![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18454 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-15.5-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
Current thread 0x00000001f7bbdf00 (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.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 (total: 53)
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"procRole" : "Background",
"version" : 2,
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"deployVersion" : 210,
"modelCode" : "MacBookPro18,2",
"coalitionID" : 76041,
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-08-15 22:33:18.5094 -0700",
"codeSigningMonitor" : 1,
"incident" : "E3B5B322-48FE-4358-AFAA-8ADE8F3D7396",
"pid" : 66016,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-15 15:11:34.1055 -0700",
"procStartAbsTime" : 68450039154933,
"procExitAbsTime" : 68767255088756,
"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":"E6DE3A76-1F19-5220-857E-92D74DDEE1D0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "85185743-89B4-AEFD-9846-12B6DC76F044",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "69BA04B9-E103-409D-90F2-3B1F46FA3603",
"wakeTime" : 1,
"sleepWakeUUID" : "ED73A5F4-E1C0-4196-92B2-E10A7B767662",
"sip" : "enabled",
"vmRegionInfo" : "0x54cb7cdc6688 is not in any region. Bytes after previous region: 92751913576073 Bytes before following region: 12320166353272\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, 0x000054cb7cdc6688","rawCodes":[1,93232949913224],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x000054cb7cdc6688"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":66016},
"vmregioninfo" : "0x54cb7cdc6688 is not in any region. Bytes after previous region: 92751913576073 Bytes before following region: 12320166353272\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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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/bethanykolody/Downloads/folds_2025_08_15_22_11/sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0/fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif
Chain information for
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> set bgColor white
> set bgColor black
> color bfactor palette alphafold
29075 atoms, 4139 residues, atom bfactor range 18.5 to 87.1
> ui tool show "Side View"
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select clear
> select /A:4122-4123
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:4122-4139
139 atoms, 138 bonds, 18 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-7
46 atoms, 46 bonds, 7 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-30
193 atoms, 195 bonds, 30 residues, 1 model selected
> select /A:31
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:31-109
550 atoms, 553 bonds, 79 residues, 1 model selected
> select /A:63-64
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:1-64
428 atoms, 432 bonds, 64 residues, 1 model selected
> select /A:1-64
428 atoms, 432 bonds, 64 residues, 1 model selected
> select /A:1-64
428 atoms, 432 bonds, 64 residues, 1 model selected
> select /A:1-64
428 atoms, 432 bonds, 64 residues, 1 model selected
> select clear
> color bychain
> rainbow
> color bypolymer
> rainbow
> select /A:1-64
428 atoms, 432 bonds, 64 residues, 1 model selected
> color #1 #76d6ffff
> select /A:4043-4088
328 atoms, 331 bonds, 46 residues, 1 model selected
> select /A:1-64
428 atoms, 432 bonds, 64 residues, 1 model selected
> select /A:4043-4088
328 atoms, 331 bonds, 46 residues, 1 model selected
> select /A:4139
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /A:4097-4139
312 atoms, 313 bonds, 43 residues, 1 model selected
> select /A:3691-4139
3337 atoms, 3387 bonds, 449 residues, 1 model selected
> set bgColor white
> color #1 #0096ffff
> select clear
> select /A:3691-4139
3337 atoms, 3387 bonds, 449 residues, 1 model selected
> select /A:3943
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:3943-4139
1405 atoms, 1419 bonds, 197 residues, 1 model selected
> select /A:3943
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:3943-4139
1405 atoms, 1419 bonds, 197 residues, 1 model selected
> select /A:3943
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:3943-4128
1318 atoms, 1332 bonds, 186 residues, 1 model selected
> select /A:3991-3992
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:3991-4083
655 atoms, 663 bonds, 93 residues, 1 model selected
> select /A:4089
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:4089
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:3993-3994
13 atoms, 12 bonds, 2 residues, 1 model selected
> select /A:3993-4085
