![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 31 hours ago
Closed 13 hours ago
#19470 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-26.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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: Bus error
Current thread 0x0000000206152080 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, 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._imaging, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 55)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,13",
"coalitionID" : 9708,
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"build" : "25B78",
"releaseType" : "User"
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"captureTime" : "2025-12-02 16:04:20.1420 -0800",
"codeSigningMonitor" : 2,
"incident" : "6D6AE9EE-0246-4C8F-AE1B-CF579853F658",
"pid" : 24620,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-12-02 13:58:18.4429 -0800",
"procStartAbsTime" : 1091530401839,
"procExitAbsTime" : 1264993296943,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F260160A-92AB-5AC9-A290-E9E6B8817C12","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C7CE9648-6482-023B-B664-5752AC9E2116",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"bootProgressRegister" : "0x2f000000",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRFOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkQng\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "859F2339-3F49-4433-87B6-80D853EE34F1",
"wakeTime" : 1,
"sleepWakeUUID" : "589DBD5E-EB8F-4410-B100-FB9A25392049",
"sip" : "enabled",
"vmRegionInfo" : "0x727272727272 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000101, 0x7272727272727272","rawCodes":[257,8246779703540740722],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"EXC_ARM_DA_ALIGN at 0x7272727272727272 -> 0x0000727272727272 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":24620},
"vmregioninfo" : "0x727272727272 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/oswanson/Desktop/RdRp/844/J198_844-dimer_init-coot-2_plusPB2.pdb
Summary of feedback from opening
/Users/oswanson/Desktop/RdRp/844/J198_844-dimer_init-coot-2_plusPB2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR a 36 GLU a 48 1 13
Start residue of secondary structure not found: HELIX 2 2 LEU a 85 GLU a 98 1
14
Start residue of secondary structure not found: HELIX 3 3 LEU a 102 VAL a 116
1 15
Start residue of secondary structure not found: HELIX 4 4 VAL a 119 THR a 123
5 5
Start residue of secondary structure not found: HELIX 5 5 ALA a 139 ASN a 153
1 15
123 messages similar to the above omitted
Chain information for J198_844-dimer_init-coot-2_plusPB2.pdb #1
---
Chain | Description
Ab | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Ca | No description available
a | No description available
> open /Users/oswanson/Desktop/RdRp/844/Lee-AF-ref.pdb
> set bgColor white
> set bgColor #ffffff00
> open /Users/oswanson/Desktop/RdRp/844/apo_dimer_reference.pdb
Chain information for apo_dimer_reference.pdb #2
---
Chain | Description
A C | No description available
B | No description available
D | No description available
> open /Users/oswanson/Desktop/RdRp/844/J198_sharp_844dimer.mrc
Opened J198_sharp_844dimer.mrc as #3, grid size 512,512,512, pixel 0.718,
shown at level 0.0467, step 2, values float32
> volume #3 step 1
> volume #3 level 0.07618
> select add #1
17056 atoms, 17370 bonds, 8 pseudobonds, 2138 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
Computing secondary structure
> open
> /Users/oswanson/Downloads/cryosparc_P605_J199_006_volume_map_sharp-2.mrc
Opened cryosparc_P605_J199_006_volume_map_sharp-2.mrc as #4, grid size
512,512,512, pixel 0.718, shown at level 0.0364, step 2, values float32
> volume #4 step 1
> volume #4 level 0.1001
> select add #4
17056 atoms, 17370 bonds, 8 pseudobonds, 2138 residues, 4 models selected
> select subtract #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,0.92101,0,1,0,7.0304,0,0,1,31.781
> ui tool show "Fit in Map"
> fitmap #4 inMap #3
Fit map cryosparc_P605_J199_006_volume_map_sharp-2.mrc in map
J198_sharp_844dimer.mrc using 162234 points
correlation = 0.3588, correlation about mean = 0.05967, overlap = 1418
steps = 104, shift = 2.26, angle = 3.04 degrees
Position of cryosparc_P605_J199_006_volume_map_sharp-2.mrc (#4) relative to
J198_sharp_844dimer.mrc (#3) coordinates:
Matrix rotation and translation
0.99876585 -0.02576584 0.04246060 -3.84658731
0.02654903 0.99948570 -0.01798566 6.77426307
-0.04197535 0.01909075 0.99893624 35.19102582
Axis 0.34970068 0.79639068 0.49342814
Axis point 579.45534725 0.00000000 283.79792798
Rotation angle (degrees) 3.03876749
Shift along axis 21.41404805
> transparency sel 50
> select add #3
4 models selected
> transparency sel 0
> transparency sel 50
> select subtract #3
2 models selected
> hide #!2 models
> view matrix models
> #4,0.99877,-0.025766,0.042461,81.38,0.026549,0.99949,-0.017986,-20.998,-0.041975,0.019091,0.99894,35.556
