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Opened 19 hours ago
Last modified 14 hours ago
#20394 assigned defect
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-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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
Thread 0x0000000305037000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030402b000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030301f000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000302013000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000301007000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017f103000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017e0f7000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017d0eb000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017c0df000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017b0d3000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000017a0c7000 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000000020795b100 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, 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, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 59)
{"app_name":"ChimeraX","timestamp":"2026-05-26 15:28:13.00 +0200","app_version":"1.10.1","slice_uuid":"9cf8124a-d876-34ad-b7ee-c011183ebc15","build_version":"1.10.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 26.3.1 (25D2128)","roots_installed":0,"name":"ChimeraX","incident_id":"19896AEB-50BB-42D2-8361-A5A552271600"}
{
"uptime" : 58000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Macmini9,1",
"coalitionID" : 2850,
"osVersion" : {
"train" : "macOS 26.3.1",
"build" : "25D2128",
"releaseType" : "User"
},
"captureTime" : "2026-05-26 15:28:02.5100 +0200",
"codeSigningMonitor" : 1,
"incident" : "19896AEB-50BB-42D2-8361-A5A552271600",
"pid" : 8188,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-05-26 13:42:42.6971 +0200",
"procStartAbsTime" : 1255003856634,
"procExitAbsTime" : 1400195099595,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"1596C622-2E3F-51B9-9047-D52D6C4F959F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "41EB562E-A196-C0AA-1FF8-4D81EBE3412B",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"bootProgressRegister" : "0x2f000000",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "DC979DCE-A667-4DE6-81DB-609043E9F572",
"sleepWakeUUID" : "35140976-555D-454A-903A-C5D749192088",
"sip" : "enabled",
"vmRegionInfo" : "0xfffffd8a1973b95d is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x16c9fd8a1973b95d","rawCodes":[1,1642122308727585117],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x16c9fd8a1973b95d -> 0xfffffd8a1973b95d (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":8188},
"vmregioninfo" : "0xfffffd8a1973b95d is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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"arch" : "arm64e",
"base" : 6928113664,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 16399392,
"uuid" : "187e7913-b154-30a7-8070-852767aac3cf",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "4302"
}
],
"sharedCache" : {
"base" : 6897254400,
"size" : 5820792832,
"uuid" : "674db25a-34b2-3c56-8bd4-7d78005b2f2e"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=1.3G written=36.5M(3%) resident=1526K(0%) swapped_out=35.0M(3%) unallocated=1.3G(97%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \n.note.gnu.proper 320 1 \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nAttributeGraph Data 1024K 1 \nCG image 192K 10 \nColorSync 96K 6 \nCoreAnimation 2240K 127 \nCoreGraphics 96K 6 \nCoreUI image data 5808K 49 \nFoundation 32K 2 \nKernel Alloc Once 48K 2 \nMALLOC 602.1M 144 \nMALLOC guard page 3984K 4 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 720K 45 \nStack 367.0M 46 \nStack Guard 56.0M 1 \nVM_ALLOCATE 273.0M 277 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__AUTH 5968K 656 \n__AUTH_CONST 90.5M 1042 \n__CTF 824 1 \n__DATA 46.7M 1157 \n__DATA_CONST 43.4M 1202 \n__DATA_DIRTY 8499K 899 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 619.3M 156 \n__OBJC_RO 78.4M 1 \n__OBJC_RW 2571K 1 \n__TEXT 1.3G 1194 \n__TEXT (graphics) 177.8M 31 \n__TPRO_CONST 128K 2 \ndyld private memory 3504K 30 \nmapped file 337.2M 70 \npage table in kernel 1526K 1 \nshared memory 3744K 28 \n=========== ======= ======= \nTOTAL 4.1G 7207 \nTOTAL, minus reserved VM space 4.0G 7207 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "adc8f3c36325ae2c48e0cb3b8f2c35dc09491a81",
"roots_installed" : 0,
