![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 months ago
Closed 4 months ago
#17978 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-12.5-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 0x00000001022f4580 (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.pdb_lib._load_libs, chimerax.surface._surface, 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 63)
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{
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"procLaunch" : "2025-06-09 17:48:28.3462 -0700",
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"version" : 2,
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"releaseType" : "User"
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"captureTime" : "2025-06-11 13:51:48.3292 -0700",
"incident" : "6589C9AE-F76B-4CC0-8768-5E0186669A0E",
"bug_type" : "309",
"pid" : 52305,
"procExitAbsTime" : 7718820724813,
"translated" : false,
"cpuType" : "ARM-64",
"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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"parentProc" : "launchd",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3B5CB510-F428-16BE-91C8-C6A2A81618AF",
"wakeTime" : 3,
"sleepWakeUUID" : "700DCCE1-A3C4-40C8-A77E-EE34DD0F8853",
"sip" : "enabled",
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"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000264311770798","rawCodes":[1,42069497677720],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000264311770798"},
"ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
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"faultingThread" : 0,
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=4.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=4.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1792K 14 \nActivity Tracing 256K 1 \nCG backing stores 5056K 8 \nCG image 544K 30 \nColorSync 640K 28 \nCoreAnimation 432K 24 \nCoreGraphics 80K 5 \nCoreUI image data 2528K 19 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 2.5G 558 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 704.0M 9 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 560K 35 \nStack 191.2M 36 \nStack Guard 56.0M 1 \nVM_ALLOCATE 461.8M 353 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__AUTH 2686K 343 \n__AUTH_CONST 21.4M 553 \n__CTF 756 1 \n__DATA 24.7M 710 \n__DATA_CONST 29.8M 716 \n__DATA_DIRTY 1968K 242 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 608.0M 162 \n__OBJC_CONST 4017K 319 \n__OBJC_RO 83.0M 1 \n__OBJC_RW 3168K 1 \n__TEXT 782.2M 734 \n__UNICODE 592K 1 \ndyld private memory 1072K 3 \nmapped file 187.1M 49 \nshared memory 3200K 28 \n=========== ======= ======= \nTOTAL 6.0G 5009 \nTOTAL, minus reserved VM space 4.9G 5009 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
},
"deploymentId" : 240000002
},
{
"rolloutId" : "607844aa04477260f58a8077",
"factorPackIds" : {
"SIRI_MORPHUN_ASSETS" : "6103050cbfe6dc472e1c982a"
},
"deploymentId" : 240000066
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> graphics silhouettes true
> lighting soft
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/jchuang/Scripps Research Dropbox/Jiachen Huang/Drifting
> H3s/Manuscript/Final maps and models/2 RBS aligned.cxs"
Opened 3.03_P341_J234_flip.mrc as #1, grid size 416,416,416, pixel 0.725,
shown at level 0.085, step 1, values float32
opened ChimeraX session
> select add #3
13734 atoms, 14025 bonds, 1715 residues, 1 model selected
> select subtract #3
Nothing selected
> show #!2 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> hide #3 models
> ui mousemode right select
Drag select of 15 atoms, 47 residues, 14 bonds
> select clear
Drag select of 89 atoms, 198 residues, 92 bonds
> select up
1653 atoms, 1676 bonds, 206 residues, 1 model selected
> select up
1674 atoms, 1699 bonds, 206 residues, 1 model selected
> select up
3425 atoms, 3477 bonds, 422 residues, 1 model selected
> select up
11711 atoms, 11957 bonds, 1474 residues, 1 model selected
> select up
12303 atoms, 12563 bonds, 1518 residues, 1 model selected
> show sel surfaces
> select clear
> select #2/G:225@CB
1 atom, 1 residue, 1 model selected
> select #2/G:137@CB
1 atom, 1 residue, 1 model selected
> select #2/G:143@CB
1 atom, 1 residue, 1 model selected
> select #2/G:142@CB
1 atom, 1 residue, 1 model selected
> select #2/G:140@CD1
1 atom, 1 residue, 1 model selected
