> select #1.1/A:164
17 atoms, 17 bonds, 1 residue, 1 model selected
> select clear
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/wt-pbond-model.cxs"
> select /A:90, 88, 161, 81
61 atoms, 57 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel #ee6677ff
> color sel byhetero
> ~display HC
> select clear
> select #1.1/A
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> color (#!1.1 & sel) dark gray
> color sel byhetero
> select clear
> select /A:90, 81, 161, 88
61 atoms, 57 bonds, 4 residues, 1 model selected
> color sel #228833ff
> color sel #ee6677ff
> select clear
Drag select of 17 residues
> hide sel cartoons
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/wt-figure1-new.tif" width 936 height 767 supersample 3
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/wt-figure1-new.cxs"
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/Figure-2.tif" width 936 height 767 supersample 4
> transparentBackground true
> select /A:90, 81, 161, 88
61 atoms, 57 bonds, 4 residues, 1 model selected
> hide sel atoms
> color sel dark gray
> select clear
> select /A:187,92,91,87,86,74,72,22,221
119 atoms, 113 bonds, 9 residues, 1 model selected
> show sel atoms
> color sel #228833ff
> color sel #ee6677ff
> color sel byhetero
> ~display HC
> select clear
> select #1.1/A
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> show sel cartoons
> select clear
> select #1.1/A:22
16 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> color sel dark gray
> select #1.1/A:222
17 atoms, 17 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:221, 222, 72, 74, 86, 87, 92, 91, 187
120 atoms, 116 bonds, 9 residues, 1 model selected
> show sel atoms
> color sel #228833ff
> color sel #ee6677ff
> color sel byhetero
> ~display HC
> select clear
> ~display H
> select clear
> transparency 60
> select #1.1/A
4320 atoms, 4365 bonds, 5 pseudobonds, 281 residues, 2 models selected
> transparency (#!1.1 & sel) 40
> select clear
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/A-scan.tif" width 4000 height 3278 supersample 4
> transparentBackground true
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/A-scan-new.cxs"
> close #1.2
> close
> open "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/wt-figure1-new.cxs" format session
opened ChimeraX session
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/Figure-2-High-res.tif" width 4000 height 3278 supersample 4
> transparentBackground true
> close
> open "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/A-scan-new.cxs" format session
opened ChimeraX session
> save "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/A-scan-newest.png" width 4000 height 3278 supersample 3
> transparentBackground true
> close
> open "/Users/ckayrouz/Desktop/Hartwig Lab Research New/WelO15
> Docking/Paper/wt-figure1-new.cxs" format session
opened ChimeraX session
> save "/Users/ckayrouz/Downloads/Figure 1-new.png" width 4000 height 3278
> supersample 3 transparentBackground true
===== 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 - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: 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: Mac15,3
Model Number: MXE03LL/A
Chip: Apple M3
Total Number of Cores: 8 (4 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: 6 days, 11 hours, 20 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Sceptre F24:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
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-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
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 , 8 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 , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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