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Opened 5 months ago
Closed 5 months ago
#17810 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-14.3-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
Thread 0x00000002a145f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002a0453000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029f447000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029e43b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029d42f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029c423000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029b417000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000029a40b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002993ff000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002983f3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000002973e7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001e2699c40 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 54)
{"app_name":"ChimeraX","timestamp":"2025-05-26 19:11:28.00 +0100","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.3 (23D2057)","roots_installed":0,"name":"ChimeraX","incident_id":"9BE6F219-41F3-4432-A714-2107DB43F8FA"}
{
"uptime" : 660000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,13",
"coalitionID" : 79791,
"osVersion" : {
"train" : "macOS 14.3",
"build" : "23D2057",
"releaseType" : "User"
},
"captureTime" : "2025-05-26 19:11:11.6046 +0100",
"codeSigningMonitor" : 1,
"incident" : "9BE6F219-41F3-4432-A714-2107DB43F8FA",
"pid" : 78621,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-26 12:30:31.2310 +0100",
"procStartAbsTime" : 15434487287260,
"procExitAbsTime" : 15897175843936,
"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":"EA9CE231-79B3-58F3-BE16-13A635E09E12","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "475CF94A-F529-C0B3-EB12-655529A86739",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "DA247172-A2C1-4F1F-AA5F-440ABDAB87BB",
"sip" : "enabled",
"vmRegionInfo" : "0x4f259880a5d8 is not in any region. Bytes after previous region: 86541854615001 Bytes before following region: 18530225314344\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000cf259880a5d8","rawCodes":[1,227760379307480],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000cf259880a5d8 -> 0x00004f259880a5d8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":78621},
"vmregioninfo" : "0x4f259880a5d8 is not in any region. Bytes after previous region: 86541854615001 Bytes before following region: 18530225314344\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"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,
"threads" : 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"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "645197bf528fbf3c3af54105",
"factorPackIds" : {
"SIRI_VALUE_INFERENCE_PERVASIVE_ENTITY_RESOLUTION" : "663e65b4a1526e1ca0e288a1"
},
"deploymentId" : 240000002
},
{
"rolloutId" : "632e3f9c01482c74ed76392d",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "6657c46161bbba17a4032c05"
},
"deploymentId" : 240000474
}
],
"experiments" : [
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}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
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/leela/Downloads/fold_vgrgtox_immunity3_with_mg/fold_vgrgtox_immunity3_with_mg_model_0.cif
Chain information for fold_vgrgtox_immunity3_with_mg_model_0.cif #1
---
Chain | Description
A B C | .
D E F | .
> hide cartoons
> show cartoons
Computing secondary structure
> style sphere
Changed 25881 atom styles
> hide atoms
> select /A:1-918
7062 atoms, 7177 bonds, 918 residues, 1 model selected
> sequence chain #1/A#1/B#1/C
Alignment identifier is 1
> select /A-C:1-2
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:1-495
11577 atoms, 11796 bonds, 1485 residues, 1 model selected
> select add #1
25881 atoms, 26313 bonds, 3342 residues, 1 model selected
> select subtract #1
Nothing selected
> ui mousemode right select
> select /B:482
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /B:481
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:482
5 atoms, 4 bonds, 1 residue, 1 model selected
> select clear
> select /B:482
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /C:483
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:483
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:486
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /A:487
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:508
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:507
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:508
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:486
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 2 residues
> select /C:707
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A-C:707
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /A-C:707-918
4929 atoms, 4998 bonds, 636 residues, 1 model selected
> select
> /A-C:9-11,46-48,50-55,102-106,122-132,159-170,209-216,225-228,275-277,286-288,356-358,373-376,508-544,547-556,558-577,582-622,625-683,707-716,751-753,784-799,827-829,849-864,900-916
6888 atoms, 6903 bonds, 891 residues, 1 model selected
> select /C:707
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A-C:707
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /A-C:1-707
16284 atoms, 16557 bonds, 2121 residues, 1 model selected
> hide sel cartoons
> hide #1 models
> show #1 models
> select add #1
25881 atoms, 26313 bonds, 3342 residues, 1 model selected
> select subtract #1
Nothing selected
> select /A-C:1-2
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /A-C:918
30 atoms, 27 bonds, 3 residues, 1 model selected
> select /A-C:871-918
1125 atoms, 1131 bonds, 144 residues, 1 model selected
> select /A-C:870-871
48 atoms, 45 bonds, 6 residues, 1 model selected
> select /A-C:91-871
17955 atoms, 18261 bonds, 2343 residues, 1 model selected
> select
> /A-C:9-11,46-48,50-55,102-106,122-132,159-170,209-216,225-228,275-277,286-288,356-358,373-376,508-544,547-556,558-577,582-622,625-683,707-716,751-753,784-799,827-829,849-864,900-916
6888 atoms, 6903 bonds, 891 residues, 1 model selected
> select /A-C:46
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /A-C:46-918
20103 atoms, 20430 bonds, 2619 residues, 1 model selected
> show sel cartoons
> ui mousemode right select
> select /A-C:918
30 atoms, 27 bonds, 3 residues, 1 model selected
> select /A-C
21186 atoms, 21531 bonds, 2754 residues, 1 model selected
> select /A-C:918
30 atoms, 27 bonds, 3 residues, 1 model selected
> select /A-C:917-918
48 atoms, 45 bonds, 6 residues, 1 model selected
> select /A:508
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A-C:917-918
48 atoms, 45 bonds, 6 residues, 1 model selected
> select /A:918
