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Opened 4 months ago
Closed 4 months ago
#18373 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.4.1-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: Segmentation fault
Current thread 0x00000001f62b0c80 (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, psutil._psutil_osx, psutil._psutil_posix, chimerax.pdb_lib._load_libs, chimerax.map._map, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 59)
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"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,7",
"coalitionID" : 141325,
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"build" : "24E263",
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"captureTime" : "2025-08-05 14:23:16.3516 +0200",
"codeSigningMonitor" : 1,
"incident" : "93AB439D-9CDA-426E-A010-9E1E18C22CFA",
"pid" : 81492,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-08-04 14:24:54.9077 +0200",
"procStartAbsTime" : 18105467270000,
"procExitAbsTime" : 18684055462326,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B362EAEC-D592-0B8A-05EB-D3BB388A7463",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["selectedLanguageDoesNotMatchSelectedSiriLanguage"]},
"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" : "AE98EC4F-661B-4FC3-9247-2524C2B02F40",
"wakeTime" : 11526,
"sleepWakeUUID" : "47309238-FA47-4625-BBCA-038312D06A36",
"sip" : "enabled",
"vmRegionInfo" : "0x1dc85a341eb0 is not in any region. Bytes after previous region: 32265307692721 Bytes before following region: 72806772236624\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, 0x00001dc85a341eb0","rawCodes":[1,32746344029872],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00001dc85a341eb0"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":81492},
"vmregioninfo" : "0x1dc85a341eb0 is not in any region. Bytes after previous region: 32265307692721 Bytes before following region: 72806772236624\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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===== Log before crash start =====
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/annguyen/ownCloud - Anh Nguyen@oc.biophys.mpg.de/Chimera
> sessions/04-08-25-ctSec63.cxs"
Opened cryosparc_P12_J364_007_volume_map.mrc as #1, grid size 224,224,224,
pixel 1.15, shown at level 0.144, step 1, values float32
Opened cryosparc_P12_J364_007_volume_map.mrc z flip as #3, grid size
224,224,224, pixel 1.15, shown at level 0.118, step 1, values float32
Log from Mon Aug 4 13:46:07 2025UCSF ChimeraX version: 1.10 (2025-06-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/tzujingyang/Downloads/cryosparc_P12_J364_007_volume_map.mrc
Opened cryosparc_P12_J364_007_volume_map.mrc as #1, grid size 224,224,224,
pixel 1.15, shown at level 0.0935, step 1, values float32
> open
> /Users/tzujingyang/Downloads/fold_2025_02_17_ct_post_translocon/fold_2025_02_17_ct_post_translocon_model_0.cif
Chain information for fold_2025_02_17_ct_post_translocon_model_0.cif #2
---
Chain | Description
A | .
B | .
C | .
D | .
E | .
F | .
G | .
> set bgColor white
[Repeated 1 time(s)]
> lighting soft
> graphics silhouettes true
> ui mousemode right zoom
> select #1
2 models selected
> select #2
17672 atoms, 18080 bonds, 2263 residues, 1 model selected
> hide sel atoms
> select #2/A-C
5104 atoms, 5209 bonds, 670 residues, 1 model selected
> show sel cartoons
Computing secondary structure
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,22.963,0,1,0,70.289,0,0,1,189.66
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.95513,-0.27821,0.10163,18.017,-0.17707,-0.26127,0.94889,44.495,-0.23743,-0.9243,-0.29881,184.53
> volume #1 level 0.1576
> view matrix models
> #2,-0.97717,0.020318,0.21151,-0.1161,-0.11033,-0.89924,-0.42332,47.062,0.18159,-0.43699,0.88094,186.75
