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Opened 6 months ago
Closed 6 months ago
#17768 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-15.3.1-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 0x000000032d493000 (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 0x000000032c487000 (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 0x000000032b47b000 (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 0x000000031ecd7000 (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 0x000000031dccb000 (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 0x000000031ccbf000 (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 0x000000031bcb3000 (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 0x000000031aca7000 (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 0x0000000319c9b000 (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 0x0000000318c8f000 (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 0x0000000317c83000 (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 0x0000000202308840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 55)
{"app_name":"ChimeraX","timestamp":"2025-05-22 11:04:59.00 +0200","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 15.3.1 (24D70)","roots_installed":0,"name":"ChimeraX","incident_id":"9296FF23-DF21-48AD-B755-561CB0027950"}
{
"uptime" : 1200000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 198721,
"osVersion" : {
"train" : "macOS 15.3.1",
"build" : "24D70",
"releaseType" : "User"
},
"captureTime" : "2025-05-22 11:00:44.4482 +0200",
"codeSigningMonitor" : 1,
"incident" : "9296FF23-DF21-48AD-B755-561CB0027950",
"pid" : 55213,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-09 11:54:11.3627 +0200",
"procStartAbsTime" : 25660715092364,
"procExitAbsTime" : 30369447056266,
"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":"5B74978C-A6B3-5669-9D1A-E03E6399210A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FE8EC029-A1A5-14E1-A513-38BA216C730B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "C50EEDBD-2F7F-474C-90DD-9A3574F0CD03",
"wakeTime" : 2431,
"sleepWakeUUID" : "FC48BEEA-6838-4C7D-ACAA-B0114A1EFEFB",
"sip" : "enabled",
"vmRegionInfo" : "0x1a504990f0d8 is not in any region. Bytes after previous region: 28451097604313 Bytes before following region: 76620982325032\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00001a504990f0d8","rawCodes":[1,28932133941464],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00001a504990f0d8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":55213},
"vmregioninfo" : "0x1a504990f0d8 is not in any region. Bytes after previous region: 28451097604313 Bytes before following region: 76620982325032\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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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
still retrieving bundle list from toolshed
> isolde shorthand
Error running startup command 'isolde shorthand': Unknown command: isolde
shorthand
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 "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_9.pdb"
Chain information for structure_model_1_9.pdb #1
---
Chain | Description
M | No description available
P | No description available
Computing secondary structure
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_0.pdb"
Chain information for structure_model_1_0.pdb #2
---
Chain | Description
M | No description available
P | No description available
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_1.pdb"
Chain information for structure_model_1_1.pdb #3
---
Chain | Description
M | No description available
P | No description available
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_2.pdb"
Chain information for structure_model_1_2.pdb #4
---
Chain | Description
M | No description available
P | No description available
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_3.pdb"
Chain information for structure_model_1_3.pdb #5
---
Chain | Description
M | No description available
P | No description available
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_4.pdb"
