![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 5 months ago
Closed 5 months ago
#18198 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-15.1.1-arm64-arm-64bit
ChimeraX Version: 1.9rc202412041747 (2024-12-04 17:47:20 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001e9c03840 (most recent call first):
File "/Applications/ChimeraX-1.9-rc2024.12.04.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-rc2024.12.04.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-rc2024.12.04.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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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)
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{
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"procRole" : "Background",
"version" : 2,
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"deployVersion" : 210,
"modelCode" : "Mac15,12",
"coalitionID" : 1419,
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"captureTime" : "2025-07-15 18:40:04.0554 +0800",
"codeSigningMonitor" : 1,
"incident" : "B6166CCE-804E-4C6C-8D95-3D4DFF487D8A",
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"cpuType" : "ARM-64",
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"bug_type" : "309",
"procLaunch" : "2025-07-15 14:31:03.4997 +0800",
"procStartAbsTime" : 598095186323,
"procExitAbsTime" : 931771760592,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"9B47FDE8-E53D-521D-9C66-EC490462E9C2","thirdParty":true},
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "52C4C778-B107-8A0A-FB4B-D4CF1C740002",
"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" : "80BB860F-BCD5-433E-B290-0CEAC4F647AF",
"sleepWakeUUID" : "2F823320-D4CF-4CC2-A241-CE08681475C4",
"sip" : "enabled",
"vmRegionInfo" : "0x658055861768 is not in any region. Bytes after previous region: 6021905258345 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600620000000-600640000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000658055861768","rawCodes":[1,111601865070440],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000658055861768"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":17845},
"vmregioninfo" : "0x658055861768 is not in any region. Bytes after previous region: 6021905258345 \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC_NANO 600620000000-600640000000 [512.0M] rw-\/rwx SM=PRV \n---> \n UNUSED SPACE AT END",
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"base" : 13204914176,
"size" : 475136,
"uuid" : "849f82aa-927d-3002-8434-8b635477d522",
"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
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"arch" : "arm64",
"base" : 13203488768,
"size" : 409600,
"uuid" : "736680db-f7b4-3d6a-92ef-c157d527fd68",
"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
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{
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"uuid" : "8abbdcef-1901-3d4b-9e6b-a38214b79214",
"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
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"uuid" : "c0aafaa1-d883-3e93-94ba-c0126088de51",
"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_sw.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/libalign_algs.dylib",
"name" : "libalign_algs.dylib"
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"uuid" : "b53185aa-f707-3b24-95dc-734406bc0611",
"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/dssp\/_dssp.cpython-311-darwin.so",
"name" : "_dssp.cpython-311-darwin.so"
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"uuid" : "178c123e-951b-3ed8-9757-a4c454c76417",
"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/alignment_algs\/_nw.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtOpenGLWidgets.abi3.so",
"name" : "QtOpenGLWidgets.abi3.so"
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{
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"size" : 49152,
"uuid" : "cd4f396b-89fe-36fd-a488-6f5b3d4b0282",
"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtOpenGLWidgets.framework\/Versions\/A\/QtOpenGLWidgets",
"name" : "QtOpenGLWidgets"
},
{
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"base" : 5964185600,
"size" : 16384,
"uuid" : "c37482c0-7aab-3517-b3ef-3bd2294eab02",
"path" : "\/Applications\/ChimeraX-1.9-rc2024.12.04.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_multiprocessing.cpython-311-darwin.so",
"name" : "_multiprocessing.cpython-311-darwin.so"
},
{
