![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18216 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x000000020177df00 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 58)
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{
"uptime" : 710000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 2951,
"osVersion" : {
"train" : "macOS 15.5",
"build" : "24F74",
"releaseType" : "User"
},
"captureTime" : "2025-07-17 13:25:54.9616 +0100",
"codeSigningMonitor" : 1,
"incident" : "6752F419-9B95-4F29-B5C2-EB366CB80F86",
"pid" : 13305,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-17 10:55:08.6853 +0100",
"procStartAbsTime" : 16961031162174,
"procExitAbsTime" : 17101156387551,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"B914EA5F-B6B8-5AE9-BCB0-309E005569B7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "CDD8368A-CB67-2368-474F-16C47B0364D2",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "706E892E-CBF4-4500-BDB4-2B8A8B37E464",
"sleepWakeUUID" : "C9707965-2872-45BE-A4C0-7E6AE3252ABB",
"sip" : "enabled",
"vmRegionInfo" : "0x582523c08dc8 is not in any region. Bytes after previous region: 96435500518857 Bytes before following region: 8636579410488\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000d82523c08dc8","rawCodes":[1,237654025211336],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000d82523c08dc8 -> 0x0000582523c08dc8 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":13305},
"vmregioninfo" : "0x582523c08dc8 is not in any region. Bytes after previous region: 96435500518857 Bytes before following region: 8636579410488\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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===== Log before crash start =====
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/javeda/Downloads/cryosparc_P146_J1717_001_volume_map_sharp.mrc
Opened cryosparc_P146_J1717_001_volume_map_sharp.mrc as #1, grid size
210,210,210, pixel 2.52, shown at level 2.03, step 1, values float32
> set bgColor white
> ui tool show "Side View"
> open
> /Users/javeda/Downloads/fold_robin_nc_p852_polyleu/fold_robin_nc_p852_polyleu_model_0.cif
Chain information for fold_robin_nc_p852_polyleu_model_0.cif #2
---
Chain | Description
A | .
> select clear
> select /A:81
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
103 atoms, 102 bonds, 14 residues, 1 model selected
> select up
922 atoms, 947 bonds, 132 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,107.16,0,1,0,127.58,0,0,1,159.09
> view matrix models #2,1,0,0,105.36,0,1,0,245.39,0,0,1,375.28
> view matrix models #2,1,0,0,148.98,0,1,0,175.51,0,0,1,386.34
> view matrix models #2,1,0,0,236.86,0,1,0,215.14,0,0,1,405.65
> view matrix models #2,1,0,0,217.77,0,1,0,282.88,0,0,1,347.4
> view matrix models #2,1,0,0,250.3,0,1,0,343.44,0,0,1,375.46
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.2164,-0.93145,-0.29253,257.23,0.72874,0.045287,-0.6833,347.78,0.6497,-0.36104,0.66898,376.57
> view matrix models
> #2,0.29897,0.91079,-0.28473,251.88,0.94897,-0.2524,0.18907,342.54,0.10034,-0.32673,-0.93978,387.71
> view matrix models
> #2,-0.10727,0.97543,-0.19245,252.23,0.95247,0.15634,0.26147,341.21,0.28513,-0.15525,-0.94583,386.9
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.10727,0.97543,-0.19245,261.46,0.95247,0.15634,0.26147,309.59,0.28513,-0.15525,-0.94583,367.21
> view matrix models
> #2,-0.10727,0.97543,-0.19245,265.95,0.95247,0.15634,0.26147,311.23,0.28513,-0.15525,-0.94583,335.01
> volume #1 level 1.166
> select clear
> select /A:80
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
103 atoms, 102 bonds, 14 residues, 1 model selected
> select ~sel & ##selected