> volume #3 level 0.1439
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.79245,0.22901,0.56531,268.38,-0.43713,-0.85962,-0.26453,373.69,0.42537,-0.45674,0.78131,60.404
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.79245,0.22901,0.56531,233.49,-0.43713,-0.85962,-0.26453,414.49,0.42537,-0.45674,0.78131,60.524
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.89879,0.38526,0.20918,297.16,-0.40703,-0.91059,-0.071834,380.17,0.1628,-0.1497,0.97524,27.447
> view matrix models
> #4,-0.82378,0.55012,-0.13695,325.18,-0.28997,-0.61645,-0.73206,441.18,-0.48714,-0.56334,0.66734,260.92
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.82378,0.55012,-0.13695,255.81,-0.28997,-0.61645,-0.73206,477.98,-0.48714,-0.56334,0.66734,290.09
> view matrix models
> #4,-0.82378,0.55012,-0.13695,255.37,-0.28997,-0.61645,-0.73206,490.33,-0.48714,-0.56334,0.66734,290.55
> fitmap #4 inMap #3
Fit map cryosparc_P605_J199_006_volume_map_sharp-2.mrc in map
J198_sharp_844dimer.mrc using 162234 points
correlation = 0.3528, correlation about mean = 0.06257, overlap = 1885
steps = 104, shift = 3.27, angle = 2.26 degrees
Position of cryosparc_P605_J199_006_volume_map_sharp-2.mrc (#4) relative to
J198_sharp_844dimer.mrc (#3) coordinates:
Matrix rotation and translation
-0.83238877 0.53501317 -0.14453320 262.99796251
-0.29204522 -0.64511626 -0.70606984 492.93211560
-0.47099737 -0.54551438 0.69323557 277.08778933
Axis 0.17769624 0.36131725 -0.91535452
Axis point 224.03957749 266.18576924 -0.00000000
Rotation angle (degrees) 153.14273416
Shift along axis -28.79493491
> view matrix models
> #4,-0.83239,0.53501,-0.14453,269.81,-0.29205,-0.64512,-0.70607,484.42,-0.471,-0.54551,0.69324,283.33
> fitmap #4 inMap #3
Fit map cryosparc_P605_J199_006_volume_map_sharp-2.mrc in map
J198_sharp_844dimer.mrc using 162234 points
correlation = 0.349, correlation about mean = 0.08891, overlap = 1822
steps = 120, shift = 2.51, angle = 1.79 degrees
Position of cryosparc_P605_J199_006_volume_map_sharp-2.mrc (#4) relative to
J198_sharp_844dimer.mrc (#3) coordinates:
Matrix rotation and translation
-0.83643465 0.53605824 -0.11409927 264.67139978
-0.31215384 -0.63707546 -0.70476581 488.32635270
-0.45048536 -0.55387401 0.70020463 281.34997623
Axis 0.16314889 0.36371109 -0.91711323
Axis point 224.42630810 263.77228896 0.00000000
Rotation angle (degrees) 152.45559949
Shift along axis -37.23923300
> view matrix models
> #4,-0.83643,0.53606,-0.1141,265.33,-0.31215,-0.63708,-0.70477,487.93,-0.45049,-0.55387,0.7002,273.28
> fitmap #4 inMap #3
Fit map cryosparc_P605_J199_006_volume_map_sharp-2.mrc in map
J198_sharp_844dimer.mrc using 162234 points
correlation = 0.8776, correlation about mean = 0.6501, overlap = 7275
steps = 256, shift = 4.78, angle = 15.9 degrees
Position of cryosparc_P605_J199_006_volume_map_sharp-2.mrc (#4) relative to
J198_sharp_844dimer.mrc (#3) coordinates:
Matrix rotation and translation
-0.75570795 0.65333370 -0.04539361 211.34363144
-0.53115608 -0.65198155 -0.54110377 502.96070912
-0.38311712 -0.38480532 0.83972980 200.79424215
Axis 0.12588748 0.27201271 -0.95402381
Axis point 212.04283583 240.91597100 0.00000000
Rotation angle (degrees) 141.62642468
Shift along axis -28.14526518
> hide #!3 models
> show #!2 models
> hide #!2 models
> close #2
> combine #1 name 844-monomer-init
> ui mousemode right select
Drag select of 1620 residues, 6 pseudobonds
> select up
13914 atoms, 14164 bonds, 6 pseudobonds, 1768 residues, 4 models selected
> select up
15632 atoms, 15922 bonds, 6 pseudobonds, 1976 residues, 4 models selected
> select up
15844 atoms, 16142 bonds, 6 pseudobonds, 1980 residues, 4 models selected
> select up
34112 atoms, 34740 bonds, 16 pseudobonds, 4276 residues, 4 models selected
> select down
15844 atoms, 16142 bonds, 6 pseudobonds, 1980 residues, 4 models selected
> select down
15632 atoms, 15922 bonds, 6 pseudobonds, 1976 residues, 4 models selected
> select add #1
24872 atoms, 25331 bonds, 11 pseudobonds, 3126 residues, 4 models selected
> select subtract #1
7816 atoms, 7961 bonds, 3 pseudobonds, 988 residues, 2 models selected
> hide #!1 models
> select clear
Drag select of 515 residues
> select up
4554 atoms, 4630 bonds, 582 residues, 1 model selected
> select up
7256 atoms, 7395 bonds, 919 residues, 1 model selected
> select up
7460 atoms, 7598 bonds, 944 residues, 1 model selected
> select down
7256 atoms, 7395 bonds, 919 residues, 1 model selected
> hide #!4 models
> delete atoms sel
> delete bonds sel
Drag select of 55 residues
> select up
508 atoms, 513 bonds, 63 residues, 1 model selected
> select down
440 atoms, 55 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!3 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> open /Users/oswanson/Desktop/RdRp/844/Lee-AF-ref.pdb
> open
> /Users/oswanson/Downloads/fold_lee_rdrp_trimer_dimer/fold_lee_rdrp_trimer_dimer_model_0.cif
Chain information for fold_lee_rdrp_trimer_dimer_model_0.cif #5
---
Chain | Description
A B | .