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:918
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:918
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /C:508
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /C:683
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:508
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:681
4 atoms, 3 bonds, 1 residue, 1 model selected
> select clear
> select /A:684
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:299
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:683
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:684
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:684
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /A:750
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select /A:750
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:751
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:918
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:752
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:751
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:918
10 atoms, 9 bonds, 1 residue, 1 model selected
> color #1 #9e56e5ff
> undo
> select /A-C:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /A-C
21186 atoms, 21531 bonds, 2754 residues, 1 model selected
> color #1 #feffa3ff
> select /C:1-918
7062 atoms, 7177 bonds, 918 residues, 1 model selected
> select /F:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /F:175
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /F:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /E:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /D:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /D:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /D:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> color white sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color white sel
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color white sel cartoons
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color white sel atoms
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color white sel models
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> rainbow sel
> white sel
Unknown command: white sel
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface
#1.1: minimum, -22.01, mean -7.61, maximum 4.10
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface
#1.1: minimum, -22.01, mean -7.61, maximum 4.10
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface
#1.1: minimum, -22.01, mean -7.61, maximum 4.10
To also show corresponding color key, enter the above coulombic command and
add key true
> mlp sel
Map values for surface "fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES
surface": minimum -27.46, mean -5.478, maximum 23.9
To also show corresponding color key, enter the above mlp command and add key
true
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface
#1.1: minimum, -22.01, mean -7.61, maximum 4.10
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface
#1.1: minimum, -22.01, mean -7.61, maximum 4.10
To also show corresponding color key, enter the above coulombic command and
add key true
> color white
> color palegreen yellow
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1 #fafba0ff
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface
#1.1: minimum, -22.01, mean -7.61, maximum 4.10
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface
#1.1: minimum, -22.01, mean -7.61, maximum 4.10
To also show corresponding color key, enter the above coulombic command and
add key true
> hide sel surfaces
> color select
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color select random
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color white select
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color white All select
Expected ',' or a keyword
> color white all, select
Missing or invalid "what" argument: Should be one of 'All', 'atoms', 'bonds',
'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or
'surfaces'
> color white All aroms select
Expected ',' or a keyword
> color white All atoms select
Expected ',' or a keyword
> color white atoms
> color white ribbons
> select /F:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /C:1-918
7062 atoms, 7177 bonds, 918 residues, 1 model selected
> select /F:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /E:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /D:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /E:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /D:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> sequence chain #1/D#1/E#1/F
Alignment identifier is 2
> select /D-F:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /D-F
4692 atoms, 4782 bonds, 585 residues, 1 model selected
> color white ribbons
> color #1.1 #ed7fe5ff
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> color #1 #feffa3ff
> show sel cartoons
> log metadata #1
No models had metadata
> log chains #1
Chain information for fold_vgrgtox_immunity3_with_mg_model_0.cif #1
---
Chain | Description
A B C | .
D E F | .
> select /E:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /D:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /F:1-195
1564 atoms, 1594 bonds, 195 residues, 1 model selected
> select /D-F:1
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /D-F
4692 atoms, 4782 bonds, 585 residues, 1 model selected
> color #1 #63633fff
> color #1 #8c8d59ff
> color #1 #feffa1ff
> Color DEF chains
Unknown command: Color DEF chains
> color red #1/D
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red :D
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color red ribbons :D
Expected ',' or a keyword
> color red /D & ribbons
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color white ribbons :D,E,F
Expected ',' or a keyword
> color white /DEF
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color white All /DEF
Expected ',' or a keyword
> ui tool show "Color Actions"
> color sel white
> show Mg
> select clear
> color mg
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
Drag select of 4 residues
> select /G:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select sel @ select sel @ select sel @ undo
> select /A:873
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:874
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /G:1@MG
1 atom, 1 residue, 1 model selected
> select sel @ ui tool show "Side View"
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting flat
> lighting full
> lighting flat
> lighting full
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> view orient
> view
> view sel
> ui tool show "Side View"
> view sel
> view
> lighting full
> set bgColor white
> set bgColor gray
> set bgColor black
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.
