![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17754 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-15.4.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x0000000201310200 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.surface._surface, chimerax.map._map, openmm._openmm, openmm.app.internal.compiled, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 58)
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{
"uptime" : 1300000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 35795,
"osVersion" : {
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"build" : "24E263",
"releaseType" : "User"
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"captureTime" : "2025-05-21 09:16:56.1996 -0500",
"codeSigningMonitor" : 1,
"incident" : "F20FCE1F-AAA2-43BE-9B3C-4A256A74CA8F",
"pid" : 37650,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-20 12:04:56.8530 -0500",
"procStartAbsTime" : 31379260431590,
"procExitAbsTime" : 33206138662290,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"ACF28FB2-42FE-58C2-8DE5-A9B04FE55DAD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5CD00815-A492-345C-021D-25B424AB78F6",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"bootSessionUUID" : "C8D5122C-1C84-4391-B3B9-DCA98D92346C",
"sleepWakeUUID" : "B70E0A05-752D-4DEE-9945-FB861EE75531",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4311375511\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100fa6000-100faa000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":37650},
"vmregioninfo" : "0x169 is not in any region. Bytes before following region: 4311375511\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 100fa6000-100faa000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7cyq
7cyq title:
Cryo-EM structure of an extended SARS-CoV-2 replication and transcription
complex reveals an intermediate state in cap synthesis [more info...]
Chain information for 7cyq #1
---
Chain | Description | UniProt
A | RNA-directed RNA polymerase | R1AB_SARS2 1-932
B D | Non-structural protein 8 | R1AB_SARS2 1-198
C | Non-structural protein 7 | R1AB_SARS2 1-83
E F | Helicase | R1AB_SARS2 1-601
G | Non-structural protein 9 | R1AB_SARS2 1-113
I | Primer |
J | Template |
Non-standard residues in 7cyq #1
---
GDP — guanosine-5'-diphosphate
MG — magnesium ion
ZN — zinc ion
16 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide atoms
> show cartoons
> color bychain
> open 7n0d
7n0d title:
Cryo-EM structure of the tetrameric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA
complex [more info...]
Chain information for 7n0d #2
---
Chain | Description | UniProt
A C E G | Non-structural protein 10 | R1AB_SARS2 1-139
B D F H | Proofreading exoribonuclease | R1AB_SARS2 1-527
I T | RNA (5'-R(*GP*GP*GP*GP*AP*UP*GP*UP*GP*AP*UP*UP*UP*UP*AP*AP*UP*AP*G)-3') |
J P | RNA (5'-R(*CP*CP*CP*CP*C)-3') |
K L | RNA (5'-R(*CP*UP*AP*UP*UP*AP*AP*AP*AP*UP*CP*AP*CP*C)-3') |
Non-standard residues in 7n0d #2
---
1N7 — chapso
(2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium)
MG — magnesium ion
ZN — zinc ion
> hide #!1 models
> hide #!2 atoms
> show #!2 cartoons
> color #!2 bychain
> combine #2
> matchmaker #3/D to #2/B
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 7n0d, chain B (#2) with copy of 7n0d, chain D (#3), sequence
alignment score = 2582.4
RMSD between 507 pruned atom pairs is 0.498 angstroms; (across all 512 pairs:
0.593)
> hide #!3 models