C D | .
E F | .
> hide #!1 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #5 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 844-monomer-init, chain Ba (#2) with
fold_lee_rdrp_trimer_dimer_model_0.cif, chain C (#5), sequence alignment score
= 2535.7
RMSD between 429 pruned atom pairs is 0.667 angstroms; (across all 538 pairs:
1.562)
> hide #!2 models
> select add #5
35830 atoms, 36512 bonds, 4496 residues, 1 model selected
> hide sel atoms
> color sel byhetero
> color sel bychain
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> select clear
Drag select of 218 residues
> select up
2781 atoms, 2813 bonds, 345 residues, 4 models selected
> select up
17915 atoms, 18256 bonds, 2248 residues, 4 models selected
> hide sel cartoons
> show #!2 models
> hide #!3 models
> hide #!5 models
> select #2/a:614
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 3 residues, 1 model selected
> select up
120 atoms, 122 bonds, 14 residues, 1 model selected
> show #!5 models
> hide #!5 models
> ui tool show "Change Chain IDs"
> changechains sel Ba
Chain IDs of 14 residues changed
> color sel bychain
> select up
4301 atoms, 4372 bonds, 552 residues, 1 model selected
> show #!1 models
> hide #!2 models
> open /Users/oswanson/Desktop/RdRp/844/J198_844-dimer_init-coot-2.pdb
Summary of feedback from opening
/Users/oswanson/Desktop/RdRp/844/J198_844-dimer_init-coot-2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 THR a 36 GLU a 48 1 13
Start residue of secondary structure not found: HELIX 2 2 LEU a 85 GLU a 98 1
14
Start residue of secondary structure not found: HELIX 3 3 LEU a 102 VAL a 116
1 15
Start residue of secondary structure not found: HELIX 4 4 VAL a 119 THR a 123
5 5
Start residue of secondary structure not found: HELIX 5 5 ALA a 139 ASN a 153
1 15
123 messages similar to the above omitted
Chain information for J198_844-dimer_init-coot-2.pdb #6
---
Chain | Description
Aa | No description available
Ab | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Ca | No description available
> close #6
> select #1/Ca:166
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
91 atoms, 91 bonds, 12 residues, 1 model selected
> select up
118 atoms, 120 bonds, 15 residues, 1 model selected
> select up
152 atoms, 155 bonds, 19 residues, 1 model selected
> select up
449 atoms, 461 bonds, 55 residues, 1 model selected
> select up
551 atoms, 564 bonds, 69 residues, 1 model selected
> select up
641 atoms, 657 bonds, 80 residues, 1 model selected
> select up
17056 atoms, 17370 bonds, 2138 residues, 1 model selected
> select down
641 atoms, 657 bonds, 80 residues, 1 model selected
> color sel orange red
> ui tool show "Color Actions"
> select #1/Ba:253
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
158 atoms, 158 bonds, 20 residues, 1 model selected
> select up
2064 atoms, 2103 bonds, 265 residues, 1 model selected
> select up
2146 atoms, 2185 bonds, 277 residues, 1 model selected
> select up
2652 atoms, 2698 bonds, 341 residues, 1 model selected
> select up
2715 atoms, 2758 bonds, 350 residues, 1 model selected
> select up
4076 atoms, 4144 bonds, 526 residues, 1 model selected
> select up
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> select up
17056 atoms, 17370 bonds, 2138 residues, 1 model selected
> select down
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> select add #1/a:613
4198 atoms, 4265 bonds, 540 residues, 1 model selected
> select up
4224 atoms, 4291 bonds, 543 residues, 1 model selected
> select up
5808 atoms, 5912 bonds, 739 residues, 1 model selected
> select down
4224 atoms, 4291 bonds, 543 residues, 1 model selected
> select clear
> select #1/a:613
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
43 atoms, 41 bonds, 5 residues, 1 model selected
> select up
1627 atoms, 1662 bonds, 201 residues, 1 model selected
> select up
1686 atoms, 1720 bonds, 209 residues, 1 model selected
> select up
2168 atoms, 2211 bonds, 270 residues, 1 model selected
> select up
2210 atoms, 2251 bonds, 276 residues, 1 model selected
> select down
2168 atoms, 2211 bonds, 270 residues, 1 model selected
> select down
1686 atoms, 1720 bonds, 209 residues, 1 model selected
> select down
1627 atoms, 1662 bonds, 201 residues, 1 model selected
> select down
43 atoms, 41 bonds, 5 residues, 1 model selected
> select down
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
43 atoms, 41 bonds, 5 residues, 1 model selected
> select up
1627 atoms, 1662 bonds, 201 residues, 1 model selected
> select down
43 atoms, 41 bonds, 5 residues, 1 model selected
> select #1/Ba:112
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
113 atoms, 113 bonds, 15 residues, 1 model selected
> select up
1165 atoms, 1186 bonds, 151 residues, 1 model selected
> select up
1174 atoms, 1194 bonds, 152 residues, 1 model selected
> select up
1337 atoms, 1358 bonds, 172 residues, 1 model selected
> select up
1358 atoms, 1378 bonds, 176 residues, 1 model selected
> select up
3401 atoms, 3461 bonds, 437 residues, 1 model selected
> select up
3468 atoms, 3529 bonds, 447 residues, 1 model selected
> select up
3817 atoms, 3884 bonds, 492 residues, 1 model selected
> select up
3864 atoms, 3929 bonds, 499 residues, 1 model selected
> select up
4076 atoms, 4144 bonds, 526 residues, 1 model selected
> select up
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> select up
17056 atoms, 17370 bonds, 2138 residues, 1 model selected
> select down
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains #* B
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (B/207/)
> select #1/Ab:466
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
159 atoms, 161 bonds, 20 residues, 1 model selected
> select up
316 atoms, 321 bonds, 39 residues, 1 model selected
> select up
453 atoms, 460 bonds, 57 residues, 1 model selected
> select up
2413 atoms, 2458 bonds, 303 residues, 1 model selected