> select #2
17672 atoms, 18080 bonds, 2263 residues, 1 model selected
> show sel cartoons
> select clear
> select #2
17672 atoms, 18080 bonds, 2263 residues, 1 model selected
> view matrix models
> #2,0.34453,0.26283,0.90123,11.89,-0.79557,-0.4279,0.42893,44.798,0.49837,-0.86477,0.061673,186.41
> view matrix models
> #2,0.89857,-0.30549,-0.31503,11.52,0.27215,-0.17521,0.94617,53.87,-0.34424,-0.93594,-0.074298,180.18
> view matrix models
> #2,0.9085,-0.28276,-0.30768,11.488,0.30843,-0.043022,0.95027,53.288,-0.28194,-0.95822,0.048128,181.55
> view matrix models
> #2,0.58344,-0.55494,-0.59299,9.1667,0.67324,-0.077903,0.73531,54.636,-0.45425,-0.82823,0.32816,181.33
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.58344,-0.55494,-0.59299,24.64,0.67324,-0.077903,0.73531,157.92,-0.45425,-0.82823,0.32816,121.65
> view matrix models
> #2,0.58344,-0.55494,-0.59299,99.716,0.67324,-0.077903,0.73531,102.26,-0.45425,-0.82823,0.32816,143.11
> view matrix models
> #2,0.58344,-0.55494,-0.59299,102.63,0.67324,-0.077903,0.73531,125.17,-0.45425,-0.82823,0.32816,125.95
> fitmap #2/A inMap #1
Fit molecule fold_2025_02_17_ct_post_translocon_model_0.cif (#2) to map
cryosparc_P12_J364_007_volume_map.mrc (#1) using 3672 atoms
average map value = 0.07813, steps = 92
shifted from previous position = 6.97
rotated from previous position = 7.15 degrees
atoms outside contour = 3102, contour level = 0.15761
Position of fold_2025_02_17_ct_post_translocon_model_0.cif (#2) relative to
cryosparc_P12_J364_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.66553909 -0.55392862 -0.50022076 106.96152025
0.60250097 0.00316975 0.79811186 125.68094581
-0.44051143 -0.83255813 0.33585212 121.20324876
Axis -0.81533711 -0.02985475 0.57821630
Axis point 0.00000000 142.79971764 21.66300902
Rotation angle (degrees) 89.86933805
Shift along axis -20.88017626
> select clear
> hide #!1 models
> show #!1 models
> hide #2 models
> volume #1 level 0.1443
> show #2 models
> select add #2
17672 atoms, 18080 bonds, 2263 residues, 1 model selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.66554,-0.55393,-0.50022,109.51,0.6025,0.0031698,0.79811,70.32,-0.44051,-0.83256,0.33585,155.11
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.18254,0.65455,0.73365,106.32,-0.74328,-0.39658,0.53876,61.958,0.64359,-0.64365,0.41412,161.87
> view matrix models
> #2,-0.9799,-0.087222,0.17942,99.534,0.053281,-0.98111,-0.18596,66.551,0.19225,-0.17266,0.96604,159.27
> view matrix models
> #2,-0.97948,-0.10009,0.1749,99.592,0.035274,-0.93968,-0.34022,65.158,0.19841,-0.32707,0.92394,160.05
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.97948,-0.10009,0.1749,97.345,0.035274,-0.93968,-0.34022,113.48,0.19841,-0.32707,0.92394,130.14
> volume flip #1
Opened cryosparc_P12_J364_007_volume_map.mrc z flip as #3, grid size
224,224,224, pixel 1.15, shown at step 1, values float32
> view matrix models
> #2,-0.97948,-0.10009,0.1749,72.066,0.035274,-0.93968,-0.34022,57.313,0.19841,-0.32707,0.92394,84.265
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.78926,-0.0074478,-0.61401,78.545,-0.38389,-0.78642,-0.48392,52.497,-0.47927,0.61765,-0.62355,63.428
> view matrix models
> #2,0.5254,-0.0024531,0.85085,86.187,0.67432,-0.60864,-0.41814,59.063,0.51889,0.79344,-0.31812,71.146
> view matrix models
> #2,0.78166,0.071995,0.61953,85.971,0.50316,-0.65976,-0.55817,57.308,0.36856,0.74802,-0.55193,68.89
> view matrix models
> #2,0.75758,0.002533,0.65274,86.471,0.3886,-0.80522,-0.44789,58.178,0.52446,0.59297,-0.611,70.589
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.75758,0.002533,0.65274,120.55,0.3886,-0.80522,-0.44789,128.77,0.52446,0.59297,-0.611,149.22
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.0024637,0.50637,0.86231,113.4,0.95074,-0.26613,0.15899,133.08,0.30999,0.82022,-0.48077,147.11