> matchmaker #4/F to #2/B
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 7n0d, chain B (#2) with copy of 7n0d, chain F (#4), sequence
alignment score = 2768.4
RMSD between 512 pruned atom pairs is 0.007 angstroms; (across all 512 pairs:
0.007)
> hide #!4 models
> matchmaker #5/H to #2/B
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 7n0d, chain B (#2) with copy of 7n0d, chain H (#5), sequence
alignment score = 2582.4
RMSD between 507 pruned atom pairs is 0.498 angstroms; (across all 512 pairs:
0.593)
> hide #!5 models
> show #!3 models
> show #!4 models
> show #!5 models
> select #2/A
957 atoms, 976 bonds, 8 pseudobonds, 133 residues, 2 models selected
Drag select of 8 residues
> select up
1135 atoms, 1152 bonds, 8 pseudobonds, 159 residues, 5 models selected
> select up
15349 atoms, 15780 bonds, 8 pseudobonds, 1945 residues, 5 models selected
Drag select of 6 residues
> select up
16377 atoms, 16896 bonds, 8 pseudobonds, 2015 residues, 5 models selected
> select up
18081 atoms, 18656 bonds, 8 pseudobonds, 2219 residues, 5 models selected
> select up
18153 atoms, 18712 bonds, 8 pseudobonds, 2243 residues, 5 models selected
> select up
87384 atoms, 90240 bonds, 103 pseudobonds, 10720 residues, 5 models selected
> select down
18153 atoms, 18712 bonds, 8 pseudobonds, 2243 residues, 5 models selected
Drag select of 8 residues
> select up
19559 atoms, 20282 bonds, 8 pseudobonds, 2309 residues, 5 models selected
> select up
87384 atoms, 90240 bonds, 103 pseudobonds, 10720 residues, 5 models selected
> select down
19559 atoms, 20282 bonds, 8 pseudobonds, 2309 residues, 5 models selected
Drag select of 2 residues
> select up
20381 atoms, 21202 bonds, 8 pseudobonds, 2347 residues, 5 models selected
> select up
87384 atoms, 90240 bonds, 103 pseudobonds, 10720 residues, 5 models selected
> select down
20381 atoms, 21202 bonds, 8 pseudobonds, 2347 residues, 5 models selected
Drag select of 2 residues
> select up
20581 atoms, 21420 bonds, 8 pseudobonds, 2357 residues, 5 models selected
> select up
87384 atoms, 90240 bonds, 103 pseudobonds, 10720 residues, 5 models selected
> select down
20581 atoms, 21420 bonds, 8 pseudobonds, 2357 residues, 5 models selected
> select ~sel & ##selected
66803 atoms, 68820 bonds, 509 pseudobonds, 8363 residues, 16 models selected
> delete sel
> show nucleic
> style stick
Changed 42422 atom styles
> ~ribbon nucleic
> hide protein-5
> ~ribbon protein-5
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!5 models
> combine #2
> delete protein
> ~show nucleic
> hide #!6 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show :mg
> color :mg green
> set bgColor white
> ui tool show "Side View"
> color #!2,6 byhetero
> save /Users/rnkirchdoerf/Desktop/7n0d_nsp1014_RNA.jpg width 769 height 772
> supersample 3
> close #3-6
> open 7kf4
Summary of feedback from opening 7kf4 fetched from pdb
---
note | Fetching compressed mmCIF 7kf4 from http://files.rcsb.org/download/7kf4.cif
7kf4 title:
Crystal structure from SARS-CoV-2 NendoU NSP15 [more info...]
Chain information for 7kf4 #3
---
Chain | Description | UniProt
A B C D E F | Uridylate-specific endoribonuclease | R1AB_SARS2 1-346
Non-standard residues in 7kf4 #3
---
CIT — citric acid
30 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> view #3
> hide
> ribbon
> delete #3/B-F
> open 7bq7
7bq7 title:
Crystal structure of 2019-nCoV nsp16-nsp10 complex [more info...]