> select up
2440 atoms, 2484 bonds, 307 residues, 1 model selected
> select up
3126 atoms, 3184 bonds, 392 residues, 1 model selected
> select up
3207 atoms, 3265 bonds, 403 residues, 1 model selected
> select up
4013 atoms, 4093 bonds, 503 residues, 1 model selected
> select up
17056 atoms, 17370 bonds, 2138 residues, 1 model selected
> select down
4013 atoms, 4093 bonds, 503 residues, 1 model selected
> changechains sel A
Chain IDs of 503 residues changed
> select #1/Ba:285
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
119 atoms, 118 bonds, 16 residues, 1 model selected
> select up
2064 atoms, 2103 bonds, 265 residues, 1 model selected
> select up
2146 atoms, 2185 bonds, 277 residues, 1 model selected
> select up
2652 atoms, 2698 bonds, 341 residues, 1 model selected
> select up
2715 atoms, 2758 bonds, 350 residues, 1 model selected
> select up
4076 atoms, 4144 bonds, 526 residues, 1 model selected
> select up
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> select up
17056 atoms, 17370 bonds, 2138 residues, 1 model selected
> select down
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> select add #1/a:613
4198 atoms, 4265 bonds, 540 residues, 1 model selected
> select up
4224 atoms, 4291 bonds, 543 residues, 1 model selected
> select add #1/a:615
4243 atoms, 4309 bonds, 545 residues, 1 model selected
> select add #1/a:616
4257 atoms, 4321 bonds, 547 residues, 1 model selected
> select add #1/a:617
4272 atoms, 4335 bonds, 549 residues, 1 model selected
> select add #1/a:618
4285 atoms, 4346 bonds, 551 residues, 1 model selected
> select add #1/a:619
4304 atoms, 4364 bonds, 553 residues, 1 model selected
> select add #1/a:620
4322 atoms, 4380 bonds, 555 residues, 1 model selected
> select add #1/a:621
4335 atoms, 4391 bonds, 557 residues, 1 model selected
> select add #1/a:622
4350 atoms, 4404 bonds, 559 residues, 1 model selected
> select add #1/a:611
4359 atoms, 4412 bonds, 560 residues, 1 model selected
> select add #1/a:610
4367 atoms, 4419 bonds, 561 residues, 1 model selected
> select add #1/a:609
4374 atoms, 4425 bonds, 562 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains sel B
Cannot reassign chain ID to only part of polymeric chain (J198_844-dimer_init-
coot-2_plusPB2.pdb #1/a)
> select #1/Ba:528
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
93 atoms, 92 bonds, 13 residues, 1 model selected
> select up
416 atoms, 423 bonds, 55 residues, 1 model selected
> select up
636 atoms, 646 bonds, 83 residues, 1 model selected
> select up
2739 atoms, 2786 bonds, 354 residues, 1 model selected
> select up
2859 atoms, 2906 bonds, 368 residues, 1 model selected
> select up
3016 atoms, 3064 bonds, 387 residues, 1 model selected
> select up
3032 atoms, 3079 bonds, 389 residues, 1 model selected
> select up
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> select up
17056 atoms, 17370 bonds, 2138 residues, 1 model selected
> select down
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> changechains sel B
Chain IDs of 538 residues changed
> changechains sel B
Chain IDs of 0 residues changed
> select #1/Ca:166
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
91 atoms, 91 bonds, 12 residues, 1 model selected
> select up
118 atoms, 120 bonds, 15 residues, 1 model selected
> select up
152 atoms, 155 bonds, 19 residues, 1 model selected
> select up
449 atoms, 461 bonds, 55 residues, 1 model selected
> select up
551 atoms, 564 bonds, 69 residues, 1 model selected
> select up
641 atoms, 657 bonds, 80 residues, 1 model selected
> select up
17056 atoms, 17370 bonds, 2138 residues, 1 model selected
> select down
641 atoms, 657 bonds, 80 residues, 1 model selected
> changechains sel C
Chain IDs of 80 residues changed
> select #1/a:483
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
79 atoms, 79 bonds, 10 residues, 1 model selected
> select up
277 atoms, 281 bonds, 35 residues, 1 model selected
> select up
333 atoms, 335 bonds, 43 residues, 1 model selected
> select up
1269 atoms, 1290 bonds, 158 residues, 1 model selected
> select up
1389 atoms, 1409 bonds, 174 residues, 1 model selected
> select up
3122 atoms, 3180 bonds, 388 residues, 1 model selected
> select up
3138 atoms, 3195 bonds, 390 residues, 1 model selected
> select up
3561 atoms, 3631 bonds, 443 residues, 1 model selected
> select up
3570 atoms, 3639 bonds, 444 residues, 1 model selected
> select up
3825 atoms, 3899 bonds, 477 residues, 1 model selected
> changechains sel D
Cannot reassign chain ID to only part of polymeric chain (J198_844-dimer_init-
coot-2_plusPB2.pdb #1/a)
> changechains sel a D
Cannot reassign chain ID to only part of polymeric chain (J198_844-dimer_init-
coot-2_plusPB2.pdb #1/a)
> select #1/Bb:141
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
73 atoms, 72 bonds, 11 residues, 1 model selected
> select up
925 atoms, 941 bonds, 120 residues, 1 model selected
> select up
1051 atoms, 1070 bonds, 136 residues, 1 model selected
> select up
1252 atoms, 1278 bonds, 161 residues, 1 model selected
> select up
1300 atoms, 1325 bonds, 167 residues, 1 model selected
> select up
1415 atoms, 1441 bonds, 181 residues, 1 model selected
> select up
1436 atoms, 1461 bonds, 185 residues, 1 model selected
> select up
3513 atoms, 3579 bonds, 450 residues, 1 model selected
> select up
3546 atoms, 3611 bonds, 455 residues, 1 model selected
> select up
3686 atoms, 3751 bonds, 475 residues, 1 model selected
> select up
3871 atoms, 3940 bonds, 497 residues, 1 model selected
> select up
17056 atoms, 17370 bonds, 2138 residues, 1 model selected
> select down
3871 atoms, 3940 bonds, 497 residues, 1 model selected
> changechains sel E
Chain IDs of 497 residues changed
> select #1/a:612
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 3 residues, 1 model selected
> select up
120 atoms, 122 bonds, 14 residues, 1 model selected
> changechains sel a E