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.0024637,0.50637,0.86231,110.46,0.95074,-0.26613,0.15899,126.68,0.30999,0.82022,-0.48077,141.34
> select clear
> fitmap #2/A inMap #3
Fit molecule fold_2025_02_17_ct_post_translocon_model_0.cif (#2) to map
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) using 3672 atoms
average map value = 0.07028, steps = 88
shifted from previous position = 2.47
rotated from previous position = 7.65 degrees
atoms outside contour = 3288, contour level = 0.14426
Position of fold_2025_02_17_ct_post_translocon_model_0.cif (#2) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.02183192 0.61273735 0.78998501 114.22628435
0.95843884 -0.23765489 0.15784536 125.93472557
0.28446154 0.75370625 -0.59245973 141.89463691
Axis 0.69734812 0.59162440 0.40458149
Axis point 0.00000000 5.45622083 37.93498054
Rotation angle (degrees) 154.70788409
Shift along axis 211.56948323
> select clear
> hide #2 models
> volume #3 level 0.1176
> show #2 models
> ui mousemode right "rotate selected models"
> select add #2
17672 atoms, 18080 bonds, 2263 residues, 1 model selected
> hide #!3 models
> view matrix models
> #2,-0.69413,0.10211,0.71257,112.11,0.68394,-0.21521,0.69707,127.39,0.22453,0.97122,0.079547,144.42
> show #!3 models
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.69413,0.10211,0.71257,126.88,0.68394,-0.21521,0.69707,114.98,0.22453,0.97122,0.079547,142.76
> fitmap #2/A inMap #3
Fit molecule fold_2025_02_17_ct_post_translocon_model_0.cif (#2) to map
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) using 3672 atoms
average map value = 0.1228, steps = 84
shifted from previous position = 7.37
rotated from previous position = 11.7 degrees
atoms outside contour = 1867, contour level = 0.11756
Position of fold_2025_02_17_ct_post_translocon_model_0.cif (#2) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
-0.79653569 0.19621692 0.57186522 126.63877416
0.55507621 -0.13755236 0.82034734 120.62018290
0.23962744 0.97086471 0.00065002 138.14374615
Axis 0.29416253 0.64930650 0.70133406
Axis point 35.95552099 2.31081827 0.00000000
Rotation angle (degrees) 165.17660668
Shift along axis 212.45676623
> select clear
> transparency #3 50
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!3 models
> select ~sel & ##selected
Nothing selected
> select #2/B:1-95
655 atoms, 667 bonds, 95 residues, 1 model selected
> hide sel cartoons
> show #!3 models
> view matrix models
> #2,-0.79654,0.19622,0.57187,127.06,0.55508,-0.13755,0.82035,121.54,0.23963,0.97086,0.00065002,136.68
> undo
> select clear
> volume #3 level 0.0962
> volume #3 level 0.1122
> volume #3 level 0.1336
> volume #3 level 0.1296
> volume zone #3 nearAtoms #2/A-C range 5
> hide #2 models
> select #2
17672 atoms, 18080 bonds, 2263 residues, 1 model selected
> show #2 models
> hide sel cartoons
> select #2/A-C
5104 atoms, 5209 bonds, 670 residues, 1 model selected
> show sel cartoons
> view matrix models
> #2,-0.79654,0.19622,0.57187,126.12,0.55508,-0.13755,0.82035,120.37,0.23963,0.97086,0.00065002,138.33
> undo
> select clear
> volume #3 level 0.09887
> open "/Users/tzujingyang/Library/Mobile
> Documents/com~apple~CloudDocs/Melanie_Lab/SND/Manuscripts/The SND3
> translocon/PDB deposition/CtSND3-translocon_20250130_rotamer_geo_clash-
> refinement-refined_043.deposit_000.cif"
Summary of feedback from opening /Users/tzujingyang/Library/Mobile
Documents/com~apple~CloudDocs/Melanie_Lab/SND/Manuscripts/The SND3
translocon/PDB deposition/CtSND3-translocon_20250130_rotamer_geo_clash-
refinement-refined_043.deposit_000.cif
---
warnings | Skipping chem_comp category: Missing column 'type' on line 617
Skipping entity category: Missing column 'type' on line 134512
Missing entity information. Treating each chain as a separate entity.
