![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 23 hours ago
Closed 21 hours ago
#20134 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-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.10rc202506100450 (2025-06-10 04:50:02 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 0x0000000206eff100 (most recent call first):
File "/Applications/ChimeraX-1.10-rc2025.06.10.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-rc2025.06.10.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-rc2025.06.10.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.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.map._map, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 61)
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"procRole" : "Background",
"version" : 2,
"userID" : 1533080713,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
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"codeSigningMonitor" : 2,
"incident" : "824EADAE-27B8-49BF-BA67-792C8DFA8D20",
"pid" : 22775,
"translated" : false,
"cpuType" : "ARM-64",
"procLaunch" : "2026-04-02 22:47:26.0355 -0400",
"procStartAbsTime" : 5193175762842,
"procExitAbsTime" : 6722574093641,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10-rc2025.06.10.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.10.0","CFBundleVersion":"1.10.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"7907C893-5782-5E7A-B003-32308BD8FC6D","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "70228687-E509-459D-AB31-FABE2482F60C",
"appleIntelligenceStatus" : {"state":"available"},
"developerMode" : 1,
"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" : "8589CC38-99E9-4D39-A76C-779C2F48B65D",
"wakeTime" : 24,
"sleepWakeUUID" : "F313F6DB-8DAE-4EBC-AA16-F54504747946",
"sip" : "enabled",
"vmRegionInfo" : "0xffffb2833dd137ec 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":"0x0000000000000001, 0x3bf5b2833dd137ec","rawCodes":[1,4320555694279440364],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x3bf5b2833dd137ec -> 0xffffb2833dd137ec (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":22775},
"vmregioninfo" : "0xffffb2833dd137ec 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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===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/bhogeba/T4_dimeric
> tRNA/Ecoli_M1RNP/3'UAA_T4_tRNA/M1_Holo_T4dimer_ternary/Intermediates_and
> active conformer_publication.cxs"
Opened cryosparc_P23_J2582_006_volume_map.mrc as #2, grid size 456,456,456,
pixel 0.909, shown at level 0.103, step 2, values float32
Opened cryosparc_P23_J2372_006_volume_map.mrc as #3, grid size 456,456,456,
pixel 0.909, shown at level 0.139, step 2, values float32
Opened Productive_Ser_5mM_Ca_HoloM1_J1524_map_1.mrc as #6, grid size
384,384,384, pixel 0.999, shown at level 0.0712, step 2, values float32
> view name session-start
opened ChimeraX session
> show #!7 models
> select #1/A
8068 atoms, 9036 bonds, 375 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #5#!7 to #1 & sel
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb, chain A (#5), sequence alignment score
= 1496
RMSD between 156 pruned atom pairs is 1.086 angstroms; (across all 374 pairs:
3.812)
Matchmaker Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb, chain A (#7),
sequence alignment score = 1491.1
RMSD between 208 pruned atom pairs is 0.979 angstroms; (across all 374 pairs:
3.576)
> matchmaker #5#!7 to #1 & sel
Using Nucleic matrix instead of BLOSUM-62 for matching
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb, chain A (#5), sequence alignment score
= 1496
RMSD between 156 pruned atom pairs is 1.086 angstroms; (across all 374 pairs:
3.812)
Matchmaker Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb, chain A (#7),
sequence alignment score = 1491.1
RMSD between 208 pruned atom pairs is 0.979 angstroms; (across all 374 pairs:
3.576)
> select clear
Drag select of 394 atoms, 698 residues, 412 bonds
> hide sel atoms
> select clear
Drag select of 238 atoms, 708 residues, 250 bonds
> hide sel atoms
> select clear
> hide #!7 models
Drag select of 120 atoms, 200 residues, 125 bonds
> hide sel atoms
> select clear
> select add #1/C:0
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #1/C:-1
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #1/C:-2
62 atoms, 66 bonds, 3 residues, 1 model selected
> hide sel atoms
> select add #1/A:333
84 atoms, 90 bonds, 4 residues, 1 model selected
> select add #1/C:76
104 atoms, 111 bonds, 5 residues, 1 model selected