"bug_type" : "309",
"trmStatus" : 8192,
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6425c75e4327780c10cc4252",
"factorPackIds" : [
"642600a457e7664b1698eb32"
],
"deploymentId" : 240000004
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{
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}
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/anushkaghosh/Documents/Documents/chimaera/Publishing/Hexamercomparison.cxs
> format session
> view name session-start
opened ChimeraX session
> select add #4/C:41
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #1/B:43
15 atoms, 13 bonds, 2 residues, 2 models selected
> select add #1/A:43
25 atoms, 22 bonds, 3 residues, 3 models selected
> select add #4/D:41
30 atoms, 26 bonds, 4 residues, 4 models selected
> select add #4/G:41
35 atoms, 30 bonds, 5 residues, 4 models selected
> select add #1/C:43
45 atoms, 39 bonds, 6 residues, 4 models selected
> select add #4/H:41
50 atoms, 43 bonds, 7 residues, 5 models selected
> select add #2.1/B:43
60 atoms, 52 bonds, 8 residues, 6 models selected
> select add #4/F:36
71 atoms, 62 bonds, 9 residues, 7 models selected
> select add #2.1/C:38
95 atoms, 85 bonds, 10 residues, 7 models selected
> select up
876 atoms, 871 bonds, 85 residues, 8 models selected
> select up
8563 atoms, 8673 bonds, 728 residues, 8 models selected
> hide sel atoms
> hide sel cartoons
> select #2.1/A:42
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #2.1/A:39
12 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2.1/A:40
34 atoms, 32 bonds, 2 residues, 2 models selected
> select subtract #2.1/A:39
22 atoms, 21 bonds, 1 residue, 2 models selected
> select add #2.1/A:39@CA
23 atoms, 21 bonds, 2 residues, 2 models selected
> select subtract #2.1/A:40
1 atom, 1 residue, 2 models selected
> hide sel atoms
> select #2.1/A:39@CG
1 atom, 1 residue, 1 model selected
> select #4/E:30
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> hide sel atoms
> select #2.1/A:37
19 atoms, 18 bonds, 1 residue, 1 model selected
> select clear
> select add #2.1/A:37
19 atoms, 18 bonds, 1 residue, 1 model selected
> select add #2.1/A:39@OD1
20 atoms, 18 bonds, 2 residues, 2 models selected
> select clear
> select #2.1/A:39@OD1
1 atom, 1 residue, 1 model selected
> select add #2.1/A:39@OD2
2 atoms, 1 residue, 2 models selected
> hide sel atoms
> select clear
> ui tool show "Side View"
> open
> /Users/anushkaghosh/Documents/Documents/chimaera/Phenix/Apo/Refine_21/HTHP_bessy050220_refine_21.pdb
Chain information for HTHP_bessy050220_refine_21.pdb #5
---
Chain | Description
A B C D F G I J L N O P R V | No description available
E K W | No description available
H M X | No description available
Q | No description available
S | No description available
T | No description available
U | No description available
39 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #5/D:7@OG
1 atom, 1 residue, 1 model selected
> select add #5/E:9@CG
2 atoms, 2 residues, 1 model selected
> select add #5/A:71@ND2
3 atoms, 3 residues, 1 model selected
> select add #5/D:75@CG
4 atoms, 4 residues, 1 model selected
> select add #5/C:74@CB
5 atoms, 5 residues, 1 model selected
> select add #5/B:9@CB
6 atoms, 6 residues, 1 model selected
> select add #5/U:37@N
7 atoms, 7 residues, 1 model selected
> select add #5/J:47@OE1
8 atoms, 8 residues, 1 model selected
> select add #5/H:45@CA
9 atoms, 9 residues, 1 model selected
> select add #5/K:43@C
10 atoms, 10 residues, 1 model selected
> select add #5/G:47@CB
11 atoms, 11 residues, 1 model selected
> select add #5/I:46@CB
12 atoms, 12 residues, 1 model selected
> select add #5/O:9@CG
13 atoms, 13 residues, 1 model selected
> select add #5/P:51@CB
14 atoms, 14 residues, 1 model selected
> select add #5/P:39@CG
15 atoms, 15 residues, 1 model selected
> select add #5/Q:7@O
16 atoms, 16 residues, 1 model selected
> select add #5/M:75@CA
17 atoms, 17 residues, 1 model selected
> select up
143 atoms, 127 bonds, 17 residues, 1 model selected
> select up
1271 atoms, 1280 bonds, 156 residues, 1 model selected
> select up
8224 atoms, 8382 bonds, 1050 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select #5/L:53@CD1
1 atom, 1 residue, 1 model selected
> select add #5/Q:63@CE2
2 atoms, 2 residues, 1 model selected
> select add #5/S:11@C
3 atoms, 3 residues, 1 model selected
> select add #5/W:22@CB
4 atoms, 4 residues, 1 model selected
> select add #5/V:38@NH1
5 atoms, 5 residues, 1 model selected
> select add #5/V:9@CD
6 atoms, 6 residues, 1 model selected
> select add #5/X:71@CB