> select #2/G:144@CB
1 atom, 1 residue, 1 model selected
> select up
6 atoms, 5 bonds, 1 residue, 2 models selected
> select clear
> hide #!2 surfaces
Drag select of 59 residues
> select up
921 atoms, 939 bonds, 119 residues, 1 model selected
> select up
1732 atoms, 1777 bonds, 227 residues, 1 model selected
> show sel surfaces
> select clear
> select #2/G:146
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/G:145
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/G:144
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #2/G:144
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Color Actions"
> color byhetero target acpf
> select #2/G:134
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #2/G:133
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/G:131
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2/G:135
14 atoms, 12 bonds, 2 residues, 2 models selected
> show sel atoms
> select add #2/G:144
20 atoms, 17 bonds, 3 residues, 2 models selected
> style sel sphere
Changed 20 atom styles
> select add #2/G:158
28 atoms, 24 bonds, 4 residues, 2 models selected
> select add #2/G:159
40 atoms, 36 bonds, 5 residues, 2 models selected
> select subtract #2/G:158
32 atoms, 29 bonds, 4 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 32 atom styles
> select clear
> select #2/G:192
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/G:190
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/G:192
16 atoms, 14 bonds, 2 residues, 2 models selected
> select subtract #2/G:192
8 atoms, 7 bonds, 1 residue, 2 models selected
> select add #2/G:193
19 atoms, 18 bonds, 2 residues, 2 models selected
> select add #2/G:192
27 atoms, 25 bonds, 3 residues, 2 models selected
> show sel atoms
> style sel sphere
Changed 27 atom styles
> select #2/G:222
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/G:226
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/G:225
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel sphere
Changed 8 atom styles
> select clear
> select #2/G:224
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/G:225@CA
1 atom, 1 residue, 1 model selected
> select add #2/G:135@CA
2 atoms, 2 residues, 2 models selected
> select add #2/G:144@CB
3 atoms, 3 residues, 2 models selected
> select add #2/G:131@CA
4 atoms, 4 residues, 2 models selected
> select add #2/G:159@CD2
5 atoms, 5 residues, 2 models selected
> select add #2/G:192@CD1
6 atoms, 6 residues, 2 models selected
> select add #2/G:190@CA
7 atoms, 7 residues, 2 models selected
> select add #2/G:193@CB
8 atoms, 8 residues, 2 models selected
> select add #2/G:190@OD2
9 atoms, 8 residues, 2 models selected
> select up
67 atoms, 62 bonds, 8 residues, 2 models selected
> style sel ball
Changed 67 atom styles
> style sel sphere
Changed 67 atom styles
> ui tool show "Color Actions"
> color sel orange target acpf
> color sel byhetero target acpf
> size ligand atomRadius -.5
Changed 1191 atom radii
> size ligand atomRadius -1
Cannot reduce atom radius to size ligand atomRadius -.3
Changed 1191 atom radii
> size ligand atomRadius -.8
Cannot reduce atom radius to ui mousemode right "resize markers"
> volume #1 level -0.2232
> style sel ball
Changed 67 atom styles
> ui mousemode right select
> select clear
> select #2/T:19@NH1
1 atom, 1 residue, 1 model selected
> select #2/S:27@OD1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
18 atoms, 17 bonds, 3 residues, 2 models selected
> select up
949 atoms, 976 bonds, 122 residues, 2 models selected
> ui tool show "Color Actions"
> color sel maroon
> color sel dark red
> color sel fire brick
> color sel dark red
> select clear
> select #2/T:59@CD
1 atom, 1 residue, 1 model selected
Drag select of 306.1.7_real_space_refined_014.pdb_T SES surface, 586 of 95370
triangles
Drag select of 306.1.7_real_space_refined_014.pdb_T SES surface, 224 of 95370
triangles
Drag select of 306.1.7_real_space_refined_014.pdb_T SES surface, 603 of 95370
triangles
> select up
12548 atoms, 3 pseudobonds, 1588 residues, 7 models selected
> select down
Nothing selected
> color tomato
> undo
Drag select of 306.1.7_real_space_refined_014.pdb_T SES surface, 409 of 95370
triangles
Drag select of 306.1.7_real_space_refined_014.pdb_T SES surface, 443 of 95370
triangles
> color sel tomato
> color sel indian red
> select clear
> select #2/G:225
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Side View"