> select add #1/C:75
124 atoms, 132 bonds, 6 residues, 1 model selected
> hide sel atoms
> select add #1/A:254
146 atoms, 156 bonds, 7 residues, 1 model selected
> hide sel atoms
> select add #1/A:332
169 atoms, 181 bonds, 8 residues, 1 model selected
> hide sel atoms
Drag select of 31 atoms, 150 residues, 28 bonds
> ~label sel residues
> select clear
> select add #1/C:-1
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #1/C:-2
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #1/C:0
62 atoms, 66 bonds, 3 residues, 1 model selected
> select add #1/C:75
82 atoms, 87 bonds, 4 residues, 1 model selected
> select add #1/A:295
104 atoms, 111 bonds, 5 residues, 1 model selected
> select add #1/C:76
124 atoms, 132 bonds, 6 residues, 1 model selected
> select add #1/A:296
147 atoms, 157 bonds, 7 residues, 1 model selected
> select add #1/A:332
170 atoms, 182 bonds, 8 residues, 1 model selected
> ~label sel residues
> select add #1/C:77
193 atoms, 207 bonds, 9 residues, 1 model selected
> select clear
> select #1/C:77
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/C:76
43 atoms, 46 bonds, 2 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide sel atoms
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show sel atoms
> hide sel atoms
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select clear
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 23 atom styles
> select clear
> select add #1/A:68
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #1/A:67
45 atoms, 49 bonds, 2 residues, 1 model selected
> select add #1/A:69
65 atoms, 70 bonds, 3 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> select add #1/C:77@O3'
66 atoms, 70 bonds, 4 residues, 1 model selected
> select up
88 atoms, 97 bonds, 4 residues, 1 model selected
> select up
90 atoms, 99 bonds, 5 residues, 1 model selected
> select up
108 atoms, 119 bonds, 5 residues, 1 model selected
> select add #1/A:352
130 atoms, 143 bonds, 6 residues, 1 model selected
> select add #1/A:351
152 atoms, 167 bonds, 7 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide sel atoms
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> color sel byhetero
> show (sel-residues & sidechain) target ab
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> hide sel atoms
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 152 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 152 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 152 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 152 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 152 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel ladder
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select Mg
26 atoms, 26 residues, 2 models selected
> show (#!1 & sel) target ab
> select clear
> select add #1/D:14@MG
1 atom, 1 residue, 1 model selected
> select add #1/C:77@OP2
2 atoms, 2 residues, 1 model selected
> ui tool show Distances
> distance #1/D:14@MG #1/C:77@OP2
Distance between Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb #1/D MG 14 MG and /C G
77 OP2: 11.76Å
> select clear
> select #1/D:14@MG
1 atom, 1 residue, 1 model selected
> color sel red
> color sel blue
> color sel cyan
> color sel orange
> color sel light sea green
> color sel forest green
> ui tool show "Color Actions"
> color sel magenta
> select clear
> hide #!1 models
> show #!1 models
> show #!7 models
> hide #!1 models
> hide #!4 models
> hide #4.1 models
> show #!4 models
> show #4.1 models
> select add #7/A:248
22 atoms, 24 bonds, 1 residue, 1 model selected
> select clear
> select add #7/A:248
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #7/A:254
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #7/A:295
66 atoms, 72 bonds, 3 residues, 1 model selected
> select add #7/C:76
86 atoms, 93 bonds, 4 residues, 1 model selected
Drag select of 2 atoms, 5 residues, 2 bonds
> select clear
Drag select of 115 atoms, 198 residues, 122 bonds
> hide sel atoms
> ~label sel residues
> select #7/A:339
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select add #7/A:248
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #7/C:165
44 atoms, 48 bonds, 2 residues, 1 model selected
> select add #7/C:166
66 atoms, 72 bonds, 3 residues, 1 model selected
> select add #7/A:253
86 atoms, 93 bonds, 4 residues, 1 model selected
> select subtract #7/A:253
66 atoms, 72 bonds, 3 residues, 1 model selected
> select add #7/A:333
88 atoms, 96 bonds, 4 residues, 1 model selected
> select add #7/A:332