7 atoms, 7 residues, 1 model selected
> select up
61 atoms, 55 bonds, 7 residues, 1 model selected
> select up
686 atoms, 695 bonds, 89 residues, 1 model selected
> select up
2701 atoms, 2754 bonds, 345 residues, 1 model selected
> hide sel atoms
> select #5/S:48@O
1 atom, 1 residue, 1 model selected
> select #5/T:73@CE3
1 atom, 1 residue, 1 model selected
> select add #5/R:37@CG1
2 atoms, 2 residues, 1 model selected
> select add #5/S:52@O
3 atoms, 3 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select up
293 atoms, 296 bonds, 37 residues, 1 model selected
> select up
1056 atoms, 1076 bonds, 134 residues, 1 model selected
> select up
1096 atoms, 1115 bonds, 139 residues, 1 model selected
> select up
1532 atoms, 1561 bonds, 196 residues, 1 model selected
> hide sel atoms
> select #5/N:32@OE1
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
22 atoms, 22 bonds, 3 residues, 1 model selected
> select up
572 atoms, 583 bonds, 73 residues, 1 model selected
> select up
13370 atoms, 13624 bonds, 1708 residues, 1 model selected
> select down
572 atoms, 583 bonds, 73 residues, 1 model selected
> hide sel atoms
> select #5/F:42@NH2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> select up
572 atoms, 583 bonds, 73 residues, 1 model selected
> cartoon sel
> style sel stick
Changed 572 atom styles
> hide sel atoms
> ui tool show "Selection Inspector"
> size =sel stickRadius 0.19
Changed 583 bond radii
> size =sel stickRadius 0.18
Changed 583 bond radii
> size =sel stickRadius 0.17
Changed 583 bond radii
> size =sel stickRadius 0.1
Changed 583 bond radii
> setattr sel r ss_type 0
Assigning ss_type attribute to 73 items
> setattr sel r ss_type 0
Assigning ss_type attribute to 73 items
> color sel #7a81ff target r
> color sel #9437ff target r
> select clear
> select add #5/F:65
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #4/E:52
12 atoms, 10 bonds, 2 residues, 2 models selected
> select clear
> select #5/F:65
7 atoms, 6 bonds, 1 residue, 1 model selected
> ui tool show Matchmaker
> matchmaker #!5 to #4
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 2oyy.pdb, chain C (#4) with HTHP_bessy050220_refine_21.pdb, chain K
(#5), sequence alignment score = 300.4
RMSD between 71 pruned atom pairs is 0.607 angstroms; (across all 71 pairs:
0.607)
> matchmaker #!1 to #5/F pairing bs
Parameters
---
Chain pairing | bs
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 HTHP_bessy050220_refine_21.pdb, chain F (#5) with
HTHP_bessy160519_refine_29.pdb, chain C (#1), sequence alignment score = 368.7
RMSD between 73 pruned atom pairs is 0.648 angstroms; (across all 73 pairs:
0.648)
> matchmaker #!1 to #5/F pairing bs
Parameters
---
Chain pairing | bs
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 HTHP_bessy050220_refine_21.pdb, chain F (#5) with
HTHP_bessy160519_refine_29.pdb, chain C (#1), sequence alignment score = 368.7
RMSD between 73 pruned atom pairs is 0.648 angstroms; (across all 73 pairs:
0.648)
> matchmaker #2.1/A to #5/F pairing ss
Parameters
---
Chain pairing | ss
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 HTHP_bessy050220_refine_21.pdb, chain F (#5) with
HTHP_bessy160519_refine_29.pdb 0 0 0 sym 9, chain A (#2.1), sequence alignment
score = 365.7
RMSD between 73 pruned atom pairs is 0.628 angstroms; (across all 73 pairs:
0.628)
> matchmaker #4/E to #5/F pairing ss
Parameters
---
Chain pairing | ss
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 HTHP_bessy050220_refine_21.pdb, chain F (#5) with 2oyy.pdb, chain E
(#4), sequence alignment score = 295.6
RMSD between 71 pruned atom pairs is 0.669 angstroms; (across all 71 pairs:
0.669)
> select clear
> select #4/E:41
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select #2.1/A:45
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/F:45
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
Unsupported scale factor (0.000000) detected on Display0
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac mini
Model Identifier: Macmini9,1
Model Number: Z12N0006DD/A
Chip: Apple M1
Total Number of Cores: 8 (4 Performance and 4 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (25D2128)
Kernel Version: Darwin 25.3.0
Time since boot: 4 days, 4 hours, 16 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
DELL U2720Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 50.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (1)
comment:1 by , 14 hours 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 |
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Reported by Anushka Ghosh