819 atoms, 845 bonds, 118 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select /A:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
103 atoms, 102 bonds, 14 residues, 1 model selected
> view matrix models
> #2,-0.10727,0.97543,-0.19245,262.46,0.95247,0.15634,0.26147,314.79,0.28513,-0.15525,-0.94583,327.96
> view matrix models
> #2,-0.10727,0.97543,-0.19245,261.19,0.95247,0.15634,0.26147,327.95,0.28513,-0.15525,-0.94583,333.99
> volume #1 level 1.088
> view matrix models
> #2,-0.10727,0.97543,-0.19245,261.9,0.95247,0.15634,0.26147,329.59,0.28513,-0.15525,-0.94583,334.32
> select clear
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened fold_robin_nc_p852_polyleu_model_0.cif map 6 as #3, grid size 31,25,24,
pixel 2, shown at level 0.0386, step 1, values float32
Opened fold_robin_nc_p852_polyleu_model_0.cif map 6 as #4, grid size 31,25,24,
pixel 2, shown at level 0.0386, step 1, values float32
> fitmap #2 inMap #1 resolution 6 metric correlation
Fit map fold_robin_nc_p852_polyleu_model_0.cif map 6 in map
cryosparc_P146_J1717_001_volume_map_sharp.mrc using 350 points
correlation = 0.759, correlation about mean = 0.2663, overlap = 95.18
steps = 84, shift = 1.66, angle = 30.4 degrees
Position of fold_robin_nc_p852_polyleu_model_0.cif map 6 (#4) relative to
cryosparc_P146_J1717_001_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.01000829 0.94823360 0.31741593 263.92466342
0.94362721 -0.09607425 0.31676082 329.34394614
0.33085875 0.30269254 -0.89381749 337.30989902
Axis -0.70355047 -0.67227163 -0.23036405
Axis point 0.00000000 39.37811514 125.43424458
Rotation angle (degrees) 179.42714374
Shift along axis -484.79698572
Average map value = 1.246 for 103 atoms, 36 outside contour
> volume #3 level 0.223
> fitmap #2 inMap #1 resolution 6 metric correlation
Fit map fold_robin_nc_p852_polyleu_model_0.cif map 6 in map
cryosparc_P146_J1717_001_volume_map_sharp.mrc using 140 points
correlation = 0.9359, correlation about mean = 0.3262, overlap = 76.12
steps = 60, shift = 0.865, angle = 9.46 degrees
Position of fold_robin_nc_p852_polyleu_model_0.cif map 6 (#3) relative to
cryosparc_P146_J1717_001_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.00295402 0.88344406 0.46852734 263.89317111
0.94253205 -0.15899737 0.29385910 329.87911324
0.33410269 0.44073397 -0.83314402 337.21560497
Axis 0.70719571 0.64724848 0.28450595
Axis point 0.00000000 36.96030436 115.84916513
Rotation angle (degrees) 174.03948011
Shift along axis 496.07771847
Average map value = 1.273 for 103 atoms, 34 outside contour
> close #3
> close #4
> volume #1 color #b2b2b267
> volume #1 level 2.442
> open /Users/javeda/Documents/Fittings/Bgal/646/20k_J1078/bgal646_AP-
> NCfit_J1078-20k_28may25_coot-3_minusN-term.pdb
Summary of feedback from opening
/Users/javeda/Documents/Fittings/Bgal/646/20k_J1078/bgal646_AP-
NCfit_J1078-20k_28may25_coot-3_minusN-term.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLY B 96 SER B 108 1 13
Cannot find LINK/SSBOND residue PRO (150 )
Cannot find LINK/SSBOND residue IAS (119 )
Cannot find LINK/SSBOND residue U (405 )
Cannot find LINK/SSBOND residue U (421 )
Cannot find LINK/SSBOND residue G (376 )
3 messages similar to the above omitted
Chain information for bgal646_AP-NCfit_J1078-20k_28may25_coot-3_minusN-
term.pdb #3
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
B | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> select #3/f:170@CD2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
83 atoms, 83 bonds, 11 residues, 1 model selected
> select up
1411 atoms, 1435 bonds, 177 residues, 1 model selected
> select up
90215 atoms, 98019 bonds, 6556 residues, 1 model selected
> ui tool show "Side View"