654 atoms, 662 bonds, 93 residues, 1 model selected
> select /A:3999
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:3999-4089
640 atoms, 647 bonds, 91 residues, 1 model selected
> select /A:4026
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:4026-4080
400 atoms, 405 bonds, 55 residues, 1 model selected
> select /A:4036-4037
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /A:4036-4087
377 atoms, 381 bonds, 52 residues, 1 model selected
> select /A:4060-4061
17 atoms, 16 bonds, 2 residues, 1 model selected
> select /A:4060-4074
114 atoms, 114 bonds, 15 residues, 1 model selected
> select /A:4055
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:4055-4076
153 atoms, 154 bonds, 22 residues, 1 model selected
> select /A:4078
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:4040-4078
279 atoms, 282 bonds, 39 residues, 1 model selected
> select /A:4080-4081
17 atoms, 17 bonds, 2 residues, 1 model selected
> select /A:4080-4084
39 atoms, 39 bonds, 5 residues, 1 model selected
> select /A:4071
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:4071-4090
134 atoms, 135 bonds, 20 residues, 1 model selected
> select /A:4079
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:4079-4093
111 atoms, 111 bonds, 15 residues, 1 model selected
> select /A:4074
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:4074-4093
136 atoms, 137 bonds, 20 residues, 1 model selected
> select /A:4079-4080
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /A:4079-4093
111 atoms, 111 bonds, 15 residues, 1 model selected
> select /A:4076
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:4076-4091
111 atoms, 111 bonds, 16 residues, 1 model selected
> select /A:4076
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:4076-4139
459 atoms, 461 bonds, 64 residues, 1 model selected
> select /A:4074
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:4011-4074
457 atoms, 461 bonds, 64 residues, 1 model selected
> select /A:4074
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /A:3931-4074
1026 atoms, 1036 bonds, 144 residues, 1 model selected
> select /A:4074-4075
11 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:3883-4075
1404 atoms, 1425 bonds, 193 residues, 1 model selected
> select /A:4075
7 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:3931-4075
1033 atoms, 1044 bonds, 145 residues, 1 model selected
> select /A:3934
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:3934-4075
1009 atoms, 1020 bonds, 142 residues, 1 model selected
> select /A:3985
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:3985-4075
642 atoms, 649 bonds, 91 residues, 1 model selected
> select /A:3977
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:3977-4075
693 atoms, 700 bonds, 99 residues, 1 model selected
> open 3HB2
Summary of feedback from opening 3HB2 fetched from pdb
---
note | Fetching compressed mmCIF 3hb2 from http://files.rcsb.org/download/3hb2.cif
3hb2 title:
PrtC methionine mutants: M226I [more info...]
Chain information for 3hb2 #2
---
Chain | Description | UniProt
P | Secreted protease C | PRTC_ERWCH 18-479
Non-standard residues in 3hb2 #2
---
CA — calcium ion
CL — chloride ion
ZN — zinc ion
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> color #2 #ff9300ff
> 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
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 3hb2, chain P (#2), sequence alignment score = 265.4
RMSD between 74 pruned atom pairs is 0.747 angstroms; (across all 362 pairs:
34.548)
> open 5K8G
Summary of feedback from opening 5K8G fetched from pdb
---
note | Fetching compressed mmCIF 5k8g from http://files.rcsb.org/download/5k8g.cif
5k8g title:
Crystal structure of a putative peptide-binding domain of MpAFP [more info...]
Chain information for 5k8g #3
---
Chain | Description | UniProt
A | Antifreeze protein | A1YIY3_9GAMM 1-519
Non-standard residues in 5k8g #3
---
CA — calcium ion
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> 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
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 3hb2, chain P (#2), sequence alignment score = 265.4
RMSD between 74 pruned atom pairs is 0.747 angstroms; (across all 362 pairs:
34.548)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 5k8g, chain A (#3), sequence alignment score = 339.9
RMSD between 11 pruned atom pairs is 1.034 angstroms; (across all 441 pairs:
71.639)
> hide #!3 models
> open 2ML3
Summary of feedback from opening 2ML3 fetched from pdb
---
note | Fetching compressed mmCIF 2ml3 from http://files.rcsb.org/download/2ml3.cif
2ml3 title:
Solution Structure of AlgE6R3 subunit from the Azotobacter vinelandii
Mannuronan C5-epimerase [more info...]