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"base" : 6520754176,
"size" : 241656,
"uuid" : "9fea25a4-e8ca-3f3d-901c-a53ff2bc7217",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"uuid" : "3b8268be-4e02-3b4a-8b41-baed2bbaacff",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202412041747 (2024-12-04)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/huan/Downloads/17-3.pdb
Chain information for 17-3.pdb #1
---
Chain | Description
A | No description available
> open "/Users/huan/Downloads/Template-guided Structure
> Prediction/rank_001.pdb"
Chain information for rank_001.pdb #2
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2 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 17-3.pdb, chain A (#1) with rank_001.pdb, chain A (#2), sequence
alignment score = 5760.4
RMSD between 1186 pruned atom pairs is 0.637 angstroms; (across all 1235
pairs: 2.696)
> set bgColor white
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting soft
> open /Users/huan/Documents/Projects/Nav1.6/open-loop-CTD.pdb
Chain information for open-loop-CTD.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show Matchmaker
> matchmaker #2#!3 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 17-3.pdb, chain A (#1) with rank_001.pdb, chain A (#2), sequence
alignment score = 5760.4
RMSD between 1186 pruned atom pairs is 0.637 angstroms; (across all 1235
pairs: 2.696)
Matchmaker 17-3.pdb, chain A (#1) with open-loop-CTD.pdb, chain A (#3),
sequence alignment score = 6262.9
RMSD between 1202 pruned atom pairs is 0.064 angstroms; (across all 1209
pairs: 1.613)
> select #3/B
1487 atoms, 1520 bonds, 178 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select #3/C
975 atoms, 999 bonds, 119 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> open /Users/huan/Downloads/rank_002_alphafold2_ptm_model_4_seed_000.pdb
Chain information for rank_002_alphafold2_ptm_model_4_seed_000.pdb #4
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #2,4#!3 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 17-3.pdb, chain A (#1) with rank_001.pdb, chain A (#2), sequence
alignment score = 5760.4
RMSD between 1186 pruned atom pairs is 0.637 angstroms; (across all 1235
pairs: 2.696)
Matchmaker 17-3.pdb, chain A (#1) with
rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain A (#4), sequence alignment
score = 5676.4
RMSD between 627 pruned atom pairs is 1.102 angstroms; (across all 1235 pairs:
4.349)
Matchmaker 17-3.pdb, chain A (#1) with open-loop-CTD.pdb, chain A (#3),
sequence alignment score = 6262.9
RMSD between 1202 pruned atom pairs is 0.064 angstroms; (across all 1209
pairs: 1.613)
> hide #2 models
> hide #1 models
> hide #4 models
> show #4 models
> hide #4 models
> view
> ui tool show "Side View"
> show #2 models
> hide #2 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #2 models
> hide #!3 models
> show #4 models
> hide #4 models
> show #!3 models
> hide #2#!3 atoms
> select down
Nothing selected
> select down
Nothing selected
> transparency 10 surfaces
> cartoon style width 1.0 thickness 0.5
> transparency 60 cartoons
> transparency 30 cartoons
> ui tool show Matchmaker
> matchmaker #!3 to #2
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 rank_001.pdb, chain A (#2) with open-loop-CTD.pdb, chain A (#3),
sequence alignment score = 6292.3
RMSD between 1325 pruned atom pairs is 0.736 angstroms; (across all 1342
pairs: 0.813)
> show #4 models
> hide #2 models
> hide #4 models
> show #!3 surfaces
> show #2 models
> show #2#!3 surfaces
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #4 models
> show #4 surfaces
> open /Users/huan/Downloads/pdbs/rank_001.pdb
Chain information for rank_001.pdb #5
---
Chain | Description
A | No description available
> open /Users/huan/Downloads/pdbs/rank_002.pdb
Chain information for rank_002.pdb #6
---
Chain | Description
A | No description available
> open /Users/huan/Downloads/pdbs/rank_003.pdb
Chain information for rank_003.pdb #7
---
Chain | Description
A | No description available
> open /Users/huan/Downloads/pdbs/rank_004.pdb
Chain information for rank_004.pdb #8
---
Chain | Description
A | No description available
> open /Users/huan/Downloads/pdbs/rank_005.pdb
Chain information for rank_005.pdb #9
---
Chain | Description
A | No description available
Computing secondary structure
> hide #!4 models
> ui tool show Matchmaker
> matchmaker #1,5-9#!3-4 to #2
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 rank_001.pdb, chain A (#2) with 17-3.pdb, chain A (#1), sequence