Invalid residue range for struct_conf "1": invalid chain "1", on line 503
Invalid residue range for struct_conf "2": invalid chain "1", on line 504
Invalid residue range for struct_conf "3": invalid chain "1", on line 505
Invalid residue range for struct_conf "4": invalid chain "1", on line 506
Invalid residue range for struct_conf "5": invalid chain "1", on line 507
51 messages similar to the above omitted
Invalid sheet range for struct_sheet_range "1 1": invalid chain "1", on line
596
Invalid sheet range for struct_sheet_range "2 1": invalid chain "1", on line
597
Invalid sheet range for struct_sheet_range "3 1": invalid chain "1", on line
598
Invalid sheet range for struct_sheet_range "4 1": invalid chain "1", on line
599
Invalid sheet range for struct_sheet_range "5 1": invalid chain "1", on line
600
14 messages similar to the above omitted
Missing or incorrect sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' on line 147388
Skipping chem_comp category: Missing column 'type' on line 147673
Skipping chem_comp category: Missing column 'type' on line 147925
Skipping chem_comp category: Missing column 'type' on line 148204
Skipping chem_comp category: Missing column 'type' on line 148465
2 messages similar to the above omitted
Chain information for CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif #4
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
6 | No description available
7 | No description available
L1 | No description available
L2 | No description available
L3 | No description available
LA | No description available
LB | No description available
LC | No description available
LD | No description available
LE | No description available
LF | No description available
LG | No description available
LH | No description available
LI | No description available
LJ | No description available
LL | No description available
LM | No description available
LN | No description available
LO | No description available
LP | No description available
LQ | No description available
LR | No description available
LS | No description available
LT | No description available
LU | No description available
LV | No description available
LX | No description available
LY | No description available
LZ | No description available
La | No description available
Lb | No description available
Lc | No description available
Ld | No description available
Le | No description available
Lf | No description available
Lg | No description available
Lh | No description available
Li | No description available
Lj | No description available
Lk | No description available
Ll | No description available
Lm | No description available
Ln | No description available
Lo | No description available
Lp | No description available
Lq | No description available
> mmaker #4/1 to #2/A
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_2025_02_17_ct_post_translocon_model_0.cif, chain A (#2) with
CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif, chain 1 (#4), sequence alignment score = 2261.8
RMSD between 199 pruned atom pairs is 0.912 angstroms; (across all 462 pairs:
4.370)
> select #4
133843 atoms, 143270 bonds, 915 pseudobonds, 11376 residues, 3 models selected
> hide sel atoms
> select #4/1-3
4821 atoms, 4923 bonds, 625 residues, 1 model selected
> show sel cartoons
> hide #2 models
> select clear
> fitmap #4/1 inMap #3
Fit molecule CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif (#4) to map cryosparc_P12_J364_007_volume_map.mrc
z flip (#3) using 3579 atoms
average map value = 0.1166, steps = 72
shifted from previous position = 0.986
rotated from previous position = 4.53 degrees
atoms outside contour = 1655, contour level = 0.09887
Position of CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif (#4) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.92522432 -0.20409499 -0.31985183 -27.77065956
-0.37089772 -0.30883687 -0.87581657 456.34574614
0.07996774 0.92895910 -0.36144176 16.46517303
Axis 0.97237838 -0.21541508 -0.08987010
Axis point 0.00000000 223.33381190 156.11302032
Rotation angle (degrees) 111.87155816
Shift along axis -126.78707277
> select #3
2 models selected
> fitmap #4/1 inMap #3
Fit molecule CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif (#4) to map cryosparc_P12_J364_007_volume_map.mrc
z flip (#3) using 3579 atoms
average map value = 0.1166, steps = 44
shifted from previous position = 0.00239
rotated from previous position = 0.0101 degrees
atoms outside contour = 1654, contour level = 0.09887
Position of CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif (#4) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.92519291 -0.20417123 -0.31989403 -27.74137314
-0.37097647 -0.30896130 -0.87573933 456.37187789
0.07996590 0.92890098 -0.36159152 16.50339602
Axis 0.97236973 -0.21545108 -0.08987739
Axis point 0.00000000 223.33681553 156.11596185
Rotation angle (degrees) 111.88099235
Shift along axis -126.78396642
> select clear
> volume unzone #3
> transparency #3 0
> volume #3 level 0.1162
> show #2 models
> volume #3 level 0.1069
> select #4
133843 atoms, 143270 bonds, 915 pseudobonds, 11376 residues, 3 models selected
> select #4/6
1444 atoms, 1471 bonds, 188 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> volume #3 level 0.1202
> select #2
17672 atoms, 18080 bonds, 2263 residues, 1 model selected
> show sel cartoons
> view matrix models
> #2,-0.79654,0.19622,0.57187,124.14,0.55508,-0.13755,0.82035,118.91,0.23963,0.97086,0.00065002,136.7
> undo
> select clear
> hide #2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #2 models
> hide #!4 models
> hide #2 models
> show #!3 models
> volume #3 level 0.1202
> show #!4 models
> volume #3 level 0.1456
> volume #3 level 0.1403
> show #2 models
> volume #3 color #b2b2b280
> transparency #3 0
> volume #3 level 0.1136
> hide #2 models
> hide #!4 models
> show #!3 models
> volume #3 level 0.1242
> volume #3 level 0.1576
> volume #3 level 0.1536
> volume #3 level 0.1122
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.1376
> volume #3 level 0.1883
> volume #3 level 0.1389
> open 7AFT
Summary of feedback from opening 7AFT fetched from pdb
---
note | Fetching compressed mmCIF 7aft from http://files.rcsb.org/download/7aft.cif
7aft title:
Cryo-EM structure of the signal sequence-engaged post-translational Sec
translocon [more info...]