Cannot reassign chain ID to only part of polymeric chain (J198_844-dimer_init-
coot-2_plusPB2.pdb #1/a)
> select up
127 atoms, 128 bonds, 15 residues, 1 model selected
> changechains #* D
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (D/207/)
> show #!3 models
> changechains #* D
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (D/207/)
> select clear
> select #1/a:207
7 atoms, 6 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/a:509
4 atoms, 3 bonds, 1 residue, 1 model selected
> changechains #* D
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (D/208/)
> select clear
> select #3/D
Nothing selected
> select #1/D
Nothing selected
> hide #!3 models
> select clear
> select #1/a:224
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
77 atoms, 78 bonds, 9 residues, 1 model selected
> select up
257 atoms, 261 bonds, 33 residues, 1 model selected
> select up
273 atoms, 276 bonds, 35 residues, 1 model selected
> select up
696 atoms, 712 bonds, 88 residues, 1 model selected
> select up
720 atoms, 735 bonds, 91 residues, 1 model selected
> select up
1718 atoms, 1750 bonds, 215 residues, 1 model selected
> select up
1728 atoms, 1759 bonds, 217 residues, 1 model selected
> select up
2034 atoms, 2071 bonds, 254 residues, 1 model selected
> select up
2055 atoms, 2092 bonds, 256 residues, 1 model selected
> select up
2311 atoms, 2352 bonds, 289 residues, 1 model selected
> select up
2341 atoms, 2381 bonds, 293 residues, 1 model selected
> select up
2987 atoms, 3040 bonds, 373 residues, 1 model selected
> select up
2996 atoms, 3048 bonds, 374 residues, 1 model selected
> select up
3818 atoms, 3892 bonds, 476 residues, 1 model selected
> select up
4044 atoms, 4124 bonds, 492 residues, 1 model selected
> select up
17049 atoms, 17363 bonds, 2137 residues, 1 model selected
> select down
4044 atoms, 4124 bonds, 492 residues, 1 model selected
> select down
3818 atoms, 3892 bonds, 476 residues, 1 model selected
> changechains sel D
Cannot reassign chain ID to only part of polymeric chain (J198_844-dimer_init-
coot-2_plusPB2.pdb #1/a)
> changechains sel a D
Cannot reassign chain ID to only part of polymeric chain (J198_844-dimer_init-
coot-2_plusPB2.pdb #1/a)
> changechains a D
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (D/507/)
> color sel cyan
> select #1/A
4013 atoms, 4093 bonds, 1 pseudobond, 503 residues, 2 models selected
> color sel cyan
> color sel dark blue
> select #1/a:456
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
159 atoms, 161 bonds, 20 residues, 1 model selected
> select up
316 atoms, 321 bonds, 39 residues, 1 model selected
> select up
448 atoms, 453 bonds, 56 residues, 1 model selected
> select up
1615 atoms, 1640 bonds, 201 residues, 1 model selected
> select up
1661 atoms, 1684 bonds, 207 residues, 1 model selected
> select up
2730 atoms, 2779 bonds, 340 residues, 1 model selected
> select up
2748 atoms, 2795 bonds, 342 residues, 1 model selected
> select up
3818 atoms, 3892 bonds, 476 residues, 1 model selected
> select up
4044 atoms, 4124 bonds, 492 residues, 1 model selected
> select down
3818 atoms, 3892 bonds, 476 residues, 1 model selected
> color sel dark blue
> select #1/B:106
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
113 atoms, 113 bonds, 15 residues, 1 model selected
> select up
1165 atoms, 1186 bonds, 151 residues, 1 model selected
> select up
1174 atoms, 1194 bonds, 152 residues, 1 model selected
> select up
1337 atoms, 1358 bonds, 172 residues, 1 model selected
> select up
1358 atoms, 1378 bonds, 176 residues, 1 model selected
> select up
3401 atoms, 3461 bonds, 437 residues, 1 model selected
> select up
3468 atoms, 3529 bonds, 447 residues, 1 model selected
> select up
3817 atoms, 3884 bonds, 492 residues, 1 model selected
> select up
3864 atoms, 3929 bonds, 499 residues, 1 model selected
> select up
4076 atoms, 4144 bonds, 526 residues, 1 model selected
> select up
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> select up
17049 atoms, 17363 bonds, 2137 residues, 1 model selected
> select down
4181 atoms, 4250 bonds, 538 residues, 1 model selected
> color sel cyan
> select #1/E:148
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
73 atoms, 72 bonds, 11 residues, 1 model selected
> select up
925 atoms, 941 bonds, 120 residues, 1 model selected
> select up
1051 atoms, 1070 bonds, 136 residues, 1 model selected
> select up
1252 atoms, 1278 bonds, 161 residues, 1 model selected
> select up
1300 atoms, 1325 bonds, 167 residues, 1 model selected
> select up
1415 atoms, 1441 bonds, 181 residues, 1 model selected
> select up
1436 atoms, 1461 bonds, 185 residues, 1 model selected
> select up
3513 atoms, 3579 bonds, 450 residues, 1 model selected
> select up
3546 atoms, 3611 bonds, 455 residues, 1 model selected
> select up
3686 atoms, 3751 bonds, 475 residues, 1 model selected
> select up
3871 atoms, 3940 bonds, 497 residues, 1 model selected
> select up
17049 atoms, 17363 bonds, 2137 residues, 1 model selected
> select down
3871 atoms, 3940 bonds, 497 residues, 1 model selected
> color sel cyan
> select clear
> select #1/a:613
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
43 atoms, 41 bonds, 5 residues, 1 model selected
> select up
1627 atoms, 1662 bonds, 201 residues, 1 model selected
> select down
43 atoms, 41 bonds, 5 residues, 1 model selected
> select add #1/a:615
62 atoms, 59 bonds, 7 residues, 1 model selected
> select add #1/a:616
76 atoms, 71 bonds, 9 residues, 1 model selected
> select add #1/a:618
89 atoms, 82 bonds, 11 residues, 1 model selected
> select add #1/a:617
104 atoms, 96 bonds, 13 residues, 1 model selected
> select add #1/a:619
123 atoms, 114 bonds, 15 residues, 1 model selected
> select add #1/a:620
141 atoms, 130 bonds, 17 residues, 1 model selected
> select add #1/a:621
154 atoms, 141 bonds, 19 residues, 1 model selected
> select add #1/a:622