Chain information for structure_model_1_4.pdb #6
---
Chain | Description
M | No description available
P | No description available
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_5.pdb"
Chain information for structure_model_1_5.pdb #7
---
Chain | Description
M | No description available
P | No description available
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_6.pdb"
Chain information for structure_model_1_6.pdb #8
---
Chain | Description
M | No description available
P | No description available
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_7.pdb"
Chain information for structure_model_1_7.pdb #9
---
Chain | Description
M | No description available
P | No description available
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_8.pdb"
Chain information for structure_model_1_8.pdb #10
---
Chain | Description
M | No description available
P | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2-10 to #1
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 structure_model_1_9.pdb, chain M (#1) with structure_model_1_0.pdb,
chain M (#2), sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.233 angstroms; (across all 182 pairs:
0.233)
Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_1.pdb,
chain M (#3), sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.210 angstroms; (across all 182 pairs:
0.210)
Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_2.pdb,
chain M (#4), sequence alignment score = 980.3
RMSD between 182 pruned atom pairs is 0.198 angstroms; (across all 182 pairs:
0.198)
Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_3.pdb,
chain M (#5), sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.169 angstroms; (across all 182 pairs:
0.169)
Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_4.pdb,
chain M (#6), sequence alignment score = 980.3
RMSD between 182 pruned atom pairs is 0.088 angstroms; (across all 182 pairs:
0.088)
Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_5.pdb,
chain M (#7), sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.226 angstroms; (across all 182 pairs:
0.226)
Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_6.pdb,
chain M (#8), sequence alignment score = 980.3
RMSD between 181 pruned atom pairs is 0.262 angstroms; (across all 182 pairs:
0.363)
Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_7.pdb,
chain M (#9), sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.181 angstroms; (across all 182 pairs:
0.181)
Matchmaker structure_model_1_9.pdb, chain M (#1) with structure_model_1_8.pdb,
chain M (#10), sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.148 angstroms; (across all 182 pairs:
0.148)
> select #1/M#2/M#3/M#4/M#5/M#6/M#7/M#8/M#9/M#10/M
14960 atoms, 15320 bonds, 1820 residues, 10 models selected
> hide sel atoms
> hide sel cartoons
> select #1/M
1496 atoms, 1532 bonds, 182 residues, 1 model selected
> select #6/M
1496 atoms, 1532 bonds, 182 residues, 1 model selected
> show sel cartoons
> color #6 #d3d3d344
> set bgColor white
> color #6 #d3d3d35e
> select #1/P#2/P#3/P#4/P#5/P#6/P#7/P#8/P#9/P#10/P
920 atoms, 950 bonds, 100 residues, 10 models selected
> hide sel cartoons
> show sel atoms
> hide #1 models
> hide #2 models
> hide #3 models
> hide #4 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> show #6 models
> select clear
> show #1 models
> hide #5 models
> show #5 models
> hide #1 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #1 models
> color bfactor palette alphafold
15880 atoms, 1920 residues, atom bfactor range 49.3 to 98.9
> select add #1
1588 atoms, 1627 bonds, 192 residues, 1 model selected
> color bfactor palette alphafold
15880 atoms, 1920 residues, atom bfactor range 49.3 to 98.9
> color #6 #d6d6d6ff
> color #6 #d6d6d631
> color #6 #d6d6d630
> hide #6 models
> show #6 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> undo
> color bfactor palette alphafold
15880 atoms, 1920 residues, atom bfactor range 49.3 to 98.9
> select clear
> show #5 models
> hide #1 models
> show #1 models
> hide #1 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> show #1 models