> view matrix models #3,1,0,0,29.31,0,1,0,229.56,0,0,1,-11.629
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.81594,0.40181,-0.41568,424.5,0.27836,0.90322,0.32667,123.98,0.50671,0.15083,-0.84882,214.35
> view matrix models
> #3,-0.78932,-0.088853,0.60752,322.39,0.31909,0.78599,0.52953,100.35,-0.52455,0.61183,-0.59204,287.81
> view matrix models
> #3,-0.84812,-0.22135,0.48135,390.29,-0.083954,0.95321,0.29042,200.18,-0.52311,0.2059,-0.82702,425.24
> view matrix models
> #3,-0.85176,0.51397,-0.10168,344.29,0.51798,0.85524,-0.015968,150.6,0.078754,-0.06627,-0.99469,386.64
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.85176,0.51397,-0.10168,355.63,0.51798,0.85524,-0.015968,-56.461,0.078754,-0.06627,-0.99469,494.72
> view matrix models
> #3,-0.85176,0.51397,-0.10168,365.33,0.51798,0.85524,-0.015968,-46.584,0.078754,-0.06627,-0.99469,493.75
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.98392,-0.019233,-0.17757,528.7,-0.0028864,0.99577,-0.09186,52.422,0.17858,-0.08987,-0.97981,473.97
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened bgal646_AP-NCfit_J1078-20k_28may25_coot-3_minusN-term.pdb map 6 as #4,
grid size 125,131,120, pixel 2, shown at level 0.1, step 1, values float32
Opened bgal646_AP-NCfit_J1078-20k_28may25_coot-3_minusN-term.pdb map 6 as #5,
grid size 125,131,120, pixel 2, shown at level 0.1, step 1, values float32
> fitmap #3 inMap #1 resolution 6 metric correlation
Fit map bgal646_AP-NCfit_J1078-20k_28may25_coot-3_minusN-term.pdb map 6 in map
cryosparc_P146_J1717_001_volume_map_sharp.mrc using 212619 points
correlation = 0.9375, correlation about mean = 0.748, overlap = 2.043e+05
steps = 88, shift = 6.91, angle = 8.88 degrees
Position of bgal646_AP-NCfit_J1078-20k_28may25_coot-3_minusN-term.pdb map 6
(#5) relative to cryosparc_P146_J1717_001_volume_map_sharp.mrc (#1)
coordinates:
Matrix rotation and translation
-0.99891328 0.01761459 -0.04315065 502.73380355
0.01863346 0.99955428 -0.02332452 30.92175279
0.04272057 -0.02410322 -0.99879627 490.34803341
Axis -0.00906720 -0.99988851 0.01186373
Axis point 245.95596914 0.00000000 250.75456147
Rotation angle (degrees) 177.53893983
Shift along axis -29.65933681
Average map value = 3.153 for 90215 atoms, 24222 outside contour
> close #4
> close #5
> select clear
> select #3/n:84@CB
1 atom, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> show cartoons
> hide atoms
> volume #1 level 1.297
> select #3/a:1321
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
59130 atoms, 66225 bonds, 2753 residues, 1 model selected
> show sel atoms
> hide sel surfaces
> color sel byhetero
> show sel atoms
> style sel stick
Changed 59130 atom styles
> select clear
> select #2/A:87
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
103 atoms, 102 bonds, 14 residues, 1 model selected
> volume #1 level 1.088
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.002954,0.88344,0.46853,263.07,0.94253,-0.159,0.29386,328.42,0.3341,0.44073,-0.83314,336.82
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened fold_robin_nc_p852_polyleu_model_0.cif map 7 as #4, grid size 29,24,24,
pixel 2.33, shown at level 0.0307, step 1, values float32
Opened fold_robin_nc_p852_polyleu_model_0.cif map 7 as #5, grid size 29,24,24,
pixel 2.33, shown at level 0.0307, step 1, values float32
> fitmap sel inMap #1 resolution 7 metric correlation
Fit map fold_robin_nc_p852_polyleu_model_0.cif map 7 in map
cryosparc_P146_J1717_001_volume_map_sharp.mrc using 262 points
correlation = 0.7272, correlation about mean = 0.2065, overlap = 60.25
steps = 84, shift = 1.22, angle = 10.9 degrees
Position of fold_robin_nc_p852_polyleu_model_0.cif map 7 (#5) relative to