169 atoms, 154 bonds, 21 residues, 1 model selected
> select add #1/a:611
178 atoms, 162 bonds, 22 residues, 1 model selected
> select add #1/a:610
186 atoms, 169 bonds, 23 residues, 1 model selected
> select add #1/a:609
193 atoms, 175 bonds, 24 residues, 1 model selected
> color sel cyan
> select clear
> show #!2 models
> hide #!2 models
> close #2
> show #!3 models
> combine #1 name 844_monomer_init
> hide #!1 models
> hide #!3 models
Drag select of 384 residues, 3 pseudobonds
> select up
4731 atoms, 4807 bonds, 3 pseudobonds, 595 residues, 2 models selected
> select up
7689 atoms, 7832 bonds, 3 pseudobonds, 973 residues, 2 models selected
> select up
7915 atoms, 8064 bonds, 3 pseudobonds, 989 residues, 2 models selected
> select up
17049 atoms, 17363 bonds, 8 pseudobonds, 2137 residues, 2 models selected
> select down
7915 atoms, 8064 bonds, 3 pseudobonds, 989 residues, 2 models selected
> select down
7689 atoms, 7832 bonds, 3 pseudobonds, 973 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> select #2/a:613
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
28 atoms, 28 bonds, 3 residues, 1 model selected
> select up
120 atoms, 122 bonds, 14 residues, 1 model selected
> select up
226 atoms, 232 bonds, 16 residues, 1 model selected
> ui tool show "Change Chain IDs"
> changechains #* B
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (B/507/)
> changechains #* D
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (D/208/)
> show #!5 models
> hide #!5 models
> select #2/Bc:9
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
57 atoms, 60 bonds, 6 residues, 1 model selected
> select up
130 atoms, 134 bonds, 16 residues, 1 model selected
> changechains #* B
Proposed chain ID change would produce multiple residues with the samechain-
ID/number/insertion-code combo (B/507/)
> color sel cyan
> select clear
> show #!4 models
> select ::name="844A"
388 atoms, 408 bonds, 4 residues, 2 models selected
> show sel & #!2 atoms
> select clear
> color #4 white models
> select clear
> surface dust #4 size 7.18
> select #2/a:806@C19
1 atom, 1 residue, 1 model selected
> select up
97 atoms, 102 bonds, 1 residue, 1 model selected
> select up
226 atoms, 232 bonds, 16 residues, 1 model selected
> select down
97 atoms, 102 bonds, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select ::name="844A"
291 atoms, 306 bonds, 3 residues, 2 models selected
> select clear
> select ::name="844A"
291 atoms, 306 bonds, 3 residues, 2 models selected
> ui tool show "Side View"
> view sel
> select clear
> select H
141 atoms, 3 residues, 2 models selected
> delete atoms (#!2 & sel)
> delete bonds (#!2 & sel)
> hide #!4 models
> show #!3 models
> hide #!2 models
> show #!1 models
> select add #1
17049 atoms, 17363 bonds, 8 pseudobonds, 2137 residues, 2 models selected
> select subtract #1
Nothing selected
> select ::name="844A"
244 atoms, 259 bonds, 3 residues, 2 models selected
> show sel & #!1 atoms
> select H
94 atoms, 2 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!3 models
> select #1/B:556
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
50 atoms, 55 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true color #797979 reveal true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
69 contacts
atom1 atom2 overlap distance
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 O49 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 455 CE 0.620 2.760
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C50 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ARG 574 CA 0.565 3.195
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C50 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 455 CE 0.510 3.250
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C06 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 455 CE 0.309 3.331
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C37 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ARG 574 CD 0.258 3.502
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C31 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B TYR 556 CD2 0.229 3.411
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C12 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 421 CD2 0.216 3.424
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C13 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 421 CD2 0.198 3.382
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C07 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 455 CE 0.189 3.391
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C32 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A THR 463 OG1 0.184 3.156
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C50 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ARG 574 CB 0.183 3.577
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C10 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE 0.160 3.420
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C01 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ASN 447 OD1 0.124 3.236
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C15 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE 0.107 3.473
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C47 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A SER 299 OG 0.083 3.137
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C11 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE 0.073 3.567
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C08 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE 0.064 3.576
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C14 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 421 CD2 0.020 3.560
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C02 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 577 CD1 0.015 3.745
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C47 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B VAL 567 CG1 0.013 3.627