Chain information for 7bq7 #4
---
Chain | Description | UniProt
A | 2'-O-methyltransferase | R1AB_SARS2 1-298
B | Non-structural protein 10 | R1AB_SARS2 1-139
Non-standard residues in 7bq7 #4
---
SAM — S-adenosylmethionine
ZN — zinc ion
> view #4
> color #4 bychain
> ~ribbon #4/B
> ~show
> hide #!4 models
> hide #3 models
> hide #!2 models
> show #!1 models
> view #1
> ~ribbon #1/A-B,D-G
> ~ribbon nucleic
> view #1
> color #1 light grey
> save /Users/rnkirchdoerf/Desktop/7cyq_nsp7.jpg width 1200 height 1205
> supersample 3
> ~ribbon #1
> ribbon #1/B
> view #1/B
> color #1/grey
> color #1 grey
> save /Users/rnkirchdoerf/Desktop/7cyq_nsp8.jpg width 1200 height 1205
> supersample 3
> ~ribbon #1
> ribbon #1/G
> view #1
> color #1/dim grey
> color #1 dim grey
> save /Users/rnkirchdoerf/Desktop/7cyq_nsp9.png width 769 height 772
> supersample 3 transparentBackground true
> ~ribbon #1
> ribbon #1/C
> view #1
> color #1/C light grey
> save /Users/rnkirchdoerf/Desktop/7cyq_nsp7.png width 1200 height 1205
> supersample 3 transparentBackground true
> ~ribbon #1
> ribbon #1/B
> view #1/B
> color #1/B grey
> ui tool show "Side View"
> save /Users/rnkirchdoerf/Desktop/7cyq_nsp8.png width 1200 height 1205
> supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> ~ribbon #2/A
> ~ribbon #2
> ribbon #2/A
> view #2
> color #2 dark grey
> color #2 black
> save /Users/rnkirchdoerf/Desktop/7n0d_nsp10.png width 1200 height 1205
> supersample 3 transparentBackground true
> hide #!2 models
> show #!1 models
> ~ribbon #1
> ribbon #1/A
> view #1
> color #1/A goldenrod
> lighting soft
> save /Users/rnkirchdoerf/Desktop/7cyq_nsp12.png width 1200 height 1205
> supersample 3 transparentBackground true
> ~ribbon #1
> ribbon #1/E
> view #1
> color #1/E light green
> hide pseudobonds
> cartoon style thickness 0.5
> cartoon style thickness 0.8
> save /Users/rnkirchdoerf/Desktop/7cyq_nsp13.png width 1200 height 1205
> supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> view #2
> ~ribbon #2/A
> ribbon #2/B
> color #2/B light grey
> view #2
> save /Users/rnkirchdoerf/Desktop/7n0d_nsp14.png width 1200 height 1205
> supersample 3 transparentBackground true
> hide #!2 models
> show #3 models
> view #3
> ui tool show "Color Actions"
> color #3 lime green
> color #3 medium sea green
> save /Users/rnkirchdoerf/Desktop/7kf4_nsp14.png width 1200 height 1205
> supersample 3 transparentBackground true
> hide #3 models
> show #!4 models
> view #4
> color #4 bychain
> select ~sel & ##selected
Nothing selected
> color #4 forest green
> save /Users/rnkirchdoerf/Desktop/7bq7_nsp16.png width 1200 height 1205
> supersample 3 transparentBackground true
> hide #!4 models
> show #!1 models
> view #1
> color #1/E yellow green
> save /Users/rnkirchdoerf/Desktop/7cyq_nsp13.png width 1200 height 1205
> supersample 3 transparentBackground true
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_13_12_32_eav_nsp5_6/fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif"
Chain information for fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif #5
---
Chain | Description
A | .
> view #5 clip false
> hide #!1 models
> show #5
> rainbow #5
> color byhetero
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_1.cif"
Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_1.cif #6
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_2.cif"
Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_2.cif #7
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_3.cif"
Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_3.cif #8
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_4.cif"
Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_4.cif #9
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_34_shfv_nsp5/fold_2025_05_21_08_34_shfv_nsp5_model_0.cif"
Chain information for fold_2025_05_21_08_34_shfv_nsp5_model_0.cif #10
---
Chain | Description
A | .