alignment score = 5760.4
RMSD between 1186 pruned atom pairs is 0.637 angstroms; (across all 1235
pairs: 2.696)
Matchmaker rank_001.pdb, chain A (#2) with rank_001.pdb, chain A (#5),
sequence alignment score = 10228.7
RMSD between 1988 pruned atom pairs is 0.000 angstroms; (across all 1988
pairs: 0.000)
Matchmaker rank_001.pdb, chain A (#2) with rank_002.pdb, chain A (#6),
sequence alignment score = 10006.7
RMSD between 1395 pruned atom pairs is 0.472 angstroms; (across all 1988
pairs: 17.820)
Matchmaker rank_001.pdb, chain A (#2) with rank_003.pdb, chain A (#7),
sequence alignment score = 9877.1
RMSD between 731 pruned atom pairs is 1.030 angstroms; (across all 1988 pairs:
24.345)
Matchmaker rank_001.pdb, chain A (#2) with rank_004.pdb, chain A (#8),
sequence alignment score = 9899.9
RMSD between 754 pruned atom pairs is 1.008 angstroms; (across all 1988 pairs:
26.552)
Matchmaker rank_001.pdb, chain A (#2) with rank_005.pdb, chain A (#9),
sequence alignment score = 9911.9
RMSD between 772 pruned atom pairs is 1.044 angstroms; (across all 1988 pairs:
29.660)
Matchmaker rank_001.pdb, chain A (#2) with open-loop-CTD.pdb, chain A (#3),
sequence alignment score = 6292.3
RMSD between 1325 pruned atom pairs is 0.736 angstroms; (across all 1342
pairs: 0.813)
Matchmaker rank_001.pdb, chain A (#2) with
rank_002_alphafold2_ptm_model_4_seed_000.pdb, chain A (#4), sequence alignment
score = 9871.1
RMSD between 716 pruned atom pairs is 1.149 angstroms; (across all 1988 pairs:
27.885)
> hide #8 models
> hide #6 models
> hide #7 models
> hide #9 models
> show #!3 models
> hide #5#!3 surfaces
> show #9 models
> hide #9 models
> show #9 models
> show #8 models
> hide #8 models
> show #8 models
> hide #9 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #7 models
> hide #8 models
> hide #7 models
> show #7 models
> hide #!3 models
> show #6 models
> hide #6 models
> hide #5 models
> show #5 models
> show #6 models
> show #8 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #8 models
> show #8 models
> hide #7 models
> hide #6 models
> open /Users/huan/Downloads/rank_005_alphafold2_ptm_model_5_seed_000.pdb
Chain information for rank_005_alphafold2_ptm_model_5_seed_000.pdb #10
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #10 to #5
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker rank_001.pdb, chain A (#5) with
rank_005_alphafold2_ptm_model_5_seed_000.pdb, chain A (#10), sequence
alignment score = 9845.9
RMSD between 845 pruned atom pairs is 1.073 angstroms; (across all 1988 pairs:
31.906)
> hide #5 models
> show #5 models
> hide #8 models
> hide #10 models
> show #10 models
> show #!3 models
> hide #5 models
> color #10 #1f8e40ff
> color #10 #1f8e408c
> show #!4 models
> hide #10#!3-4 surfaces
> hide #10 models
> show #10 models
> hide #!4 models
> cartoon style width 1.0 thickness 0.5
> hide #10 models
> show #!4 models
> show #!2 models
> hide #!2-4 surfaces
> show #10 models
> hide #10 models
> show #10 models
> hide #!4 models
> show #9 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> show #8 models
> hide #8 models
> show #8 models
> show #7 models
> show #6 models
> show #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> show #8 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #10 models
> show #10 models
> hide #5 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #10 models
> show #10 models
> hide #8 models
> show #!3 models
> hide #10 models
> show #10 models
> ui tool show Matchmaker
> matchmaker #10 to #3
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 open-loop-CTD.pdb, chain A (#3) with
rank_005_alphafold2_ptm_model_5_seed_000.pdb, chain A (#10), sequence
alignment score = 6185.5
RMSD between 806 pruned atom pairs is 1.071 angstroms; (across all 1342 pairs:
7.649)
> ui tool show Matchmaker
> matchmaker #9 to #3
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 open-loop-CTD.pdb, chain A (#3) with rank_005.pdb, chain A (#9),
sequence alignment score = 6213.7
RMSD between 734 pruned atom pairs is 1.092 angstroms; (across all 1342 pairs:
7.885)
> ui tool show Matchmaker
> matchmaker #10 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 rank_005.pdb, chain A (#9) with
rank_005_alphafold2_ptm_model_5_seed_000.pdb, chain A (#10), sequence
alignment score = 10030.7
RMSD between 1283 pruned atom pairs is 0.909 angstroms; (across all 1988
pairs: 29.583)
> hide #9 models
> hide #10 models
Alignment identifier is 1/A
Alignment identifier is 1
Alignment identifier is 3/A