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 F17 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 419 O 0.010 2.750
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C11 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 421 CD2 0.002 3.638
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C41 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 419 CD1 -0.004 3.644
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C38 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B ALA 552 CB -0.010 3.770
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C06 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A PHE 637 CZ -0.017 3.537
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C36 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE -0.020 3.780
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C31 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B ASP 553 OD1 -0.046 3.406
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 F16 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ALA 418 CB -0.087 3.247
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C50 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 455 CG -0.101 3.861
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C02 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 577 CD2 -0.116 3.876
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 F17 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ASP 420 O -0.129 2.889
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C14 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE -0.140 3.720
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C38 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B ALA 552 O -0.143 3.503
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C01 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ILE 446 CG2 -0.151 3.911
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 S46 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B HIS 561 CE1 -0.173 3.715
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 O49 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 455 CG -0.181 3.561
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C12 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE -0.181 3.821
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 F17 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ASP 420 C -0.185 3.165
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 F16 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 419 O -0.188 2.948
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 N48 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A SER 299 OG -0.194 2.879
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C36 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 SD -0.200 3.862
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C15 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 421 CD2 -0.202 3.782
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C05 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A SER 452 CB -0.207 3.847
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C32 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A THR 463 CG2 -0.209 3.969
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 O18 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A PRO 422 CD -0.216 3.596
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 F17 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 419 C -0.223 3.203
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C10 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 421 CD2 -0.224 3.804
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C31 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B TYR 556 CE2 -0.234 3.874
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C01 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ASN 447 CA -0.239 3.999
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C37 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B ALA 552 CB -0.258 4.018
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C29 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A LEU 460 CD2 -0.272 4.032
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C50 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 455 SD -0.272 3.934
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C31 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B TYR 556 CG -0.275 3.855
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C27 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B TYR 556 CD1 -0.279 3.919
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 N48 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A SER 299 CB -0.283 3.788
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C32 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A THR 463 CB -0.292 4.052
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C20 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ASP 420 O -0.292 3.532
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C09 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE -0.301 3.881
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C13 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE -0.307 3.887
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C32 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A VAL 459 CG1 -0.334 4.094
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C38 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B ALA 552 CA -0.336 4.096
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C50 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A VAL 459 CG2 -0.339 4.099
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 N48 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B VAL 567 CG1 -0.345 3.850
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C06 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A SER 452 CA -0.347 3.987