> matchmaker #7-10 to #6
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 fold_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6) with
fold_2025_05_21_08_34_shfv_nsp5_model_2.cif, chain A (#7), sequence alignment
score = 865.4
RMSD between 163 pruned atom pairs is 0.468 angstroms; (across all 166 pairs:
0.573)
Matchmaker fold_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6) with
fold_2025_05_21_08_34_shfv_nsp5_model_3.cif, chain A (#8), sequence alignment
score = 868.4
RMSD between 160 pruned atom pairs is 0.443 angstroms; (across all 166 pairs:
0.761)
Matchmaker fold_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6) with
fold_2025_05_21_08_34_shfv_nsp5_model_4.cif, chain A (#9), sequence alignment
score = 865.4
RMSD between 161 pruned atom pairs is 0.442 angstroms; (across all 166 pairs:
0.621)
Matchmaker fold_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6) with
fold_2025_05_21_08_34_shfv_nsp5_model_0.cif, chain A (#10), sequence alignment
score = 864.8
RMSD between 156 pruned atom pairs is 0.375 angstroms; (across all 166 pairs:
1.587)
> matchmaker #6-10 to #5
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 fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_34_shfv_nsp5_model_1.cif, chain A (#6), sequence alignment
score = 311.1
RMSD between 85 pruned atom pairs is 0.891 angstroms; (across all 155 pairs:
4.763)
Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_34_shfv_nsp5_model_2.cif, chain A (#7), sequence alignment
score = 321.9
RMSD between 86 pruned atom pairs is 0.911 angstroms; (across all 155 pairs:
4.587)
Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_34_shfv_nsp5_model_3.cif, chain A (#8), sequence alignment
score = 318.3
RMSD between 87 pruned atom pairs is 0.892 angstroms; (across all 155 pairs:
4.682)
Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_34_shfv_nsp5_model_4.cif, chain A (#9), sequence alignment
score = 321.9
RMSD between 83 pruned atom pairs is 0.886 angstroms; (across all 155 pairs:
4.690)
Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_34_shfv_nsp5_model_0.cif, chain A (#10), sequence alignment
score = 314.7
RMSD between 85 pruned atom pairs is 0.899 angstroms; (across all 155 pairs:
5.107)
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> show #6 models
> select #5:50-75
206 atoms, 211 bonds, 26 residues, 1 model selected
> hide #6 models
> select #6:50-75
201 atoms, 205 bonds, 26 residues, 1 model selected
> hide #5 models
> show #6 models
> hide #6 models
> show #5 models
> close #7-10
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_1.cif"
Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_1.cif #7
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_2.cif"
Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_2.cif #8
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_3.cif"
Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_3.cif #9
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_4.cif"
Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_4.cif #10
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_08_43_sars2_nsp6/fold_2025_05_21_08_43_sars2_nsp6_model_0.cif"
Chain information for fold_2025_05_21_08_43_sars2_nsp6_model_0.cif #11
---
Chain | Description
A | .
> matchmaker #7-11 to #5
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 fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7), sequence alignment
score = 145.5
RMSD between 10 pruned atom pairs is 1.212 angstroms; (across all 168 pairs:
18.928)
Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_43_sars2_nsp6_model_2.cif, chain A (#8), sequence alignment
score = 145
RMSD between 19 pruned atom pairs is 1.055 angstroms; (across all 172 pairs:
17.976)
Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_43_sars2_nsp6_model_3.cif, chain A (#9), sequence alignment
score = 145.5
RMSD between 10 pruned atom pairs is 1.222 angstroms; (across all 168 pairs:
18.972)
Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_43_sars2_nsp6_model_4.cif, chain A (#10), sequence
alignment score = 145
RMSD between 22 pruned atom pairs is 1.085 angstroms; (across all 172 pairs:
17.958)
Matchmaker fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_43_sars2_nsp6_model_0.cif, chain A (#11), sequence
alignment score = 145
RMSD between 15 pruned atom pairs is 1.479 angstroms; (across all 172 pairs:
16.979)
> matchmaker #7 to #5
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 fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7), sequence alignment
score = 145.5
RMSD between 10 pruned atom pairs is 1.212 angstroms; (across all 168 pairs:
18.928)
> matchmaker #8-11 to #7
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 fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with
fold_2025_05_21_08_43_sars2_nsp6_model_2.cif, chain A (#8), sequence alignment
score = 1541.1
RMSD between 290 pruned atom pairs is 0.452 angstroms; (across all 290 pairs:
0.452)
Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with