Chain information for 7aft #5
---
Chain | Description | UniProt
A | Protein transport protein SEC61 | SC61A_YEAST 1-480
B | Protein transport protein SBH1 | SC6B1_YEAST 1-82
C | Protein transport protein SSS1 | SC61G_YEAST 1-80
D | Protein translocation protein SEC63 | SEC63_YEAST 1-663
E | Translocation protein SEC66 | SEC66_YEAST 1-206
F | Translocation protein SEC72 | SEC72_YEAST 1-193
G | Translocation protein SEC62,Translocation protein SEC62 | SEC62_YEAST -124-149
H | Mating factor alpha-1,Mating factor alpha-1 | MFAL1_YEAST -164-0
> select #5
6691 atoms, 6676 bonds, 7 pseudobonds, 1353 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select #5/A to #4/1
Expected a keyword
> mmaker #5/A to #4/1
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 CtSND3-translocon_20250130_rotamer_geo_clash-refinement-
refined_043.deposit_000.cif, chain 1 (#4) with 7aft, chain A (#5), sequence
alignment score = 1590.6
RMSD between 118 pruned atom pairs is 0.994 angstroms; (across all 388 pairs:
5.498)
> select clear
> select #5
6691 atoms, 6676 bonds, 7 pseudobonds, 1353 residues, 2 models selected
> select #5/H
65 atoms, 64 bonds, 13 residues, 1 model selected
> fitmap #5/1 inMap #3
No atoms or maps for #5/1
> fitmap #5/A inMap #3
Fit molecule 7aft (#5) to map cryosparc_P12_J364_007_volume_map.mrc z flip
(#3) using 1922 atoms
average map value = 0.149, steps = 84
shifted from previous position = 2.12
rotated from previous position = 8.11 degrees
atoms outside contour = 869, contour level = 0.13892
Position of 7aft (#5) relative to cryosparc_P12_J364_007_volume_map.mrc z flip
(#3) coordinates:
Matrix rotation and translation
-0.72201031 -0.56105533 0.40486791 222.89438450
-0.30547912 0.78354717 0.54105115 18.48906784
-0.62079273 0.26696582 -0.73711982 237.51717785
Axis -0.25099834 0.93926632 0.23404830
Axis point 150.85135772 0.00000000 80.52896731
Rotation angle (degrees) 146.90763543
Shift along axis 17.01053023
> select clear
> hide #!5 models
> volume #3 level 0.1456
> volume #3 level 0.1443
> show #!4 models
> show #2 models
> hide #!3 models
> hide #2 models
> show #!5 models
> hide #!4 models
> show #!4 models
> show #!3 models
> hide #!5 models
> hide #!4 models
> volume #3 level 0.1309
> volume #3 level 0.1176
> volume #3 level 0.1136
> volume #3 level 0.1403
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> volume #3 level 0.1296
> volume #3 level 0.1176
> save /Users/tzujingyang/Downloads/ctSec63.cxs includeMaps true
——— End of log from Mon Aug 4 13:46:07 2025 ———
> view name session-start
opened ChimeraX session
Cell requested for row 4 is out of bounds for table with 6 rows! Resizing
table model.
> show #!5 models
> rename #5 "7aft Tsai"
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #2 models
> show #!5 models
> color #3 #b2b2b2d2 models
> color #3 #b2b2b2de models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #2 models
> select #2/A
3672 atoms, 3752 bonds, 476 residues, 1 model selected
> volume #3 level 0.1416
> show #!5 models
> hide #!5 models
> select #5/B
158 atoms, 157 bonds, 32 residues, 1 model selected
> hide #!3 models
> hide #2 models
> show #!5 models
> select #5/B
158 atoms, 157 bonds, 32 residues, 1 model selected
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!3 models
> show #2 models
> show #!5 models
> hide #2 models
> show #2 models
> hide #!5 models
> hide #!3 models
> show #!3 models
> show #!5 models
> hide #!5 models
> ui tool show "Side View"
> open /Users/annguyen/Downloads/cryosparc_P12_J369_005_volume_map.mrc
Opened cryosparc_P12_J369_005_volume_map.mrc as #6, grid size 224,224,224,
pixel 1.15, shown at level 0.0937, step 1, values float32
> hide #!3 models
> hide #2 models
> volume #6 level 0.1367
> volume #6 level 0.1238
> show #!5 models
> hide #!5 models
> volume #6 level 0.08371
> volume #6 level 0.1324
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> hide #!6 models
> show #2 models
> hide #2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> show #2 models
> show #!6 models
> select add #6
158 atoms, 157 bonds, 32 residues, 3 models selected
> select add #5
6691 atoms, 6676 bonds, 7 pseudobonds, 1353 residues, 4 models selected
> show #!5 models
> select subtract #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.91504,-0.34874,0.20269,32.05,-0.39981,-0.71766,0.57019,206.86,-0.053387,-0.60278,-0.79612,301.07
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.91504,-0.34874,0.20269,32.446,-0.39981,-0.71766,0.57019,202.96,-0.053387,-0.60278,-0.79612,314.95