> hide #1 models
> hide #5 models
> hide #6 models
> show #6 models
> hide #7 models
> show #5 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #1 models
> hide #1 models
> show #1 models
> hide #1 models
> show #9 models
> hide #9 models
> show #8 models
> hide #8 models
> show #7 models
> hide #5 models
> hide #7 models
> show #5 models
> hide #6 models
> show #6 models
> hide #5 models
> close #1-5
> close #7-10
> rename #6 mhc
> select /P
92 atoms, 95 bonds, 10 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /M
1496 atoms, 1532 bonds, 182 residues, 1 model selected
> set bgColor black
> select clear
> set bgColor white
> set bgColor black
> set bgColor white
> open
> /Users/philippnawrath/Desktop/alphafold/results/MOG_peps/MOG_peps/outputs/0/structure_model_1_12.pdb
Chain information for structure_model_1_12.pdb #1
---
Chain | Description
M | No description available
P | No description available
Computing secondary structure
> open
> /Users/philippnawrath/Desktop/alphafold/results/MOG_peps/MOG_peps/outputs/1/structure_model_1_4.pdb
Chain information for structure_model_1_4.pdb #2
---
Chain | Description
M | No description available
P | No description available
Computing secondary structure
> open
> /Users/philippnawrath/Desktop/alphafold/results/MOG_peps/MOG_peps/outputs/2/structure_model_1_0.pdb
Chain information for structure_model_1_0.pdb #3
---
Chain | Description
M | No description available
P | No description available
Computing secondary structure
> matchmaker #1-3 to #6
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 mhc, chain M (#6) with structure_model_1_12.pdb, chain M (#1),
sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.187 angstroms; (across all 182 pairs:
0.187)
Matchmaker mhc, chain M (#6) with structure_model_1_4.pdb, chain M (#2),
sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.168 angstroms; (across all 182 pairs:
0.168)
Matchmaker mhc, chain M (#6) with structure_model_1_0.pdb, chain M (#3),
sequence alignment score = 977.3
RMSD between 181 pruned atom pairs is 0.209 angstroms; (across all 182 pairs:
0.310)
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/9/structure_model_1_5.pdb"
Chain information for structure_model_1_5.pdb #4
---
Chain | Description
M | No description available
P | No description available
Computing secondary structure
> rename #4 RPPIFIRRLH
> rename #1 MASLSRPSLP
> rename #2 LSRPSLPSCL
> rename #3 KVTLRIRNVR
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E21_40/outputs/21/structure_model_1_9.pdb"
Chain information for structure_model_1_9.pdb #5
---
Chain | Description
M | No description available
P | No description available
Computing secondary structure
> rename #5 APHTPLPPVS
> rename #5 "APHTPLPPVS (1-B09)"
> rename #4 "RPPIFIRRLH (1-A09)"
> rename #3 "KVTLRIRNVR MOG109_118"
> rename #1 "MASLSRPSLP MOG1_10"
> rename #2 "LSRPSLPSCL (MOG4_13)"
> rename #1 "MASLSRPSLP (MOG1_10)"
> rename #3 "KVTLRIRNVR (MOG109_118)"
> matchmaker #1-5 to #6
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 mhc, chain M (#6) with MASLSRPSLP (MOG1_10), chain M (#1), sequence
alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.187 angstroms; (across all 182 pairs:
0.187)
Matchmaker mhc, chain M (#6) with LSRPSLPSCL (MOG4_13), chain M (#2), sequence
alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.168 angstroms; (across all 182 pairs:
0.168)
Matchmaker mhc, chain M (#6) with KVTLRIRNVR (MOG109_118), chain M (#3),
sequence alignment score = 977.3
RMSD between 181 pruned atom pairs is 0.209 angstroms; (across all 182 pairs:
0.310)
Matchmaker mhc, chain M (#6) with RPPIFIRRLH (1-A09), chain M (#4), sequence
alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.237 angstroms; (across all 182 pairs:
0.237)
Matchmaker mhc, chain M (#6) with APHTPLPPVS (1-B09), chain M (#5), sequence
alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.121 angstroms; (across all 182 pairs:
0.121)
> select #1/P#2/P#3/P#4/P#5/P
395 atoms, 403 bonds, 50 residues, 5 models selected
> select #1/M#2/M#3/M#4/M#5/M#6/M
8976 atoms, 9192 bonds, 1092 residues, 6 models selected