> transparency 50
> volume hide
No volumes specified
> volume hide
No volumes specified
> volume hide
No volumes specified
> save /Users/leela/Desktop/image1.png supersample 3
> set bgColor white
> set bgColor black
> view orient
> set bgColor white
> save /Users/leela/Desktop/image2.png supersample 3
> select clear
> select /H:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> select /I:1@MG
1 atom, 1 residue, 1 model selected
> color sel red
> save /Users/leela/Desktop/image3.png supersample 3
> select /G:1@MG
1 atom, 1 residue, 1 model selected
> select sel @ show sel atoms
> hide sel atoms
> show sel atoms
> style sel stick
Changed 18 atom styles
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> style sel stick
Changed 18 atom styles
> style sel stick
Changed 18 atom styles
> style sel sphere
Changed 18 atom styles
> style sel stick
Changed 18 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel atoms
> style sel ball
Changed 18 atom styles
> style sel ball
Changed 18 atom styles
> style sel stick
Changed 18 atom styles
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> show sel atoms
> select /A:828
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> show sel atoms
> volume hide
No volumes specified
> volume style surface
No volumes specified
> volume style mesh
No volumes specified
> volume style mesh
No volumes specified
> volume style image
No volumes specified
> transparency 0
> volume showOutlineBox true
No volumes specified
> hide sel surfaces
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> select /A:873@CG
1 atom, 1 residue, 1 model selected
> select /A:873@CB
1 atom, 1 residue, 1 model selected
> select /A:873
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:873
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /G:1@MG
1 atom, 1 residue, 1 model selected
> select sel @ coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface
#1.2: minimum, -24.71, mean -2.57, maximum 15.92
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface
#1.2: minimum, -24.71, mean -2.57, maximum 15.92
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface
#1.2: minimum, -24.71, mean -2.57, maximum 15.92
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface
#1.2: minimum, -24.71, mean -2.57, maximum 15.92
To also show corresponding color key, enter the above coulombic command and
add key true
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface
#1.2: minimum, -24.71, mean -2.57, maximum 15.92
To also show corresponding color key, enter the above coulombic command and
add key true
> undo
> select /A:873@NE2
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select /A:873@OE1
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select /A:873@CB
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select clear
> select /G:1@MG
1 atom, 1 residue, 1 model selected
> select sel @ select /A:873@N
1 atom, 1 residue, 1 model selected
> hide sel surfaces
> select /G:1@MG
1 atom, 1 residue, 1 model selected
> select sel @ select /A:873
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel surfaces
> hide sel atoms
> show sel atoms
> hide sel surfaces
> style sel sphere
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> show sel surfaces
> show sel atoms
> hide sel atoms
> select /A:871
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:871
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel atoms
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
> style sel stick
Changed 8 atom styles
> select clear
> select /G:1@MG
1 atom, 1 residue, 1 model selected
> select sel @ select /A:828
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> style sel stick
Changed 9 atom styles
> show sel atoms
Drag select of 32 residues
> select clear
> save /Users/leela/Desktop/image4.png supersample 3
> select clear
> select /G:1@MG
1 atom, 1 residue, 1 model selected
> select sel @ label residues
> save /Users/leela/Desktop/image5.png supersample 3
> label (#!1 & sel) attribute name
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> save /Users/leela/Desktop/image6.png supersample 3
> save /Users/leela/Desktop/image7.png supersample 3
> coulombic sel
Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface
#1.2: minimum, -24.71, mean -2.57, maximum 15.92
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> save /Users/leela/Desktop/image8.png supersample 3
> save /Users/leela/Desktop/image9.png supersample 3
> select /A:622
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui tool show Distances
> select clear
> select /B:69
8 atoms, 7 bonds, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select /A:622
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select /B:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add /A:622
17 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:622
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:69
8 atoms, 7 bonds, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select /A:622
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 9 atom styles
> show sel atoms
> select /A:622@OE1
1 atom, 1 residue, 1 model selected
> select /A:622@OE1
1 atom, 1 residue, 1 model selected
> select clear
> select /B:69
8 atoms, 7 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 8 atom styles
> style sel sphere
Changed 8 atom styles
> show sel atoms
> select /B:69@CB
1 atom, 1 residue, 1 model selected
> select add /A:622@OE1
2 atoms, 2 residues, 1 model selected
> select /A:622@CA
1 atom, 1 residue, 1 model selected
> select add /B:69@ND2
2 atoms, 2 residues, 2 models selected
> distance /A:622@CA /B:69@ND2
Distance between /A GLU 622 CA and /B ASN 69 ND2: 172.230Å
===== 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
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 Air
Model Identifier: Mac15,13
Model Number: MRYN3ZP/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.81.1
OS Loader Version: 10151.81.1
Software:
System Software Overview:
System Version: macOS 14.3 (23D2057)
Kernel Version: Darwin 23.3.0
Time since boot: 27 days, 20 hours, 59 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:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL P2419H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-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 , 5 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 5 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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