111 atoms, 121 bonds, 5 residues, 1 model selected
> hide sel atoms
> select add #7/B:17
122 atoms, 132 bonds, 6 residues, 1 model selected
> select add #7/B:86
133 atoms, 142 bonds, 7 residues, 1 model selected
> select add #7/B:26
144 atoms, 152 bonds, 8 residues, 1 model selected
> select add #7/B:25
152 atoms, 159 bonds, 9 residues, 1 model selected
> select add #7/B:13
163 atoms, 170 bonds, 10 residues, 1 model selected
> hide sel atoms
> select clear
> show #!1 models
> hide #!1 models
> select clear
> select Mg
26 atoms, 26 residues, 2 models selected
> show (#!7 & sel) target ab
> select clear
> select #7/D:14@MG
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> select add #7/C:76
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #7/C:77
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #7/A:68
66 atoms, 71 bonds, 3 residues, 1 model selected
> select add #7/A:67
88 atoms, 95 bonds, 4 residues, 1 model selected
> select add #7/A:69
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #7/A:352
130 atoms, 140 bonds, 6 residues, 1 model selected
> select add #7/A:351
152 atoms, 164 bonds, 7 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> show #!1 models
> hide #!1 models
> color sel byhetero
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> transparency #7/a 80 rings
> transparency #7/a 0 rings
> transparency #7/b 0 rings
> transparency #7/c 0 rings
> show #!1 models
> hide #!1 models
> label sel text "{0.name} {0.number}{0.insertion_code}"
> show #!1 models
> hide #!1 models
> show #5 models
> hide #!7 models
> select add #7
12689 atoms, 14097 bonds, 670 residues, 2 models selected
> transparency #7/c 80 ribbons
> transparency #5/c 80 ribbons
> transparency #5/a 80 ribbons
> transparency #5/b 80 ribbons
> hide #5 atoms
> select clear
> select Ca
5 atoms, 5 residues, 1 model selected
> show sel target ab
> select clear
> select #5/F:5@CA
1 atom, 1 residue, 1 model selected
> select add #5/A:68
24 atoms, 25 bonds, 2 residues, 1 model selected
> select add #5/A:67
46 atoms, 49 bonds, 3 residues, 1 model selected
> select add #5/A:69
66 atoms, 70 bonds, 4 residues, 1 model selected
> select add #5/C:77
89 atoms, 95 bonds, 5 residues, 1 model selected
> select add #5/C:76
109 atoms, 116 bonds, 6 residues, 1 model selected
> select add #5/A:351
131 atoms, 140 bonds, 7 residues, 1 model selected
> select add #5/A:352
153 atoms, 164 bonds, 8 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #5/F:5@CA
1 atom, 1 residue, 1 model selected
> ~label sel residues
> select clear
> select #5/F:5@CA
1 atom, 1 residue, 1 model selected
> color sel magenta
> select clear
> show #!1 models
> show #!7 models
> hide #!1 models
> hide #!5 models
> hide #!7 models
> show #!5 models
> select clear
> select #5/C:77@OP1
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #5/C:76@O3'
24 atoms, 25 bonds, 2 residues, 1 model selected
> select up
43 atoms, 47 bonds, 2 residues, 1 model selected
> select add #5/A:67@P
44 atoms, 47 bonds, 3 residues, 1 model selected
> select up
65 atoms, 71 bonds, 3 residues, 1 model selected
> select add #5/A:68@OP1
66 atoms, 71 bonds, 4 residues, 1 model selected
> select up
88 atoms, 97 bonds, 4 residues, 1 model selected
> select add #5/A:351@O3'
89 atoms, 97 bonds, 5 residues, 1 model selected
> select up
110 atoms, 121 bonds, 5 residues, 1 model selected
> select add #5/A:352@C4'
111 atoms, 122 bonds, 6 residues, 1 model selected
> select subtract #5/A:352@C4'
110 atoms, 121 bonds, 5 residues, 1 model selected
> select add #5/A:352@C4'
111 atoms, 121 bonds, 6 residues, 1 model selected
> select up
132 atoms, 146 bonds, 6 residues, 1 model selected
> select add #5/A:69@O5'
133 atoms, 146 bonds, 7 residues, 1 model selected
> select up
152 atoms, 168 bonds, 7 residues, 1 model selected
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> color sel byhetero
> select clear
> select #5/F:5@CA
1 atom, 1 residue, 1 model selected
> select add #5/C:77@OP1
2 atoms, 2 residues, 1 model selected
> distance #5/F:5@CA #5/C:77@OP1
Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /C G
77 OP1: 2.14Å
> select clear
> show #!1 models
> show #!7 models
> hide #!5 models
> hide #!1 models
> select add #7/C:77@OP1
1 atom, 1 residue, 1 model selected
> select add #7/D:14@MG
2 atoms, 2 residues, 1 model selected
> distance #7/C:77@OP1 #7/D:14@MG
Distance between Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb
#7/C G 77 OP1 and /D MG 14 MG: 10.79Å
> show #!1 models
> show #!5 models