> view matrix models
> #6,0.91504,-0.34874,0.20269,34.814,-0.39981,-0.71766,0.57019,202.52,-0.053387,-0.60278,-0.79612,313.3
> ui tool show "Fit in Map"
> fitmap #6 inMap #1
Fit map cryosparc_P12_J369_005_volume_map.mrc in map
cryosparc_P12_J364_007_volume_map.mrc using 46864 points
correlation = 0.7436, correlation about mean = 0.07993, overlap = 603.8
steps = 60, shift = 3.81, angle = 2.63 degrees
Position of cryosparc_P12_J369_005_volume_map.mrc (#6) relative to
cryosparc_P12_J364_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.91602817 -0.32807524 0.23077913 29.45651043
-0.40100174 -0.73541368 0.54622733 204.65652088
-0.00948553 -0.59290246 -0.80521839 305.26117423
Axis -0.97655807 0.20597512 -0.06251874
Axis point 0.00000000 155.67490962 117.77245564
Rotation angle (degrees) 144.32145282
Shift along axis -5.69638643
> color #6 #6a6a6aff models
> undo
> color #6 #6a6a6abf models
> color #6 #6a6a6ad2 models
> color #6 #6a6a6ad1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!3 models
> hide #!5 models
> color #6 #a5a5a5d1 models
> hide #2 models
> show #!3 models
> fitmap #6 inMap #3
Fit map cryosparc_P12_J369_005_volume_map.mrc in map
cryosparc_P12_J364_007_volume_map.mrc z flip using 46864 points
correlation = 0.6934, correlation about mean = 0.08096, overlap = 653.8
steps = 140, shift = 5.84, angle = 10.2 degrees
Position of cryosparc_P12_J369_005_volume_map.mrc (#6) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.89059252 -0.41985823 0.17482562 45.87397832
-0.42552460 -0.63354903 0.64617676 184.26921694
-0.16054203 -0.64987281 -0.74289404 327.71666014
Axis -0.96810520 0.25050830 -0.00423259
Axis point 0.00000000 163.07355093 127.22582210
Rotation angle (degrees) 137.98120473
Shift along axis 0.36304043
> volume flip #6
Opened cryosparc_P12_J369_005_volume_map.mrc z flip as #7, grid size
224,224,224, pixel 1.15, shown at step 1, values float32
> fitmap #7 inMap #3
Fit map cryosparc_P12_J369_005_volume_map.mrc z flip in map
cryosparc_P12_J364_007_volume_map.mrc z flip using 46864 points
correlation = 0.6754, correlation about mean = 0.05638, overlap = 543.7
steps = 156, shift = 14.5, angle = 7.31 degrees
Position of cryosparc_P12_J369_005_volume_map.mrc z flip (#7) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.91091097 -0.40937649 0.05149827 54.18018317
-0.33423477 -0.65894287 0.67385560 167.24216477
-0.24192623 -0.63103498 -0.73706616 347.07625424
Axis -0.97410180 0.21904161 0.05609335
Axis point 0.00000000 158.15300023 142.24540846
Rotation angle (degrees) 137.94900990
Shift along axis 3.32464895
> close #6
> close #1
> color #7 #a5a5a5ff models
> ui mousemode right "rotate selected models"
> select add #7
2 models selected
> view matrix models
> #7,0.98734,0.026146,0.15644,-26.648,-0.025494,0.99966,-0.0061751,3.4773,-0.15655,0.0021087,0.98767,19.815
> fitmap #7 inMap #3
Fit map cryosparc_P12_J369_005_volume_map.mrc z flip in map
cryosparc_P12_J364_007_volume_map.mrc z flip using 46864 points
correlation = 0.9946, correlation about mean = 0.9205, overlap = 1712
steps = 92, shift = 2.57, angle = 9.28 degrees
Position of cryosparc_P12_J369_005_volume_map.mrc z flip (#7) relative to
cryosparc_P12_J364_007_volume_map.mrc z flip (#3) coordinates:
Matrix rotation and translation
0.99976784 0.02110035 -0.00435981 -2.35330290
-0.02107072 0.99975529 0.00673369 1.86561627
0.00450082 -0.00664025 0.99996780 0.31585649
Axis -0.29641125 -0.19638121 -0.93465223
Axis point 87.57532457 111.98744505 0.00000000
Rotation angle (degrees) 1.29268927
Shift along axis 0.03595749
> show #2 models
> hide #!3 models
> color #7 #a5a5a5de models
> show #!5 models
> hide #!5 models
> color #7 #a5a5a5bb models
> color #7 #a5a5a5ba models
> lighting soft
> lighting flat
> color #7 #a5a5a5c4 models
> lighting soft
> volume #7 level 0.1117
> volume #7 level 0.03172
> volume #7 level 0.1304
> volume #7 level 0.1146
> show #!3 models
> hide #!7 models
> volume #3 level 0.1113
> volume #3 level 0.1463
> hide #2 models
> show #!5 models
> select #5/B
158 atoms, 157 bonds, 32 residues, 1 model selected
> hide #!5 models
> show #2 models
> open 7kal
Summary of feedback from opening 7kal fetched from pdb
---
note | Fetching compressed mmCIF 7kal from http://files.rcsb.org/download/7kal.cif
7kal title:
Cryo-EM structure of the Sec complex from T. lanuginosus, wild-type, class
with Sec62, plug-open conformation [more info...]