Chain information for 2ml3
---
Chain | Description | UniProt
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A | Poly(beta-D-mannuronate) C5 epimerase 6 | ALGE6_AZOVI 2-181
> color #4 #ff2f92ff models
> color #4 #00f900ff models
> ui tool show Matchmaker
> matchmaker #!2-3#!4.1-20 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
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 3hb2, chain P (#2), sequence alignment score = 265.4
RMSD between 74 pruned atom pairs is 0.747 angstroms; (across all 362 pairs:
34.548)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 5k8g, chain A (#3), sequence alignment score = 339.9
RMSD between 11 pruned atom pairs is 1.034 angstroms; (across all 441 pairs:
71.639)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.1), sequence alignment score = 197
RMSD between 18 pruned atom pairs is 1.221 angstroms; (across all 156 pairs:
14.254)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.2), sequence alignment score = 193.9
RMSD between 65 pruned atom pairs is 0.875 angstroms; (across all 148 pairs:
8.019)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.3), sequence alignment score = 191.3
RMSD between 16 pruned atom pairs is 1.159 angstroms; (across all 156 pairs:
14.128)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.4), sequence alignment score = 196.9
RMSD between 14 pruned atom pairs is 0.860 angstroms; (across all 156 pairs:
14.064)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.5), sequence alignment score = 191
RMSD between 16 pruned atom pairs is 1.100 angstroms; (across all 156 pairs:
14.326)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.6), sequence alignment score = 197
RMSD between 18 pruned atom pairs is 1.085 angstroms; (across all 156 pairs:
14.202)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.7), sequence alignment score = 193.2
RMSD between 18 pruned atom pairs is 1.129 angstroms; (across all 162 pairs:
14.207)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.8), sequence alignment score = 196.2
RMSD between 65 pruned atom pairs is 0.847 angstroms; (across all 155 pairs:
7.611)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.9), sequence alignment score = 202.2
RMSD between 71 pruned atom pairs is 0.938 angstroms; (across all 155 pairs:
7.359)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.10), sequence alignment score = 185.3
RMSD between 18 pruned atom pairs is 1.208 angstroms; (across all 156 pairs:
14.119)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.11), sequence alignment score = 190.9
RMSD between 16 pruned atom pairs is 1.253 angstroms; (across all 162 pairs:
14.205)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.12), sequence alignment score = 191.3
RMSD between 18 pruned atom pairs is 1.203 angstroms; (across all 156 pairs:
14.161)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.13), sequence alignment score = 201.8
RMSD between 70 pruned atom pairs is 0.977 angstroms; (across all 161 pairs:
8.018)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.14), sequence alignment score = 184.9
RMSD between 17 pruned atom pairs is 1.250 angstroms; (across all 162 pairs:
14.301)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.15), sequence alignment score = 188.6
RMSD between 18 pruned atom pairs is 1.248 angstroms; (across all 156 pairs:
14.195)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.16), sequence alignment score = 187.2
RMSD between 16 pruned atom pairs is 1.178 angstroms; (across all 162 pairs:
14.338)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.17), sequence alignment score = 194.6
RMSD between 17 pruned atom pairs is 1.168 angstroms; (across all 156 pairs:
14.136)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.18), sequence alignment score = 190.9
RMSD between 16 pruned atom pairs is 1.253 angstroms; (across all 162 pairs:
14.320)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.19), sequence alignment score = 184.9
RMSD between 17 pruned atom pairs is 1.190 angstroms; (across all 156 pairs:
14.240)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.20), sequence alignment score = 197.3
RMSD between 16 pruned atom pairs is 1.214 angstroms; (across all 156 pairs:
14.210)
> hide #!2 models
> hide #!4.20 models
> hide #!4.19 models
> hide #!4.18 models
> hide #!4.17 models
> hide #!4.16 models
> hide #!4.15 models
> hide #!4.14 models
> hide #!4.13 models
> hide #!4.12 models
> hide #!4.11 models
> hide #!4.10 models
> hide #!4.9 models
> hide #!4.7 models
> hide #!4.8 models
> hide #!4.6 models
> hide #!4.5 models
> hide #!4.4 models
> hide #!4.3 models
> hide #!4.2 models
> hide #!4.1 models
> show #!4.1 models
> ui tool show "Side View"
> color #4 #ff9300ff models
> open
> /Users/bethanykolody/Downloads/folds_2025_08_15_23_20/alg_like_domain_with_6_ca/fold_alg_like_domain_with_6_ca_model_0.cif
Chain information for fold_alg_like_domain_with_6_ca_model_0.cif #5
---
Chain | Description
A | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #5#!2-3#!4.1-20 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
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with fold_alg_like_domain_with_6_ca_model_0.cif, chain A (#5),
sequence alignment score = 473.2