> select
> #3/A:17-33,68-70,80-83,114-123,126-144,150-172,183-185,187-204,210-227,231-266,270-272,286-290,296-301,347-359,363-374,376-413,735-741,744-763,770-796,800-805,807-824,832-847,850-863,867-894,896-899,913-925,929-939,941-972,1176-1189,1192-1211,1214-1218,1220-1247,1249-1254,1257-1278,1285-1287,1290-1300,1305-1342,1367-1376,1392-1404,1408-1416,1431-1460,1503-1512,1515-1534,1541-1575,1577-1601,1608-1624,1628-1639,1641-1665,1684-1695,1700-1707,1733-1761
6713 atoms, 6822 bonds, 826 residues, 1 model selected
> select #3/A:1331-1376
366 atoms, 377 bonds, 46 residues, 1 model selected
> select #3/A:1331-1380
396 atoms, 407 bonds, 50 residues, 1 model selected
> select #3/A:1509
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:1509-1514
49 atoms, 49 bonds, 6 residues, 1 model selected
> select #3/A:1472
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:1472-1474
27 atoms, 27 bonds, 3 residues, 1 model selected
> style sel stick
Changed 27 atom styles
> style sel sphere
Changed 27 atom styles
> style sel ball
Changed 27 atom styles
> show sel atoms
> style sel ball
Changed 27 atom styles
> show #10 models
Alignment identifier is 3/A
> select add #10
15941 atoms, 16291 bonds, 1991 residues, 3 models selected
Alignment identifier is 3/A
Alignment identifier is 10/A
> select #10/A:1472
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #10/A:1472-1474
27 atoms, 27 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 27 atom styles
> view #10 clip false
> open /Users/huan/Downloads/rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for rank_001_alphafold2_ptm_model_3_seed_000.pdb #11
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #11 to #3
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 open-loop-CTD.pdb, chain A (#3) with
rank_001_alphafold2_ptm_model_3_seed_000.pdb, chain A (#11), sequence
alignment score = 6190.3
RMSD between 609 pruned atom pairs is 0.964 angstroms; (across all 1342 pairs:
7.532)
> select add #11
15941 atoms, 16291 bonds, 1991 residues, 2 models selected
Alignment identifier is 1
> select add #10
31828 atoms, 32528 bonds, 3976 residues, 2 models selected
> select subtract #10
15914 atoms, 16264 bonds, 1988 residues, 1 model selected
> select subtract #11
Nothing selected
> select #10/A:1472 #11/A:1472
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #10/A:1472-1474 #11/A:1472-1474
54 atoms, 54 bonds, 6 residues, 2 models selected
1 [ID: 1] region 2 chains [1472-1474] RMSD: 19.881
> style sel ball
Changed 54 atom styles
> show sel atoms
> hide #10 models
> show #10 models
> hide #!3 models
> color #11 #a57a9eff
> color #11 #a58c88ff
> color #11 #97a547ff
> color #11 #d8eb65ff
> hide #10 models
> hide #11 models
> show #11 models
> show #10 models
> hide #11 models
> hide #10 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
Alignment identifier is 2
> select #10/A:1472 #11/A:1472
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #10/A:1472-1474 #11/A:1472-1474
54 atoms, 54 bonds, 6 residues, 2 models selected
2 [ID: 2] region 2 chains [1472-1474] RMSD: 19.881
> show #6-9 atoms
> undo
Alignment identifier is 3
> select add #6
31993 atoms, 32343 bonds, 1994 residues, 3 models selected
> select add #7
63932 atoms, 64632 bonds, 3982 residues, 4 models selected
> select add #8
95871 atoms, 96921 bonds, 5970 residues, 5 models selected
> select add #9
127810 atoms, 129210 bonds, 7958 residues, 6 models selected
Alignment identifier is 1
> select clear
> select #6/A:1472 #7/A:1472 #8/A:1472 #9/A:1472 #10/A:1472 #11/A:1472
92 atoms, 86 bonds, 6 residues, 6 models selected
> select #6/A:1472-1474 #7/A:1472-1474 #8/A:1472-1474 #9/A:1472-1474
> #10/A:1472-1474 #11/A:1472-1474
278 atoms, 278 bonds, 18 residues, 6 models selected
1 [ID: 1] region 6 chains [1472-1474] RMSD: 13.168
> show sel & #6-9 atoms
> style sel & #6-9 ball
Changed 224 atom styles
> hide #6 models
> hide #7 models
> hide #8 models
> show #11 models
> hide #9 models
> show #7 models
> show #6 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> hide #6 models
> hide #7 models
> show sel & #11 surfaces
> select add #11
16165 atoms, 16515 bonds, 2003 residues, 7 models selected
> show sel & #!11 surfaces
> show #10 models
> hide #!11 models
> show #9 models
> show #8 models
> show #7 models
> show #6 models
> show #5 models
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
Alignment identifier is 1
> select #6/A:1472-1473 #7/A:1472-1473 #8/A:1472-1473 #9/A:1472-1473
> #10/A:1472-1473 #11/A:1472-1473