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C23 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 456 CE -0.350 3.990
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C32 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A MET 571 CG -0.382 4.142
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 C19 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ASP 420 O -0.389 3.479
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 O33 J198_844-dimer_init-coot-2_plusPB2.pdb #1/A ARG 574 CD -0.398 3.778
J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 O18 J198_844-dimer_init-coot-2_plusPB2.pdb #1/B ALA 552 CB -0.398 3.778
69 contacts
> style sel stick
Changed 76 atom styles
> select up
232 atoms, 226 bonds, 24 residues, 1 model selected
> style sel stick
Changed 232 atom styles
> color sel byhetero
> show #!3 models
> hide #1.2 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
50 atoms, 55 bonds, 1 residue, 1 model selected
> color sel dark magenta
> color sel hot pink
> color sel byhetero
> select clear
> select add #3
4 models selected
> color zone #3 near #1 distance 4.31
> transparency sel 0
> select subtract #3
Nothing selected
> select add #3
4 models selected
> transparency #3 70
> color sel bychain
> color zone #3 near #1 distance 4.31
> select #1/B
4181 atoms, 4250 bonds, 2 pseudobonds, 538 residues, 2 models selected
> color sel cyan
> select #1/b
122 atoms, 118 bonds, 11 residues, 1 model selected
> color magenta
> color sel magenta
> select #1/A
4013 atoms, 4093 bonds, 1 pseudobond, 503 residues, 2 models selected
> color sel dark blue
> select #3
4 models selected
> color zone #3 near #1 distance 4.31
> transparency #3 80
> select #1
16955 atoms, 17269 bonds, 77 pseudobonds, 2137 residues, 3 models selected
> color sel byhetero
> undo
> color sel byhetero
> select clear
> select add #3
4 models selected
> ui tool show "Volume Viewer"
> select #3
4 models selected
> select clear
> lighting soft
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
50 atoms, 55 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #fffb00 restrict cross interModel false intraMol false
> intraRes false select true reveal true log true
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 J198_844-dimer_init-coot-2_plusPB2.pdb
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
J198_844-dimer_init-coot-2_plusPB2.pdb #1/A SER 299 OG J198_844-dimer_init-coot-2_plusPB2.pdb #1/b 844A 801 N48 no hydrogen 2.879 N/A
1 hydrogen bonds found
> hide #!3 models
> hide #1.3 models
> show #1.2 models
> show #1.3 models
> select clear
> ui tool show "Side View"
> open /Users/oswanson/Downloads/cryosparc_P605_J205_map_locres.mrc
Opened cryosparc_P605_J205_map_locres.mrc as #6, grid size 512,512,512, pixel
0.718, shown at level 3.74, step 2, values float32
> ui tool show "Volume Viewer"
> hide #!1 models
> combine #3 name dimer_map_localres
No structures specified
> ui tool show "Surface Color"
> color sample #3.1 map #6 palette 3.5,#ff0000:3,#ffffff:2.5,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 1.836, mean 2.821, maximum 12.66
> show #!1 models
> select add #3
2 models selected
> transparency sel 50
> hide #!1 models
> select clear
> select #3
2 models selected
> select clear
> show #!1 models
> select #1/b:801@C38
1 atom, 1 residue, 1 model selected
> select up
50 atoms, 55 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> select ~sel & ##selected
16905 atoms, 17214 bonds, 78 pseudobonds, 2136 residues, 4 models selected
> hide sel atoms
> hide sel cartoons
> select clear
> select add #1
16955 atoms, 17269 bonds, 78 pseudobonds, 2137 residues, 4 models selected
> show sel cartoons
> select clear
> select ::name="844A"
150 atoms, 165 bonds, 3 residues, 2 models selected
> show sel & #!1 atoms
> select clear
> select #3
2 models selected
> hide #!1 models
> show #!1 models
> hide #!3 models
> select #1/a:806@C43
1 atom, 1 residue, 1 model selected
> select up
50 atoms, 55 bonds, 1 residue, 1 model selected
> select up
3997 atoms, 4077 bonds, 492 residues, 1 model selected
> select down
50 atoms, 55 bonds, 1 residue, 1 model selected
> color sel magenta
> color sel byhetero
> show #!3 models
> select clear
> surface dust #3 size 7.18
> volume #3 level 0.1078
> color sample #3.1 map #6 palette 3.5,#ff0000:3,#ffffff:2.5,#0000ff
> outsideColor #808080
Map values for surface "surface": minimum 0, mean 2.902, maximum 26.12
> transparency #3.1 50
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/oswanson/Desktop/movie4.mp4
Movie saved to /Users/oswanson/Desktop/movie4.mp4
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac15,13
Model Number: Z1BP0006TLL/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 13822.41.1
OS Loader Version: 13822.41.1
Software:
System Software Overview:
System Version: macOS 26.1 (25B78)
Kernel Version: Darwin 25.1.0
Time since boot: 23 hours, 41 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2880 x 1864 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
LG Ultra HD:
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
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 2.5.1
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: 1.6.2
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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: 1.19.1
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: 2.5.2
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: 1.45.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 14 hours 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 , 13 hours ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
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."
The current ChimeraX release candidate and daily build use a newer Qt version where this crash has not been reported so you may want to try those.