cryosparc_P146_J1717_001_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.12308702 0.92764386 0.35259956 262.44489375
0.90793501 -0.03817106 0.41736912 328.77169123
0.40062900 0.37151021 -0.83754198 338.05882526
Axis -0.66203323 -0.69336765 -0.28452296
Axis point -28.18786064 0.00000000 100.73464369
Rotation angle (degrees) 178.01516939
Shift along axis -497.89239002
Average map value = 1.22 for 103 atoms, 39 outside contour
> show sel atoms
> view matrix models
> #2,-0.12309,0.92764,0.3526,261.48,0.90794,-0.038171,0.41737,326.67,0.40063,0.37151,-0.83754,337.29
> view matrix models
> #2,-0.12309,0.92764,0.3526,261.71,0.90794,-0.038171,0.41737,327.65,0.40063,0.37151,-0.83754,337.78
> close #4
> close #5
> volume #1 level 0.5838
> volume #1 level 1.088
> volume #1 level 1.315
> select clear
> select #3/s:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
67 atoms, 66 bonds, 9 residues, 1 model selected
> select up
700 atoms, 706 bonds, 88 residues, 1 model selected
> colour sel orange
> select clear
> open /Users/javeda/Documents/Fittings/Bgal/bgal510-gabia_70SRNC_jan25.pdb
Summary of feedback from opening
/Users/javeda/Documents/Fittings/Bgal/bgal510-gabia_70SRNC_jan25.pdb
---
warning | Start residue of secondary structure not found: HELIX 1 1 GLY B 96 SER B 108 1 13
Chain information for bgal510-gabia_70SRNC_jan25.pdb #4
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
A | No description available
AB | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
n | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #3 to #4
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 bgal510-gabia_70SRNC_jan25.pdb, chain a (#4) with bgal646_AP-
NCfit_J1078-20k_28may25_coot-3_minusN-term.pdb, chain a (#3), sequence
alignment score = 16206
RMSD between 2753 pruned atom pairs is 0.001 angstroms; (across all 2753
pairs: 0.001)
> show cartoons
> hide atoms
> hide #!4 models
> show #!4 models
> volume #1 level 0.8986
> undo
> select #1
4 models selected
> select clear
> volume #1 level 2.591
> select #1
4 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #4/a:1366@OP1
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
59130 atoms, 66225 bonds, 2753 residues, 1 model selected
> select up
59436 atoms, 66225 bonds, 3059 residues, 1 model selected
> select up
141989 atoms, 153867 bonds, 10592 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> show #!1 models
> view matrix models #4,1,0,0,68.861,0,1,0,77.396,0,0,1,41.989
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.6717,0.26226,-0.69285,488.95,0.45245,0.88578,-0.10335,33.608,0.58661,-0.3829,-0.71364,364.88
> view matrix models
> #4,-0.98097,0.0066471,-0.19404,497.78,-0.036527,0.97525,0.21807,43.935,0.19068,0.22101,-0.95645,369.34
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.98097,0.0066471,-0.19404,512.95,-0.036527,0.97525,0.21807,23.418,0.19068,0.22101,-0.95645,386.6
> hide #3 models
> view matrix models
> #4,-0.98097,0.0066471,-0.19404,511.25,-0.036527,0.97525,0.21807,17.865,0.19068,0.22101,-0.95645,387.37
> view matrix models
> #4,-0.98097,0.0066471,-0.19404,507.85,-0.036527,0.97525,0.21807,19.303,0.19068,0.22101,-0.95645,382.18
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.96211,-0.083067,-0.25971,536.39,-0.10478,0.99197,0.070869,60.158,0.25174,0.095395,-0.96308,397.43
> view matrix models
> #4,-0.99439,-0.072755,-0.076723,502.23,-0.074201,0.99711,0.016163,64.56,0.075326,0.021766,-0.99692,454.38
> view matrix models
> #4,-0.99483,0.0081075,-0.10119,490.8,0.0097393,0.99983,-0.015642,54.164,0.10105,-0.016547,-0.99474,456.75
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Opened bgal510-gabia_70SRNC_jan25.pdb map 5 as #5, grid size 147,163,179,