> hide sel atoms
> hide sel cartoons
> select #6/M
1496 atoms, 1532 bonds, 182 residues, 1 model selected
> show sel cartoons
> select #1/P#2/P#3/P#4/P#5/P
395 atoms, 403 bonds, 50 residues, 5 models selected
> hide sel cartoons
> show sel atoms
> select clear
> hide #1 models
> hide #2 models
> hide #5 models
> hide #4 models
> show #5 models
> hide #3 models
> show #2 models
> hide #2 models
> show #1 models
> hide #1 models
> show #2 models
> hide #2 models
> show #3 models
> hide #5 models
> show #4 models
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/8/structure_model_1_4.pdb"
Chain information for structure_model_1_4.pdb #7
---
Chain | Description
M | No description available
P | No description available
Computing secondary structure
> open "/Volumes/FS/Common/RAT project/_pMHC
> alphafold/pnawrath/E1_20/outputs/10/structure_model_1_3.pdb"
Chain information for structure_model_1_3.pdb #8
---
Chain | Description
M | No description available
P | No description available
Computing secondary structure
> matchmaker #1-5,7-8 to #6
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 mhc, chain M (#6) with MASLSRPSLP (MOG1_10), chain M (#1), sequence
alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.187 angstroms; (across all 182 pairs:
0.187)
Matchmaker mhc, chain M (#6) with LSRPSLPSCL (MOG4_13), chain M (#2), sequence
alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.168 angstroms; (across all 182 pairs:
0.168)
Matchmaker mhc, chain M (#6) with KVTLRIRNVR (MOG109_118), chain M (#3),
sequence alignment score = 977.3
RMSD between 181 pruned atom pairs is 0.209 angstroms; (across all 182 pairs:
0.310)
Matchmaker mhc, chain M (#6) with RPPIFIRRLH (1-A09), chain M (#4), sequence
alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.237 angstroms; (across all 182 pairs:
0.237)
Matchmaker mhc, chain M (#6) with APHTPLPPVS (1-B09), chain M (#5), sequence
alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.121 angstroms; (across all 182 pairs:
0.121)
Matchmaker mhc, chain M (#6) with structure_model_1_4.pdb, chain M (#7),
sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.121 angstroms; (across all 182 pairs:
0.121)
Matchmaker mhc, chain M (#6) with structure_model_1_3.pdb, chain M (#8),
sequence alignment score = 977.3
RMSD between 182 pruned atom pairs is 0.172 angstroms; (across all 182 pairs:
0.172)
> select #1/M#2/M#3/M#4/M#5/M#6/M#7/M#8/M
11968 atoms, 12256 bonds, 1456 residues, 8 models selected
> hide sel & #3-4,6-8 cartoons
> hide sel & #3-4,6-8 atoms
> select #6/M
1496 atoms, 1532 bonds, 182 residues, 1 model selected
> show sel cartoons
> rename #7 "KPTPPPSRR (1-A08)"
> rename #8 "TPTPPPQVP (A-A10)"
> hide #4 models
> select clear
> hide #3 models
> hide #8 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #3 models
> show #5 models
> hide #7 models
> hide #3 models
> show #4 models
> hide #5 models
> select #4/P
92 atoms, 95 bonds, 10 residues, 1 model selected
> label sel attribute name
> label sel attribute label_specifier
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> color #4 #ff2600ff
> undo
> color #4 #797979ff
> color #4 #212121ff
> color #4 #9437ffff
> color #4 #00fdffff
> color #4 #d99090ff
> select #4/P
92 atoms, 95 bonds, 10 residues, 1 model selected
> color sel byhetero
> select clear
> save /Users/philippnawrath/Desktop/image1.png supersample 3
> labelopt bold true
Unknown command: labelopt bold true
> label text @/name style bold
Expected a keyword
> select #4/P
92 atoms, 95 bonds, 10 residues, 1 model selected
> label sel text @/name style bold
Expected a keyword
> open 6VMX
6vmx title:
Structure of HD14 TCR in complex with HLA-B7 presenting an EBV epitope [more
info...]
Chain information for 6vmx #9
---
Chain | Description | UniProt
A F | HLA class I histocompatibility antigen, B-7 alpha chain | 1B07_HUMAN 1-276
B G | Beta-2-microglobulin | B2MG_HUMAN 1-99
C H | Epstein-Barr nuclear antigen 3 | EBNA3_EBVB9 1-9
D I | HD14 alpha chain |
E J | HD14 beta chain |
Non-standard residues in 6vmx #9
---
EDO — 1,2-ethanediol (ethylene glycol)