194 atoms, 194 bonds, 12 residues, 6 models selected
> select #6/A:1472-1474 #7/A:1472-1474 #8/A:1472-1474 #9/A:1472-1474
> #10/A:1472-1474 #11/A:1472-1474
278 atoms, 278 bonds, 18 residues, 6 models selected
1 [ID: 1] region 6 chains [1472-1474] RMSD: 13.168
> style #5 ball
Changed 31939 atom styles
> show #5 atoms
> hide #5 atoms
> show #5 atoms
> hide #5 atoms
> select
> #6/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #7/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #8/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #9/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #10/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #11/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
96864 atoms, 97764 bonds, 7002 residues, 6 models selected
> select clear
> select #6/A:1472-1474 #7/A:1472-1474 #8/A:1472-1474 #9/A:1472-1474
> #10/A:1472-1474 #11/A:1472-1474
278 atoms, 278 bonds, 18 residues, 6 models selected
> select #6/A:1472 #7/A:1472 #8/A:1472 #9/A:1472 #10/A:1472 #11/A:1472
92 atoms, 86 bonds, 6 residues, 6 models selected
> select #6/A:1472 #7/A:1472 #8/A:1472 #9/A:1472 #10/A:1472 #11/A:1472
92 atoms, 86 bonds, 6 residues, 6 models selected
1 [ID: 1] region 6 chains [1472] RMSD: 10.672
> select #6/A:1472 #7/A:1472 #8/A:1472 #9/A:1472 #10/A:1472 #11/A:1472
92 atoms, 86 bonds, 6 residues, 6 models selected
> select #6/A:1472-1474 #7/A:1472-1474 #8/A:1472-1474 #9/A:1472-1474
> #10/A:1472-1474 #11/A:1472-1474
278 atoms, 278 bonds, 18 residues, 6 models selected
1 [ID: 1] region 6 chains [1472-1474] RMSD: 13.168
> select
> #6/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #7/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #8/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #9/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #10/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #11/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
96864 atoms, 97764 bonds, 7002 residues, 6 models selected
> select #6/A:1417-1602 #7/A:1417-1602 #8/A:1417-1602 #9/A:1417-1602
> #10/A:1417-1602 #11/A:1417-1602
15422 atoms, 15644 bonds, 1116 residues, 6 models selected
> select #6/A:1417-1602 #7/A:1417-1602 #8/A:1417-1602 #9/A:1417-1602
> #10/A:1417-1602 #11/A:1417-1602
15422 atoms, 15644 bonds, 1116 residues, 6 models selected
1 [ID: 1] region 6 chains [1417-1602] RMSD: 4.366
> select #6/A:1472 #7/A:1472 #8/A:1472 #9/A:1472 #10/A:1472 #11/A:1472
92 atoms, 86 bonds, 6 residues, 6 models selected
> select #6/A:1472-1474 #7/A:1472-1474 #8/A:1472-1474 #9/A:1472-1474
> #10/A:1472-1474 #11/A:1472-1474
278 atoms, 278 bonds, 18 residues, 6 models selected
1 [ID: 1] region 6 chains [1472-1474] RMSD: 13.168
> select add #5
32217 atoms, 32567 bonds, 2006 residues, 8 models selected
> select clear
> select
> #6/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #7/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #8/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #9/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #10/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
> #11/A:9-11,17-33,51-53,61-63,68-70,80-84,105-107,114-124,126-144,150-174,183-185,187-204,210-227,229-267,270-272,286-292,296-302,338-340,347-359,363-374,376-454,475-481,683-707,712-722,728-741,744-763,770-805,807-825,831-848,850-898,913-925,929-939,941-981,983-1014,1157-1162,1164-1166,1173-1190,1192-1211,1214-1248,1250-1255,1257-1278,1280-1303,1305-1343,1367-1376,1392-1404,1408-1417,1431-1471,1476-1490,1503-1513,1515-1534,1541-1575,1577-1602,1606-1626,1628-1666,1684-1696,1700-1708,1733-1771,1776-1788,1799-1808,1819-1825,1838-1850,1854-1870,1872-1877,1883-1918
96864 atoms, 97764 bonds, 7002 residues, 6 models selected
> select #6/A:1472 #7/A:1472 #8/A:1472 #9/A:1472 #10/A:1472 #11/A:1472
92 atoms, 86 bonds, 6 residues, 6 models selected
> select #6/A:1472-1474 #7/A:1472-1474 #8/A:1472-1474 #9/A:1472-1474
> #10/A:1472-1474 #11/A:1472-1474
278 atoms, 278 bonds, 18 residues, 6 models selected
1 [ID: 1] region 6 chains [1472-1474] RMSD: 13.168
> select add #6
32161 atoms, 32511 bonds, 2003 residues, 7 models selected
> select subtract #6
222 atoms, 222 bonds, 15 residues, 6 models selected
> select add #5
32161 atoms, 32511 bonds, 2003 residues, 7 models selected
> select clear
> select add #5
31939 atoms, 32289 bonds, 1988 residues, 1 model selected
Alignment identifier is 5/A
> select clear
> select #5/A:1472
19 atoms, 18 bonds, 1 residue, 1 model selected
> select #5/A:1472-1474
56 atoms, 56 bonds, 3 residues, 1 model selected