> select clear
Drag select of 1 bonds
Drag select of 1 atoms, 2 bonds
> select up
8 atoms, 5 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> hide sel atoms
> select clear
> select #2/A:619@C3
1 atom, 1 residue, 1 model selected
> select add #2/A:615@C3
2 atoms, 2 residues, 1 model selected
> select up
28 atoms, 28 bonds, 2 residues, 1 model selected
> select up
4126 atoms, 4215 bonds, 508 residues, 1 model selected
> select down
28 atoms, 28 bonds, 2 residues, 2 models selected
> hide sel atoms
Drag select of 12 atoms, 81 residues, 10 bonds
> select up
677 atoms, 683 bonds, 84 residues, 2 models selected
> select up
705 atoms, 715 bonds, 84 residues, 2 models selected
> select up
1319 atoms, 1355 bonds, 160 residues, 2 models selected
> select up
2530 atoms, 2589 bonds, 321 residues, 2 models selected
> select up
2683 atoms, 2747 bonds, 341 residues, 2 models selected
> select up
3914 atoms, 3997 bonds, 492 residues, 2 models selected
> select up
8216 atoms, 8390 bonds, 1013 residues, 2 models selected
> select down
3914 atoms, 3997 bonds, 492 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
Drag select of 28 atoms, 29 bonds
> select up
4126 atoms, 4215 bonds, 508 residues, 1 model selected
> select up
14035 atoms, 14340 bonds, 1745 residues, 2 models selected
> select down
4126 atoms, 4215 bonds, 508 residues, 6 models selected
> select down
28 atoms, 29 bonds, 2 residues, 2 models selected
> hide sel atoms
> select #2/G:218
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
Drag select of 306.1.7_real_space_refined_014.pdb_T SES surface, 1465 of 95370
triangles, 6 residues
> select up
105 atoms, 102 bonds, 14 residues, 2 models selected
> select up
783 atoms, 801 bonds, 105 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
Drag select of 306.1.7_real_space_refined_014.pdb_S SES surface, 1871 of
109832 triangles, cap far, 68 of 4526 triangles, 2 residues
> select up
32 atoms, 32 bonds, 5 residues, 3 models selected
> select up
949 atoms, 976 bonds, 122 residues, 3 models selected
> hide sel cartoons
> hide sel surfaces
> select #2/G:198
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 5 residues, 2 models selected
> select up
2485 atoms, 2542 bonds, 318 residues, 2 models selected
> show sel surfaces
> hide sel surfaces
> select clear
> select add #2/G:159
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #2/G:192
20 atoms, 19 bonds, 2 residues, 2 models selected
> select add #2/G:193
31 atoms, 30 bonds, 3 residues, 2 models selected
> select add #2/G:190
39 atoms, 37 bonds, 4 residues, 2 models selected
> select add #2/G:225
47 atoms, 44 bonds, 5 residues, 2 models selected
> select add #2/G:144
53 atoms, 49 bonds, 6 residues, 2 models selected
> select add #2/G:135
60 atoms, 55 bonds, 7 residues, 2 models selected
> select add #2/G:131
67 atoms, 61 bonds, 8 residues, 2 models selected
> select up
404 atoms, 412 bonds, 51 residues, 2 models selected
> select down
67 atoms, 61 bonds, 8 residues, 2 models selected
> ui tool show "Color Actions"
> color sel orange
> color sel byhetero
> color sel orange
> color sel byhetero target acpf
> select clear
> show #4#!2 surfaces
Drag select of 306.1.7_real_space_refined_014.pdb_S SES surface, 3958 of
109832 triangles, 306.1.7_real_space_refined_014.pdb_T SES surface, 6844 of
95370 triangles
Drag select of 306.1.7_real_space_refined_014.pdb_S SES surface, 977 of 109832
triangles, 306.1.7_real_space_refined_014.pdb_T SES surface, 1160 of 95370
triangles
> hide #4#!2 surfaces
Drag select of 3 residues
> select up
181 atoms, 186 bonds, 21 residues, 2 models selected
> select up
2485 atoms, 2542 bonds, 318 residues, 2 models selected
> show sel surfaces
> select clear
Drag select of 3 atoms, 47 residues, 2 bonds
> select up
385 atoms, 389 bonds, 49 residues, 2 models selected
> select up
409 atoms, 415 bonds, 49 residues, 2 models selected
> select clear
Drag select of 2 atoms, 10 residues, 2 bonds
> select up
96 atoms, 94 bonds, 11 residues, 2 models selected
> select up
107 atoms, 106 bonds, 11 residues, 2 models selected
> select up
384 atoms, 392 bonds, 48 residues, 2 models selected
> select up
2499 atoms, 2556 bonds, 319 residues, 2 models selected
> select clear
Drag select of 13 atoms, 24 residues, 12 bonds
> select up
216 atoms, 218 bonds, 26 residues, 2 models selected
> select up