PEG — di(hydroxyethyl)ether
6vmx mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
53 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!4 models
> hide #6 models
> select add #9
13603 atoms, 13843 bonds, 1 pseudobond, 1795 residues, 3 models selected
> hide sel & #!9 atoms
> show sel & #!9 cartoons
> select #9/B
842 atoms, 860 bonds, 105 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/C
83 atoms, 85 bonds, 9 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/D
1600 atoms, 1630 bonds, 212 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/E
1984 atoms, 2006 bonds, 278 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #9/A
2291 atoms, 2336 bonds, 295 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> matchmaker #6 to #9
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 6vmx, chain F (#9) with mhc, chain M (#6), sequence alignment score
= 953.9
RMSD between 181 pruned atom pairs is 0.492 angstroms; (across all 182 pairs:
0.514)
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> matchmaker #1-3,5-8#!4 to #9
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 6vmx, chain F (#9) with MASLSRPSLP (MOG1_10), chain M (#1),
sequence alignment score = 957.5
RMSD between 182 pruned atom pairs is 0.498 angstroms; (across all 182 pairs:
0.498)
Matchmaker 6vmx, chain F (#9) with LSRPSLPSCL (MOG4_13), chain M (#2),
sequence alignment score = 957.5
RMSD between 182 pruned atom pairs is 0.542 angstroms; (across all 182 pairs:
0.542)
Matchmaker 6vmx, chain F (#9) with KVTLRIRNVR (MOG109_118), chain M (#3),
sequence alignment score = 957.5
RMSD between 181 pruned atom pairs is 0.477 angstroms; (across all 182 pairs:
0.533)
Matchmaker 6vmx, chain F (#9) with APHTPLPPVS (1-B09), chain M (#5), sequence
alignment score = 957.5
RMSD between 181 pruned atom pairs is 0.521 angstroms; (across all 182 pairs:
0.548)
Matchmaker 6vmx, chain F (#9) with mhc, chain M (#6), sequence alignment score
= 953.9
RMSD between 181 pruned atom pairs is 0.492 angstroms; (across all 182 pairs:
0.514)
Matchmaker 6vmx, chain F (#9) with KPTPPPSRR (1-A08), chain M (#7), sequence
alignment score = 957.5
RMSD between 181 pruned atom pairs is 0.526 angstroms; (across all 182 pairs:
0.546)
Matchmaker 6vmx, chain F (#9) with TPTPPPQVP (A-A10), chain M (#8), sequence
alignment score = 957.5
RMSD between 181 pruned atom pairs is 0.508 angstroms; (across all 182 pairs:
0.530)
Matchmaker 6vmx, chain F (#9) with RPPIFIRRLH (1-A09), chain M (#4), sequence
alignment score = 957.5
RMSD between 182 pruned atom pairs is 0.485 angstroms; (across all 182 pairs:
0.485)
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> select #9/H
83 atoms, 85 bonds, 9 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain #9/I
Alignment identifier is 9/I
> sequence chain #9/J
Alignment identifier is 9/J
> select #9/J:25
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/J:25-39
65 atoms, 66 bonds, 8 residues, 1 model selected
> select #9/J:64-65
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #9/J:64-68
39 atoms, 38 bonds, 5 residues, 1 model selected
> select #9/J:69
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/J:69-75
46 atoms, 46 bonds, 6 residues, 1 model selected
> select #9/J:80
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/J:80-85
33 atoms, 33 bonds, 5 residues, 1 model selected
> select #9/J:92-93
15 atoms, 15 bonds, 2 residues, 1 model selected
> select #9/J:92-94
23 atoms, 23 bonds, 3 residues, 1 model selected
> select #9/J:105
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #9/J:105-115
80 atoms, 81 bonds, 11 residues, 1 model selected
> select #9/J:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/J:108-111
36 atoms, 36 bonds, 4 residues, 1 model selected
> select #9/J:46
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #9/J:46-48
23 atoms, 22 bonds, 3 residues, 1 model selected
> select #9/J:108-109
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #9/J:108-115
63 atoms, 64 bonds, 8 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 63 atom styles
> style sel ball
Changed 63 atom styles