Chain information for 7kal #1
---
Chain | Description
A | Protein transport channel Sec61 complex, alpha subunit (Sec61)
B | Protein transport channel Sec61 complex, beta subunit (Sbh1)
C | Protein transport channel Sec61 complex, gamma subunit (Sss1)
D | Protein transport protein Sec63
E | Protein transport protein Sec66/Sec71
F | Protein transport protein Sec72
G | Protein transport protein Sec62
> show #2#!1 cartoons
> hide #2#!1 atoms
> select add #5
6691 atoms, 6676 bonds, 7 pseudobonds, 1353 residues, 2 models selected
> show #!5 models
> select subtract #5
Nothing selected
> select add #1
10789 atoms, 11024 bonds, 11 pseudobonds, 1429 residues, 2 models selected
> hide #2 models
> view matrix models
> #1,0.88239,0.40211,-0.24431,-11.455,0.35912,-0.91107,-0.20246,265.91,-0.30399,0.090914,-0.94833,290.99
> view matrix models
> #1,0.9093,0.33777,-0.24308,-5.751,0.28851,-0.93264,-0.21668,281.45,-0.29989,0.1269,-0.9455,284.53
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9093,0.33777,-0.24308,-23.762,0.28851,-0.93264,-0.21668,264.93,-0.29989,0.1269,-0.9455,291.41
> view matrix models
> #1,0.9093,0.33777,-0.24308,-17.687,0.28851,-0.93264,-0.21668,263.06,-0.29989,0.1269,-0.9455,291.76
> mmaker 1/A to #5/A
> matchmaker 1/A to #5/A
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker #1/A to #5/A
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 7aft Tsai, chain A (#5) with 7kal, chain A (#1), sequence alignment
score = 1682.4
RMSD between 287 pruned atom pairs is 1.164 angstroms; (across all 387 pairs:
2.284)
> hide #!5 models
> volume #3 level 0.1009
> volume #3 level 0.1208
> volume #7 level 0.1117
> volume #7 level 0.1709
> hide #!7 models
> show #2 models
> hide #!1 models
> select subtract #1
Nothing selected
> rename #1 "7kal Cryo-EM structure of the Sec complex from T. lanuginosus,
> wild-type, class with Sec62, plug-open conformation"
> rename #1 "7kal T. lanuginosus WT with Sec62, plug-open conformation"
> rename #1 "7kal T. lanuginosus WT with Sec62 plug-open conformation"
> open 7kam
Summary of feedback from opening 7kam fetched from pdb
---
note | Fetching compressed mmCIF 7kam from http://files.rcsb.org/download/7kam.cif
7kam title:
Cryo-EM structure of the Sec complex from T. lanuginosus, wild-type, class
with Sec62, plug-closed conformation [more info...]