pixel 1.67, shown at level 0.105, step 1, values float32
Opened bgal510-gabia_70SRNC_jan25.pdb map 5 as #6, grid size 147,163,179,
pixel 1.67, shown at level 0.105, step 1, values float32
> fitmap #4 inMap #1 resolution 5 metric correlation
Fit map bgal510-gabia_70SRNC_jan25.pdb map 5 in map
cryosparc_P146_J1717_001_volume_map_sharp.mrc using 518828 points
correlation = 0.9082, correlation about mean = 0.6079, overlap = 5.674e+05
steps = 72, shift = 4.12, angle = 3.48 degrees
Position of bgal510-gabia_70SRNC_jan25.pdb map 5 (#6) relative to
cryosparc_P146_J1717_001_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99882279 0.02220353 -0.04312808 477.46908555
0.02328992 0.99941980 -0.02485279 54.09410162
0.04255123 -0.02582798 -0.99876038 467.78909543
Axis -0.01138024 -0.99985487 0.01267787
Axis point 233.40567666 0.00000000 239.34844724
Rotation angle (degrees) 177.54436047
Shift along axis -53.58939690
Average map value = 3.07 for 141989 atoms, 46900 outside contour
> volume #6 level 0.3378
> fitmap #4 inMap #1 resolution 5 metric correlation
Fit map bgal510-gabia_70SRNC_jan25.pdb map 5 in map
cryosparc_P146_J1717_001_volume_map_sharp.mrc using 518828 points
correlation = 0.9082, correlation about mean = 0.6078, overlap = 5.674e+05
steps = 40, shift = 0.0533, angle = 0.014 degrees
Position of bgal510-gabia_70SRNC_jan25.pdb map 5 (#5) relative to
cryosparc_P146_J1717_001_volume_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
-0.99882664 0.02217180 -0.04305530 477.48508893
0.02326618 0.99941454 -0.02508534 54.16078702
0.04247391 -0.02605764 -0.99875771 467.89875646
Axis -0.01136636 -0.99985356 0.01279349
Axis point 233.42122519 0.00000000 239.39806261
Rotation angle (degrees) 177.54866181
Shift along axis -53.59406698
Average map value = 3.07 for 141989 atoms, 46919 outside contour
> close #6
> close #5
> select clear
> close #3
> select #4/s:71
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
13 atoms, 12 bonds, 2 residues, 1 model selected
> select up
729 atoms, 735 bonds, 93 residues, 1 model selected
> colour sel orange
> select clear
> volume #1 level 0.9341
> volume #1 level 1.165
> volume #1 level 0.5872
> ui tool show "Show Sequence Viewer"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> sequence chain #4/AB
Alignment identifier is 4/AB
> select #4/AB:150
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #4/AB:142-150
90 atoms, 97 bonds, 9 residues, 1 model selected
> colour sel orange
> select clear
> select #4/AB:141
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/AB:111-141
214 atoms, 217 bonds, 31 residues, 1 model selected
> colour sel green
> select clear
> volume #1 level 0.3945
> volume #1 level 0.9533
> volume #1 level 1.05
> select clear
> select #4/s:21
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
67 atoms, 66 bonds, 9 residues, 1 model selected
> select add #4/s:27
73 atoms, 71 bonds, 10 residues, 1 model selected
> select add #4/s:28
81 atoms, 78 bonds, 11 residues, 1 model selected
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/javeda/Downloads/cryosparc_P146_J1724_001_volume_map_sharp.mrc
Opened cryosparc_P146_J1724_001_volume_map_sharp.mrc as #1, grid size
210,210,210, pixel 2.52, shown at level 2.02, step 1, values float32
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac15,6
Model Number: MRX33B/A
Chip: Apple M3 Pro
Total Number of Cores: 11 (5 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 52 days, 15 hours, 32 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 3
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 P2723D:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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