> style sel ball
Changed 56 atom styles
> show sel atoms
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> ui tool show "Side View"
> show #10 models
> style sel sphere
Changed 56 atom styles
> hide #6 models
> hide #7 models
> hide #8 models
> hide #9 models
> hide #10 models
> show #10 models
> style sel ball
Changed 56 atom styles
> hide #10 models
> show #!11 models
> hide sel surfaces
> select add #11
15970 atoms, 16320 bonds, 1991 residues, 4 models selected
> hide sel surfaces
> select subtract #11
56 atoms, 56 bonds, 3 residues, 2 models selected
> hide #!11 models
> show #10 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #10 models
> show #10 models
> hide #10 models
> show #!11 models
> hide #!11 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #8 models
> hide #9 models
> hide #5 models
> show #!11 models
> hide #!11 models
> show #!11 models
> cartoon style width 1.0 thickness 0.5
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #9 models
> show #6 models
> show #7 models
> show #5 models
> hide #5 models
> show #5 models
> show #!3 models
> hide #8 models
> hide #7 models
> hide #9 models
> show #8 models
> show #10 models
> hide #10 models
> show #!11 models
> hide #!11 models
> hide #8 models
> hide #6 models
> show #10 models
> hide #5 models
> transparency 60 cartoons
> lighting gentle
> show #9 models
> hide #10 models
> show #10 models
> hide #10 models
> show #8 models
> hide #8 models
> show #7 models
> hide #7 models
> show #5 models
> hide #9 models
> select clear
> lighting gentle
> color #5 #efdf1b66
> color #5 #ef996d66
> color #5 #deef4b66
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> hide #6 models
> hide #8 models
> hide #9 models
> hide #5 models
> color #7 #3cedcf66
> show #5 models
> hide #5 models
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> show #8 models
> hide #8 models
> show #5 models
> hide #5 models
> show #10 models
> hide #7 models
> hide #10 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #!11 models
> show #8 models
> color #8 #25fa1b66
> color #8 #bc92fa66
> color #8 #fa646666
> color #8 #fa854166
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> hide #!11 models
> show #9 models
> hide #9 models
> show #8 models
> hide #8 models
> show #7 models
> show #6 models
> hide #6 models
> hide #7 models
> show #8 models
> hide #8 models
> show #8 models
> show #1 models
> hide #8 models
> hide #1 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #9 models
> hide #9 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #!11 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #!3 models
> color #11 #e7ec2866
> color #11 #deec8666
> color #11 #d4eca966
> show #5 models
> hide #!11 models
> hide #8 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #!3 models
> hide #5 models
> show #10 models
> show #!11 models
> hide #!3 models
> show #!3 models
> hide #10 models
> show #8 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #5 models
> color #5 #efa1e966
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202412041747 (2024-12-04)
© 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 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: Mac15,12
Model Number: MC8N4CH/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.41.5
OS Loader Version: 11881.41.5
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 1天4小时41分钟
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: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
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: 2.7.1
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: 1.58.7
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: 2.4.7
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: 1.9rc202412041747
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: 1.1.13
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: 4.55.1
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
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: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
narwhals: 1.34.1
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: 2.2.4
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
plotly: 6.0.1
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
pyKVFinder: 0.7.3
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
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
toml: 0.10.2
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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