> style sel stick
Changed 63 atom styles
> color sel byhetero
> select #9/J:69-70
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/J:69-75
46 atoms, 46 bonds, 6 residues, 1 model selected
> select #9/J:45-46
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #9/J:45-50
46 atoms, 47 bonds, 6 residues, 1 model selected
> select #9/J:25-26
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #9/J:25-37
52 atoms, 53 bonds, 6 residues, 1 model selected
> select #9/J:15
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/J:15-18
32 atoms, 31 bonds, 4 residues, 1 model selected
> select #9/J:69
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/J:69-75
46 atoms, 46 bonds, 6 residues, 1 model selected
> select #9/J:80
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/J:80-85
33 atoms, 33 bonds, 5 residues, 1 model selected
> select #9/I:45
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/I:45-50
43 atoms, 43 bonds, 6 residues, 1 model selected
> select #9/I:57
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/I:57-64
35 atoms, 34 bonds, 5 residues, 1 model selected
> select #9/I:68-74
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #9/I:68-75
24 atoms, 23 bonds, 3 residues, 1 model selected
> select #9/I:82-83
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #9/I:82-85
29 atoms, 28 bonds, 4 residues, 1 model selected
> select #9/I:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #9/I:15-18
27 atoms, 26 bonds, 4 residues, 1 model selected
> select #9/I:25-26
18 atoms, 19 bonds, 2 residues, 1 model selected
> select #9/I:25-29
38 atoms, 39 bonds, 5 residues, 1 model selected
> select #9/I:141-142
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/I:141-146
44 atoms, 43 bonds, 6 residues, 1 model selected
> select #9/I:109-110
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #9/I:109-113
34 atoms, 33 bonds, 5 residues, 1 model selected
> select #9/I:83-84
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #9/I:83-85
22 atoms, 21 bonds, 3 residues, 1 model selected
> select #9/I:109
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #9/I:109-113
34 atoms, 33 bonds, 5 residues, 1 model selected
> style sel stick
Changed 34 atom styles
> show sel atoms
> hide sel cartoons
> show sel cartoons
> color sel byhetero
> select #9/F
2214 atoms, 2255 bonds, 1 pseudobond, 287 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dark salmon
> color sel light slate gray
> color sel slate gray
> ui tool show "Color Actions"
> color (#!9 & sel) #fffffffe
> color (#!9 & sel) #ffffffd5
> color (#!9 & sel) #ffffffcc
> color (#!9 & sel) #ffffffb8
> color (#!9 & sel) #ffffff9f
> color (#!9 & sel) #ffffff8e
> color (#!9 & sel) #ffffff88
> color (#!9 & sel) #ffffff87
> color (#!9 & sel) #ffffff85
> color (#!9 & sel) #ffffff83
> color (#!9 & sel) #ffffff82
> color (#!9 & sel) #ffffff81
> color (#!9 & sel) #ffffff80
> color (#!9 & sel) #ffffff88
> color (#!9 & sel) #ffffff8c
> color (#!9 & sel) #ffffff8f
> color (#!9 & sel) #ffffff91
> color (#!9 & sel) #ffffff93
> color (#!9 & sel) #ffffff96
> color (#!9 & sel) #ffffff98
> color (#!9 & sel) #ffffff9c
> color (#!9 & sel) #ffffffa4
> color (#!9 & sel) #ffffffa9
> color (#!9 & sel) #ffffffab
> color (#!9 & sel) #ffffffac
> color (#!9 & sel) #ffffffad
> color (#!9 & sel) #ffffffaf
> color (#!9 & sel) #ffffffb1
> color (#!9 & sel) #ffffffb5
> color (#!9 & sel) #ffffffb6
> color (#!9 & sel) #ffffffb7
> color (#!9 & sel) #ffffffba
> color (#!9 & sel) #ffffffbb
> color (#!9 & sel) #ffffffb9
> color (#!9 & sel) #ffffffb8
> color (#!9 & sel) #ffffffb6
> color (#!9 & sel) #ffffffb1
> color (#!9 & sel) #ffffffae
> color (#!9 & sel) #ffffffab
> color (#!9 & sel) #ffffffaa
> color (#!9 & sel) #ffffffa8
> color (#!9 & sel) #ffffffa6
> color (#!9 & sel) #ffffffa4
> color (#!9 & sel) #ffffffa3
> color (#!9 & sel) #ffffffa2
> color (#!9 & sel) #ffffffa1
> color (#!9 & sel) #ffffffa0
> color (#!9 & sel) #ffffff9e
> color (#!9 & sel) #ffffff9d
> color (#!9 & sel) #ffffff9c
> color (#!9 & sel) #ffffff9b
> color (#!9 & sel) #ffffff99
> color (#!9 & sel) #ffffff98