fold_2025_05_21_08_43_sars2_nsp6_model_3.cif, chain A (#9), sequence alignment
score = 1544.1
RMSD between 290 pruned atom pairs is 0.342 angstroms; (across all 290 pairs:
0.342)
Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with
fold_2025_05_21_08_43_sars2_nsp6_model_4.cif, chain A (#10), sequence
alignment score = 1541.1
RMSD between 273 pruned atom pairs is 0.334 angstroms; (across all 290 pairs:
1.134)
Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with
fold_2025_05_21_08_43_sars2_nsp6_model_0.cif, chain A (#11), sequence
alignment score = 1541.1
RMSD between 290 pruned atom pairs is 0.400 angstroms; (across all 290 pairs:
0.400)
> hide #5 models
> select clear
> hide #8 models
> hide #9 models
> hide #10 models
> hide #11 models
> show #5 models
> rainbow #7
> matchmaker #7 to #5
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 fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7), sequence alignment
score = 145.5
RMSD between 10 pruned atom pairs is 1.212 angstroms; (across all 168 pairs:
18.928)
> ui tool show Matchmaker
> matchmaker #8 to #5 ssFraction 0.8088
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.8088
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 fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_43_sars2_nsp6_model_2.cif, chain A (#8), sequence alignment
score = 589.859
RMSD between 8 pruned atom pairs is 1.430 angstroms; (across all 170 pairs:
16.553)
> matchmaker #8 to #5 ssFraction 0.8088
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.8088
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 fold_2025_05_13_12_32_eav_nsp5_6_model_0.cif, chain A (#5) with
fold_2025_05_21_08_43_sars2_nsp6_model_2.cif, chain A (#8), sequence alignment
score = 589.859
RMSD between 8 pruned atom pairs is 1.430 angstroms; (across all 170 pairs:
16.553)
> hide #5 models
> select #7:157
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #7 models
> select up
120 atoms, 121 bonds, 16 residues, 1 model selected
> select up
2321 atoms, 2383 bonds, 290 residues, 1 model selected
> select up
48150 atoms, 49268 bonds, 6157 residues, 11 models selected
> select up
48150 atoms, 49268 bonds, 6157 residues, 11 models selected
> select up
48150 atoms, 49268 bonds, 6157 residues, 11 models selected
> close #8-11
> select clear
> show #5 models
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_1.cif"
Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_1.cif #8
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_2.cif"
Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_2.cif #9
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_3.cif"
Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_3.cif #10
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_4.cif"
Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_4.cif #11
---
Chain | Description
A | .
> open "/Users/rnkirchdoerf/Library/CloudStorage/Box-Box/Wisconsin/2025 Arteri
> nsp9
> grant/AlphaFold/fold_2025_05_21_09_00_mhv_nsp6/fold_2025_05_21_09_00_mhv_nsp6_model_0.cif"
Chain information for fold_2025_05_21_09_00_mhv_nsp6_model_0.cif #12
---
Chain | Description
A | .
> matchmaker #8-12 to #7
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 fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with
fold_2025_05_21_09_00_mhv_nsp6_model_1.cif, chain A (#8), sequence alignment
score = 36
RMSD between 5 pruned atom pairs is 1.030 angstroms; (across all 101 pairs:
17.951)
Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with
fold_2025_05_21_09_00_mhv_nsp6_model_2.cif, chain A (#9), sequence alignment
score = 48.9
RMSD between 4 pruned atom pairs is 1.448 angstroms; (across all 99 pairs:
18.180)
Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with
fold_2025_05_21_09_00_mhv_nsp6_model_3.cif, chain A (#10), sequence alignment
score = 45.3
RMSD between 5 pruned atom pairs is 1.205 angstroms; (across all 99 pairs:
18.905)
Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with
fold_2025_05_21_09_00_mhv_nsp6_model_4.cif, chain A (#11), sequence alignment
score = 48.9
RMSD between 4 pruned atom pairs is 1.003 angstroms; (across all 99 pairs:
18.713)
Matchmaker fold_2025_05_21_08_43_sars2_nsp6_model_1.cif, chain A (#7) with
fold_2025_05_21_09_00_mhv_nsp6_model_0.cif, chain A (#12), sequence alignment
score = 48.9
RMSD between 4 pruned atom pairs is 1.450 angstroms; (across all 99 pairs:
18.091)
> hide #5 models
> show #7 models
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> hide #7 models
> hide #8 models
> show #9 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: Z14Z00105LL/A
Chip: Unknown
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 34 days, 9 hours, 48 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
ChimeraX-Clipper: 0.23.1
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: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
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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