RMSD between 91 pruned atom pairs is 0.620 angstroms; (across all 99 pairs:
2.322)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 3hb2, chain P (#2), sequence alignment score = 265.4
RMSD between 74 pruned atom pairs is 0.747 angstroms; (across all 362 pairs:
34.548)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 5k8g, chain A (#3), sequence alignment score = 339.9
RMSD between 11 pruned atom pairs is 1.034 angstroms; (across all 441 pairs:
71.639)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.1), sequence alignment score = 197
RMSD between 18 pruned atom pairs is 1.221 angstroms; (across all 156 pairs:
14.254)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.2), sequence alignment score = 193.9
RMSD between 65 pruned atom pairs is 0.875 angstroms; (across all 148 pairs:
8.019)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.3), sequence alignment score = 191.3
RMSD between 16 pruned atom pairs is 1.159 angstroms; (across all 156 pairs:
14.128)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.4), sequence alignment score = 196.9
RMSD between 14 pruned atom pairs is 0.860 angstroms; (across all 156 pairs:
14.064)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.5), sequence alignment score = 191
RMSD between 16 pruned atom pairs is 1.100 angstroms; (across all 156 pairs:
14.326)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.6), sequence alignment score = 197
RMSD between 18 pruned atom pairs is 1.085 angstroms; (across all 156 pairs:
14.202)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.7), sequence alignment score = 193.2
RMSD between 18 pruned atom pairs is 1.129 angstroms; (across all 162 pairs:
14.207)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.8), sequence alignment score = 196.2
RMSD between 65 pruned atom pairs is 0.847 angstroms; (across all 155 pairs:
7.611)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.9), sequence alignment score = 202.2
RMSD between 71 pruned atom pairs is 0.938 angstroms; (across all 155 pairs:
7.359)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.10), sequence alignment score = 185.3
RMSD between 18 pruned atom pairs is 1.208 angstroms; (across all 156 pairs:
14.119)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.11), sequence alignment score = 190.9
RMSD between 16 pruned atom pairs is 1.253 angstroms; (across all 162 pairs:
14.205)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.12), sequence alignment score = 191.3
RMSD between 18 pruned atom pairs is 1.203 angstroms; (across all 156 pairs:
14.161)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.13), sequence alignment score = 201.8
RMSD between 70 pruned atom pairs is 0.977 angstroms; (across all 161 pairs:
8.018)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.14), sequence alignment score = 184.9
RMSD between 17 pruned atom pairs is 1.250 angstroms; (across all 162 pairs:
14.301)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.15), sequence alignment score = 188.6
RMSD between 18 pruned atom pairs is 1.248 angstroms; (across all 156 pairs:
14.195)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.16), sequence alignment score = 187.2
RMSD between 16 pruned atom pairs is 1.178 angstroms; (across all 162 pairs:
14.338)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.17), sequence alignment score = 194.6
RMSD between 17 pruned atom pairs is 1.168 angstroms; (across all 156 pairs:
14.136)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.18), sequence alignment score = 190.9
RMSD between 16 pruned atom pairs is 1.253 angstroms; (across all 162 pairs:
14.320)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.19), sequence alignment score = 184.9
RMSD between 17 pruned atom pairs is 1.190 angstroms; (across all 156 pairs:
14.240)
Matchmaker
fold_sde_1294_vcbs_domain_protein_from_nitricoxidoreducens_64_0_model_0.cif,
chain A (#1) with 2ml3, chain A (#4.20), sequence alignment score = 197.3
RMSD between 16 pruned atom pairs is 1.214 angstroms; (across all 156 pairs:
14.210)
> hide #1 models
> color #5 #d783ffff
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/bethanykolody/Downloads/folds_2025_08_16_05_55/ricemega_all12creps_fn_pb_15730_l_63_rtx_cadhesin/fold_ricemega_all12creps_fn_pb_15730_l_63_rtx_cadhesin_model_0.cif
Chain information for
fold_ricemega_all12creps_fn_pb_15730_l_63_rtx_cadhesin_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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 Pro
Model Identifier: MacBookPro18,2
Model Number: Z14Y0016GLL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 48 days, 7 hours, 40 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
DELL S2722QC:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
DELL S2722QC:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 3 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 , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel said what we know about this crash:
"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."
You may want to try the ChimeraX daily build which uses a newer version of the Qt window toolkit (6.9) where these multi-display Mac crashes may have been fixed.
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Reported by Bethany Kolody