> color (#!9 & sel) #ffffff97
> color (#!9 & sel) #ffffff98
> color (#!9 & sel) #ffffff99
> color (#!9 & sel) #ffffff9a
> color (#!9 & sel) #ffffff9c
> color (#!9 & sel) #ffffff9d
> color (#!9 & sel) #ffffff9e
> color (#!9 & sel) #ffffff9f
> color (#!9 & sel) #ffffffa1
> color (#!9 & sel) #ffffffa6
> color (#!9 & sel) #ffffffa8
> color (#!9 & sel) #ffffffa9
> color (#!9 & sel) #ffffffaa
> color (#!9 & sel) #ffffffac
> color (#!9 & sel) #ffffffae
> color (#!9 & sel) #ffffffaf
> color (#!9 & sel) #ffffffb0
> color (#!9 & sel) #ffffffb2
> color (#!9 & sel) #ffffffb3
> color (#!9 & sel) #ffffffb2
> color (#!9 & sel) #a9a9a9ff
> color (#!9 & sel) #76d6ffff
> color (#!9 & sel) #76d6ffde
> color (#!9 & sel) #76d6ffbc
> color (#!9 & sel) #76d6ffa3
> color (#!9 & sel) #76d6ff99
> color (#!9 & sel) #76d6ff8e
> color (#!9 & sel) #76d6ff81
> color (#!9 & sel) #76d6ff77
> color (#!9 & sel) #76d6ff72
> color (#!9 & sel) #76d6ff70
> color (#!9 & sel) #76d6ff6f
> color (#!9 & sel) #76d6ff6e
> color (#!9 & sel) #76d6ff6b
> color (#!9 & sel) #76d6ff60
> color (#!9 & sel) #76d6ff55
> color (#!9 & sel) #76d6ff4f
> color (#!9 & sel) #76d6ff4e
> color (#!9 & sel) #76d6ff4d
> color (#!9 & sel) #76d6ff4c
> color (#!9 & sel) #76d6ff4b
> color (#!9 & sel) #76d6ff4a
> color (#!9 & sel) #76d6ff49
> color (#!9 & sel) #76d6ff48
> color (#!9 & sel) #76d6ff47
> color (#!9 & sel) #76d6ff46
> color (#!9 & sel) #76d6ff45
> color (#!9 & sel) #76d6ff46
> color (#!9 & sel) #76d6ff47
> color (#!9 & sel) #76d6ff48
> color (#!9 & sel) #76d6ff49
> color (#!9 & sel) #76d6ff4b
> color (#!9 & sel) #76d6ff4c
> color (#!9 & sel) #76d6ff4e
> color (#!9 & sel) #76d6ff4f
> color (#!9 & sel) #76d6ff50
> color (#!9 & sel) #76d6ff51
> color (#!9 & sel) #76d6ff53
> color (#!9 & sel) #76d6ff54
> color (#!9 & sel) #76d6ff56
> color (#!9 & sel) #76d6ff58
> color (#!9 & sel) #76d6ff59
> color (#!9 & sel) #76d6ff5b
> color (#!9 & sel) #76d6ff5c
> color (#!9 & sel) #76d6ff5e
> color (#!9 & sel) #76d6ff5f
> color (#!9 & sel) #76d6ff61
> color (#!9 & sel) #76d6ff62
> color (#!9 & sel) #76d6ff63
> color (#!9 & sel) #76d6ff5e
> color (#!9 & sel) #76d6ff5b
> color (#!9 & sel) #76d6ff58
> color (#!9 & sel) #76d6ff55
> color (#!9 & sel) #76d6ff52
> color (#!9 & sel) #76d6ff4d
> color (#!9 & sel) #76d6ff43
> color (#!9 & sel) #76d6ff3e
> color (#!9 & sel) #76d6ff3c
> color (#!9 & sel) #76d6ff3b
> color (#!9 & sel) #76d6ff39
> color (#!9 & sel) #76d6ff35
> color (#!9 & sel) #76d6ff31
> color (#!9 & sel) #76d6ff2f
> color (#!9 & sel) #76d6ff2e
> color (#!9 & sel) #76d6ff2f
> color (#!9 & sel) #76d6ff33
> color (#!9 & sel) #76d6ff34
> color (#!9 & sel) #76d6ff36
> color (#!9 & sel) #76d6ff39
> color (#!9 & sel) #76d6ff3d
> color (#!9 & sel) #76d6ff40
> color (#!9 & sel) #76d6ff3f
> color (#!9 & sel) #76d6ff3e
> color (#!9 & sel) #76d6ff3c
> color (#!9 & sel) #76d6ff3b
> color (#!9 & sel) #76d6ff3c
> color (#!9 & sel) #76d6ff3d
> color (#!9 & sel) #76d6ff46
> color (#!9 & sel) #76d6ff51
> color (#!9 & sel) #76d6ff58
> color (#!9 & sel) #76d6ff5a
> color (#!9 & sel) #76d6ff5b
> color (#!9 & sel) #76d6ff5f
> color (#!9 & sel) #76d6ff63
> color (#!9 & sel) #76d6ff64
> color (#!9 & sel) #76d6ff66
> color (#!9 & sel) #76d6ff68
> color (#!9 & sel) #76d6ff6a
> color (#!9 & sel) #76d6ff6b
> color (#!9 & sel) #76d6ff68
> color (#!9 & sel) #76d6ff67
> color (#!9 & sel) #76d6ff66
> color (#!9 & sel) #76d6ff64
> color (#!9 & sel) #76d6ff63
> color (#!9 & sel) #76d6ff61
> color (#!9 & sel) #76d6ff60
> color (#!9 & sel) #76d6ff5f
> color (#!9 & sel) #76d6ff5d
> color (#!9 & sel) #76d6ff60
> color (#!9 & sel) #76d6ff62
> color (#!9 & sel) #76d6ff6c
> color (#!9 & sel) #76d6ff7a
> color (#!9 & sel) #76d6ff84
> color (#!9 & sel) #76d6ff86
> color (#!9 & sel) #76d6ff85
> color (#!9 & sel) #76d6ff84
> color (#!9 & sel) #76d6ff83
> color (#!9 & sel) #76d6ff82
> color (#!9 & sel) #76d6ff81
> color (#!9 & sel) #76d6ff80
> color (#!9 & sel) #76d6ff76
> color (#!9 & sel) #76d6ff72
> color (#!9 & sel) #76d6ff6d
> color (#!9 & sel) #76d6ff66
> color (#!9 & sel) #76d6ff61
> color (#!9 & sel) #76d6ff5f