> hide #!1 models
> hide #!7 models
> hide #!5 models
> show #!1 models
> show #!7 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!7 models
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> save /Users/bhogeba/Desktop/image4.png supersample 3
> hide #!7 models
> show #!1 models
> show #!5 models
> hide #!1 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!5 models
> hide #!7 models
> show #!5 models
> save /Users/bhogeba/Desktop/image5.png supersample 3
> show #!1 models
> hide #!5 models
> save /Users/bhogeba/Desktop/image6.png supersample 3
> hide #!1 models
> show #!6 models
> show #!7 models
> hide #!6 models
> save /Users/bhogeba/Desktop/image7.png supersample 3
> show #!5 models
> hide #!7 models
> select add #7
12689 atoms, 14097 bonds, 1 pseudobond, 670 residues, 3 models selected
> select subtract #7
Nothing selected
> select #5/C:161
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/C:162
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #5/C:163
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #5/C:164
83 atoms, 88 bonds, 4 residues, 1 model selected
> select add #5/C:165
105 atoms, 112 bonds, 5 residues, 1 model selected
> select subtract #5/C:161
85 atoms, 91 bonds, 4 residues, 1 model selected
> select subtract #5/C:162
65 atoms, 70 bonds, 3 residues, 1 model selected
> show sel atoms
> nucleotides sel ladder
> nucleotides sel atoms
> style nucleic & sel stick
Changed 65 atom styles
> select add #5/A:294
85 atoms, 91 bonds, 4 residues, 1 model selected
> select add #5/A:295
107 atoms, 115 bonds, 5 residues, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 107 atom styles
> select add #5/A:293
130 atoms, 140 bonds, 6 residues, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 130 atom styles
> select #5/A:50
20 atoms, 21 bonds, 1 residue, 1 model selected
> select clear
> select #5/A:296
23 atoms, 25 bonds, 1 residue, 1 model selected
> select add #5/A:297
46 atoms, 50 bonds, 2 residues, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 46 atom styles
> hide sel atoms
> select clear
> select #5/A:295
22 atoms, 24 bonds, 1 residue, 1 model selected
> select add #5/A:294
42 atoms, 45 bonds, 2 residues, 1 model selected
> select add #5/A:293
65 atoms, 70 bonds, 3 residues, 1 model selected
> select add #5/C:165
87 atoms, 94 bonds, 4 residues, 1 model selected
> select add #5/C:164
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #5/C:163
130 atoms, 140 bonds, 6 residues, 1 model selected
> select subtract #5/C:164
110 atoms, 119 bonds, 5 residues, 1 model selected
> select add #5/C:164
130 atoms, 140 bonds, 6 residues, 1 model selected
> select subtract #5/C:163
107 atoms, 115 bonds, 5 residues, 1 model selected
> select add #5/C:163
130 atoms, 140 bonds, 6 residues, 1 model selected
> color sel byhetero
> select clear
> select add #5/C:164
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/C:165
42 atoms, 45 bonds, 2 residues, 1 model selected
> select subtract #5/C:165
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/A:293
43 atoms, 46 bonds, 2 residues, 1 model selected
> select add #5/A:294
63 atoms, 67 bonds, 3 residues, 1 model selected
> select add #5/A:295
85 atoms, 91 bonds, 4 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select add #5/C:163
108 atoms, 116 bonds, 5 residues, 1 model selected
> select add #5/C:165
130 atoms, 140 bonds, 6 residues, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #5/C:164@O2
1 atom, 1 residue, 1 model selected
> select add #5/A:295@N6
2 atoms, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 select true reveal true retainCurrent true
0 hydrogen bonds found
> select clear
> select add #5/C:164@O4
1 atom, 1 residue, 1 model selected
> select add #5/A:295@N6
2 atoms, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 select true reveal true retainCurrent true
0 hydrogen bonds found
> select clear
> select #5/C:164@O2
1 atom, 1 residue, 1 model selected
> select add #5/A:294@O2
2 atoms, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 select true reveal true retainCurrent true
0 hydrogen bonds found
> select #5/A:295@N1
1 atom, 1 residue, 1 model selected
> select add #5/C:164@N3
2 atoms, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 select true reveal true retainCurrent true
1 hydrogen bonds found
> select clear
> select add #5/C:163@O2'
1 atom, 1 residue, 1 model selected
> select clear
> select #5/C:163@O2'
1 atom, 1 residue, 1 model selected
> select add #5/C:164@O2