230 atoms, 234 bonds, 26 residues, 2 models selected
> select up
450 atoms, 459 bonds, 56 residues, 2 models selected
> select up
2513 atoms, 2570 bonds, 320 residues, 2 models selected
> select up
2666 atoms, 2728 bonds, 340 residues, 2 models selected
> hide sel cartoons
Drag select of 38 atoms, 38 bonds
> select up
39 atoms, 39 bonds, 3 residues, 1 model selected
> select up
42 atoms, 42 bonds, 3 residues, 1 model selected
> hide sel atoms
Drag select of 18 atoms, 21 bonds
> select clear
Drag select of 6 atoms, 8 bonds
Drag select of 1 atoms
Drag select of 10 atoms, 12 bonds
> select up
24 atoms, 21 bonds, 4 residues, 1 model selected
> select up
53 atoms, 53 bonds, 4 residues, 1 model selected
> select up
106 atoms, 110 bonds, 8 residues, 1 model selected
> hide sel atoms
Drag select of 3 atoms, 2 residues, 4 bonds
> select up
22 atoms, 19 bonds, 4 residues, 2 models selected
> select up
44 atoms, 44 bonds, 4 residues, 2 models selected
> select #2/G:401
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
184 atoms, 186 bonds, 22 residues, 2 models selected
> select up
1384 atoms, 1408 bonds, 171 residues, 2 models selected
> show sel surfaces
> select clear
> hide #!2 models
> open 9cb1
Summary of feedback from opening 9cb1 fetched from pdb
---
note | Fetching compressed mmCIF 9cb1 from http://files.rcsb.org/download/9cb1.cif
9cb1 title:
Cryo-EM Structure of the Human Neutralizing Antibody 5-1 in Complex with
Prefusion Human Metapneumovirus F Glycoprotein [more info...]
Chain information for 9cb1 #5
---
Chain | Description | UniProt
A B C | 5-1 Fab Heavy Chain Variable Domain |
D E F | 5-1 Fab Light Chain Variable Domain |
G H I | Fusion glycoprotein F0 | H6X1Z1_9MONO 1-490
Non-standard residues in 9cb1 #5
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> open 7tl0
Summary of feedback from opening 7tl0 fetched from pdb
---
note | Fetching compressed mmCIF 7tl0 from http://files.rcsb.org/download/7tl0.cif
7tl0 title:
Cryo-EM structure of hMPV preF bound by Fabs MPE8 and SAN32-2 [more info...]
Chain information for 7tl0 #6
---
Chain | Description | UniProt
A B C | Fusion glycoprotein F0 | H6X1Z0_9MONO 1-490
D F H | SAN32-2 Fab heavy chain |
E G I | SAN32-2 Fab light chain |
J L N | MPE8 Fab heavy chain |
K M O | MPE8 Fab light chain |
Non-standard residues in 7tl0 #6
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> ui tool show Matchmaker
> matchmaker #!6 to #5
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9cb1, chain I (#5) with 7tl0, chain B (#6), sequence alignment
score = 2579.7
RMSD between 401 pruned atom pairs is 1.037 angstroms; (across all 429 pairs:
1.240)
> matchmaker #!6 to #5
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 9cb1, chain I (#5) with 7tl0, chain B (#6), sequence alignment
score = 2579.7
RMSD between 401 pruned atom pairs is 1.037 angstroms; (across all 429 pairs:
1.240)
> hide #4#!5-6 atoms
> show #4#!5-6 cartoons
> hide #!5 models
> select ::name="BMA"::name="MAN"::name="NAG"
1608 atoms, 1636 bonds, 105 residues, 4 models selected
> show sel & #!6 atoms
> show #!5 models
> select clear
> hide #4 models
> select subtract #4
Nothing selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> graphics silhouettes true
> lighting soft
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/jchuang/Downloads/cryosparc_P7_J79_005_volume_map_sharp.mrc
Opened cryosparc_P7_J79_005_volume_map_sharp.mrc as #1, grid size 440,440,440,
pixel 0.721, shown at level 0.0299, step 2, values float32
> open /Users/jchuang/Downloads/cryosparc_P7_J81_006_volume_map_sharp.mrc
Opened cryosparc_P7_J81_006_volume_map_sharp.mrc as #2, grid size 440,440,440,
pixel 0.721, shown at level 0.0286, step 2, values float32
OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M2
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: Mac14,7
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 7459.141.1
OS Loader Version: 7459.141.1
Software:
System Software Overview:
System Version: macOS 12.5 (21G72)
Kernel Version: Darwin 21.6.0
Time since boot: 15 days 22:09
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
LG UltraFine:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 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 , 4 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 , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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