> color (#!9 & sel) #76d6ff5e
> color (#!9 & sel) #76d6ff59
> color (#!9 & sel) #76d6ff51
> color (#!9 & sel) #76d6ff4a
> color (#!9 & sel) #76d6ff48
> color (#!9 & sel) #76d6ff47
> color sel sea green
> color sel medium sea green
> color sel sea green
> select #9/I
1608 atoms, 1630 bonds, 220 residues, 1 model selected
> color sel chocolate
> color sel sienna
> color sel byhetero
> select #9/J
1964 atoms, 1998 bonds, 265 residues, 1 model selected
> color sel coral
> color sel tomato
> color sel salmon
> color sel dodger blue
> color sel turquoise
> color sel medium turquoise
> color sel orange
> color sel dark orange
> color sel goldenrod
> color sel sandy brown
> color sel byhetero
> select #9/H
83 atoms, 85 bonds, 9 residues, 1 model selected
> color sel spring green
> color sel blue
> color sel medium blue
> color sel slate gray
> color sel dark blue
> color sel medium blue
> color sel dark blue
> color sel navy
> color sel indigo
> color sel royal blue
> color sel deep sky blue
> color sel royal blue
> color sel slate blue
> color sel dark violet
> color sel deep pink
> color sel dark slate blue
> color sel slate blue
> color sel dark slate blue
> color sel slate blue
> color sel medium slate blue
> color sel dark slate gray
> color sel aquamarine
> color sel sky blue
> color sel light sky blue
> color sel honeydew
> color sel alice blue
> color sel light pink
> color sel lavender
> color sel rebecca purple
> color sel dark slate blue
> color sel rebecca purple
> color sel midnight blue
> color sel royal blue
> color sel byhetero
> color sel medium orchid
> color sel orchid
> color sel pale violet red
> color sel byhetero
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/philippnawrath/Desktop/movie1.mp4
Movie saved to /Users/philippnawrath/Desktop/movie1.mp4
> ui tool show "Side View"
> view orient
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting full
> lighting flat
> lighting full
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting full
> lighting flat
> lighting soft
> lighting simple
> lighting soft
> lighting full
> undo
> set bgColor white
> set bgColor black
> set bgColor gray
> set bgColor black
> set bgColor white
> select clear
> lighting simple
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting full
> graphics silhouettes false
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting simple
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting flat
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> select #9/H
83 atoms, 85 bonds, 9 residues, 1 model selected
> center sel
Unknown command: center sel
> cofr
Center of rotation: -71.854 -9.2962 5.222 front center
> select clear
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/philippnawrath/Desktop/movie2.mp4
Movie saved to /Users/philippnawrath/Desktop/movie2.mp4
> show #5 models
> hide #!9 models
> show #6 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #6 models
> show #!9 models
> hide #5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!9 models
> hide #!4 models
> show #3 models
> hide #3 models
> show #6 models
> show #3 models
> hide #3 models
> show #3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
===== Log before crash end =====
Log:
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
still retrieving bundle list from toolshed
> isolde shorthand
Error running startup command 'isolde shorthand': Unknown command: isolde
shorthand
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 - 89.3
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 Air
Model Identifier: Mac14,2
Model Number: Z15S000LJSM/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.4
OS Loader Version: 11881.81.4
Software:
System Software Overview:
System Version: macOS 15.3.1 (24D70)
Kernel Version: Darwin 24.3.0
Time since boot: 77 days, 6 hours, 25 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2423DE:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 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 , 6 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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