2 atoms, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 select true reveal true retainCurrent true
1 hydrogen bonds found
> select clear
> select add #5/C:165@O4'
1 atom, 1 residue, 1 model selected
> select add #5/A:293@O6
2 atoms, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 select true reveal true retainCurrent true
1 hydrogen bonds found
> hbonds sel dashes 6 select true reveal true retainCurrent true
1 hydrogen bonds found
> select #5/A:295
22 atoms, 24 bonds, 1 residue, 1 model selected
> select #5/A:294
20 atoms, 21 bonds, 1 residue, 1 model selected
> save /Users/bhogeba/Desktop/image8.png supersample 3
> select clear
> select #5/A:294
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/C:164
40 atoms, 42 bonds, 2 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 select true reveal true retainCurrent true
8 hydrogen bonds found
> hbonds sel dashes 6 select true reveal true retainCurrent true
15 hydrogen bonds found
> select clear
> select #5/A:295
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> select clear
> select add #5/A:294@O2'
1 atom, 1 pseudobond, 1 residue, 2 models selected
> select add #5/A:295
23 atoms, 24 bonds, 1 pseudobond, 2 residues, 2 models selected
> hbonds delete
> select clear
> select #5/C:164@N3
1 atom, 1 residue, 1 model selected
> select add #5/A:294@O2
2 atoms, 2 residues, 1 model selected
> hbonds select
Missing "select" keyword's argument
> ui tool show H-Bonds
> hbonds sel restrict both select true reveal true
0 hydrogen bonds found
> select #5/C:163@O2'
1 atom, 1 residue, 1 model selected
> select add #5/C:164@N3
2 atoms, 2 residues, 1 model selected
> hbonds sel restrict both select true reveal true
0 hydrogen bonds found
> select #5/A:294@O2
1 atom, 1 residue, 1 model selected
> select #5/A:294@N3
1 atom, 1 residue, 1 model selected
> select #5/A:294
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #5/C:164@N3
1 atom, 1 residue, 1 model selected
> select add #5/A:294@O2
2 atoms, 2 residues, 1 model selected
> hbonds sel restrict both select true reveal true
0 hydrogen bonds found
> select add #5/C:164@N3
1 atom, 1 residue, 1 model selected
> select #5/C:164@O4
1 atom, 1 residue, 1 model selected
> select add #5/A:295@N1
2 atoms, 2 residues, 1 model selected
> select clear
> select #5/A:295@N1
1 atom, 1 residue, 1 model selected
> select add #5/C:164@N3
2 atoms, 2 residues, 1 model selected
> hbonds sel restrict both select true reveal true
1 hydrogen bonds found
> select clear
> select #5/C:163@O2'
1 atom, 1 residue, 1 model selected
> select clear
> select #5/C:164@O2'
1 atom, 1 residue, 1 model selected
> select add #5/A:293@N2
2 atoms, 2 residues, 1 model selected
> hbonds sel restrict both select true reveal true
0 hydrogen bonds found
> select #5/A:295@N1
1 atom, 1 residue, 1 model selected
> select add #5/C:164@N3
2 atoms, 2 residues, 1 model selected
> hbonds sel restrict both select true reveal true
1 hydrogen bonds found
> select clear
> save /Users/bhogeba/Desktop/image9.png supersample 3
> save /Users/bhogeba/Desktop/image10.png supersample 3
> select add #5/C:0
22 atoms, 24 bonds, 1 residue, 1 model selected
> show sel atoms
> nucleotides sel atoms
> style nucleic & sel stick
Changed 22 atom styles
> select clear
> select #5/C:158
20 atoms, 21 bonds, 1 residue, 1 model selected
> select add #5/C:159
40 atoms, 42 bonds, 2 residues, 1 model selected
> select add #5/C:157
63 atoms, 67 bonds, 3 residues, 1 model selected
> show sel atoms
> hide sel atoms
> select clear
> select #5/C:0
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel byhetero
> save /Users/bhogeba/Desktop/image11.png supersample 3
> ui tool show "Model Panel"
> ui tool show "Side View"
> select clear
> select #5/F:2@CA
1 atom, 1 residue, 1 model selected
> color sel hot pink
> color sel orange
> color sel red
> color sel orange red
> color sel orange
> color sel yellow
> color sel orange
> color sel cornflower blue
> color sel light sea green
> color sel dodger blue
> color sel blue
> color sel pale violet red
> color sel deep pink
> color sel magenta
> color sel rebecca purple
> color sel dark slate blue
> color sel slate blue
> color sel medium slate blue
> color sel dim gray
> color sel pale green
> color sel light green
> color sel burly wood
> color sel light coral
> color sel burly wood
> color sel tan
> color sel burly wood
> color sel aquamarine
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel light steel blue
> color sel silver
> color sel thistle
> color sel rosy brown
> ui tool show Distances
> select #5/F:5@CA
1 atom, 1 residue, 1 model selected
> select add #5/A:67@OP1
2 atoms, 2 residues, 1 model selected
> distance #5/F:5@CA #5/A:67@OP1
Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
67 OP1: 1.88Å
> select clear
> select #5/A:67@OP2
1 atom, 1 residue, 1 model selected
> select add #5/F:2@CA
2 atoms, 2 residues, 1 model selected
> distance #5/A:67@OP2 #5/F:2@CA
Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A A 67 OP2 and /F
CA 2 CA: 2.12Å
> select #5/F:5@CA
1 atom, 1 residue, 1 model selected
> select add #5/A:352@OP2
2 atoms, 2 residues, 1 model selected
> distance #5/F:5@CA #5/A:352@OP2
Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
352 OP2: 1.95Å
> select #5/F:5@CA
1 atom, 1 residue, 1 model selected
> select add #5/A:351@OP1
2 atoms, 2 residues, 1 model selected
> distance #5/F:5@CA #5/A:351@OP1
Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
351 OP1: 1.91Å
> distance style symbol false
> distance style symbol true
> label size 2
> label size 1
> label size 150
> label height 1.5
> label height 1
> label height 0.5
> select #5/F:5@CA
1 atom, 1 residue, 1 model selected
> select add #5/C:76@O3'
2 atoms, 2 residues, 1 model selected
> distance #5/F:5@CA #5/C:76@O3'
Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /C U
76 O3': 2.21Å
> label height 0.5
> select #5/F:2@CA
1 atom, 1 residue, 1 model selected
> select add #5/C:77@OP1
2 atoms, 2 residues, 1 model selected
> distance #5/F:2@CA #5/C:77@OP1
Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 2 CA and /C G
77 OP1: 2.71Å
> label height 0.5
> select #5/A:68@OP2
1 atom, 1 residue, 1 model selected
> select add #5/F:2@CA
2 atoms, 2 residues, 1 model selected
> distance #5/A:68@OP2 #5/F:2@CA
Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A G 68 OP2 and /F
CA 2 CA: 2.89Å
> label height 0.5
> select add #5/F:2@CA
21 atoms, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> nucleotides sel atoms
> style nucleic & sel stick
Changed 20 atom styles
> show sel atoms
> select clear
> select #5/A:69@O4
1 atom, 1 residue, 1 model selected
> select add #5/F:2@CA
2 atoms, 2 residues, 1 model selected
> distance #5/A:69@O4 #5/F:2@CA
Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A U 69 O4 and /F CA
2 CA: 1.91Å
> label height 0.5
> select clear
> select #5/F:2@CA
1 atom, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> style sel ball
Changed 1 atom style
> style sel stick
Changed 1 atom style
> style sel ball
Changed 1 atom style
> style sel sphere
Changed 1 atom style
> select down
1 atom, 1 residue, 1 model selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/J1387_GstRNR.pdb"
Chain information for J1387_GstRNR.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Pro
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 Pro
Model Identifier: Mac15,6
Model Number: Z1AU00299LL/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 Performance and 6 Efficiency)
Memory: 18 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3.1 (25D2128)
Kernel Version: Darwin 25.3.0
Time since boot: 9 days, 19 hours, 58 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2715Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
DELL P2715Q:
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
auditwheel: 6.4.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.4
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: 14.1.18
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: 1.10rc202506100450
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: 2.2.1
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
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: 1.45.1
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: 7.8.2
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.2
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: 4.4.4
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
pyelftools: 0.32
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: 8.4.0
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 26.4.0
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: 4.14.0
tzdata: 2025.2
urllib3: 2.4.0
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 , 21 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 , 21 hours 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."
We have not seen this crash in Qt 6.10 which is used by the ChimeraX daily build so you may want to try that.
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Reported by Bapurao Bhoge