Chain information for 7kam #6
---
Chain | Description
A | Protein transport channel Sec61 complex, alpha subunit (Sec61)
B | Protein transport channel Sec61 complex, beta subunit (Sbh1)
C | Protein transport channel Sec61 complex, gamma subunit (Sss1)
D | Protein transport protein Sec63
E | Protein transport protein Sec66/Sec71
F | Protein transport protein Sec72
G | Protein transport protein Sec62
> rename #6 "7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation"
> mmaker #1/A to #6/A
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 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)
> show #2#!6 cartoons
> hide #2#!6 atoms
> select add #6
10916 atoms, 11157 bonds, 9 pseudobonds, 1445 residues, 2 models selected
> view matrix models #6,1,0,0,36.367,0,1,0,-148.94,0,0,1,-51.128
> view matrix models #6,1,0,0,33.364,0,1,0,-145.72,0,0,1,-55.655
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.56918,0.65785,0.49322,96.147,0.68596,0.71066,-0.15626,-180.81,-0.45331,0.24939,-0.85575,219.94
> view matrix models
> #6,-0.51104,0.85707,-0.065353,131.76,-0.30202,-0.10786,0.94718,-58.919,0.80475,0.50379,0.31397,-158.45
> view matrix models
> #6,0.71818,0.13655,-0.68233,144.65,0.34299,-0.92264,0.17637,74.113,-0.60546,-0.36069,-0.70945,315.72
> view matrix models
> #6,0.70134,0.36268,-0.61366,103.44,0.52853,-0.84223,0.10629,44.117,-0.4783,-0.39889,-0.78238,312.72
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.70134,0.36268,-0.61366,125.48,0.52853,-0.84223,0.10629,132.15,-0.4783,-0.39889,-0.78238,308.63
> view matrix models
> #6,0.70134,0.36268,-0.61366,100.94,0.52853,-0.84223,0.10629,125.12,-0.4783,-0.39889,-0.78238,303.35
> view matrix models
> #6,0.70134,0.36268,-0.61366,59.233,0.52853,-0.84223,0.10629,127.48,-0.4783,-0.39889,-0.78238,309.7
> view matrix models
> #6,0.70134,0.36268,-0.61366,83.991,0.52853,-0.84223,0.10629,165.86,-0.4783,-0.39889,-0.78238,356.63
> mmaker #1/A to #6/A
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 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)
> view matrix models
> #6,0.70134,0.36268,-0.61366,84.018,0.52853,-0.84223,0.10629,149.4,-0.4783,-0.39889,-0.78238,367.32
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.36878,0.9289,-0.033825,-31.2,0.91986,-0.36994,-0.1304,51.795,-0.13364,0.016975,-0.99088,281.38
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.36878,0.9289,-0.033825,-67.306,0.91986,-0.36994,-0.1304,60.252,-0.13364,0.016975,-0.99088,284.19
> mmaker #1/A to #6/A
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 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)
> view matrix models
> #6,0.36878,0.9289,-0.033825,-70.459,0.91986,-0.36994,-0.1304,57.715,-0.13364,0.016975,-0.99088,279.62
> view matrix models
> #6,0.36878,0.9289,-0.033825,-66.6,0.91986,-0.36994,-0.1304,59.871,-0.13364,0.016975,-0.99088,287.05
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.75101,0.65467,0.085978,-96.5,0.65998,-0.74023,-0.12843,154.03,-0.020434,0.15319,-0.98799,249.36
> mmaker #1/A to #6/A
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 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.75101,0.65467,0.085978,-95.623,0.65998,-0.74023,-0.12843,159.12,-0.020434,0.15319,-0.98799,246.71
> mmaker #1/A to #6/A
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 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain A (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain A (#1), sequence alignment score = 2347
RMSD between 427 pruned atom pairs is 0.827 angstroms; (across all 437 pairs:
1.506)
> mmaker #1 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation,
chain D (#6) with 7kal T. lanuginosus WT with Sec62 plug-open conformation,
chain D (#1), sequence alignment score = 3216.3
RMSD between 470 pruned atom pairs is 0.543 angstroms; (across all 475 pairs:
0.654)
> hide #2 models
> show #!1 models
> hide #!1 models
> fitmap #6/A inMap #3
Fit molecule 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation
(#6) to map cryosparc_P12_J364_007_volume_map.mrc z flip (#3) using 3386 atoms
average map value = 0.1176, steps = 84
shifted from previous position = 4.61
rotated from previous position = 11.5 degrees
atoms outside contour = 1840, contour level = 0.12075
Position of 7kam 7kal T. lanuginosus WT with Sec62 plug-close conformation
(#6) relative to cryosparc_P12_J364_007_volume_map.mrc z flip (#3)
coordinates:
Matrix rotation and translation
0.82602362 0.56150897 -0.04891494 -67.86582856
0.53971147 -0.81299405 -0.21852274 202.24385256
-0.16247004 0.15410500 -0.97460512 266.94351827
Axis 0.95507491 0.29105086 -0.05586872
Axis point 0.00000000 97.75952528 142.22737827
Rotation angle (degrees) 168.75073396
Shift along axis -20.86749542
> select #6/G
354 atoms, 360 bonds, 62 residues, 1 model selected
> show #2 models
> open 7kai
7kai title:
Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with
Sec62, conformation 1 (C1) [more info...]
Chain information for 7kai #8
---
Chain | Description | UniProt
A | Protein transport protein SEC61 | SC61A_YEAST 1-480
B | Protein transport protein SBH1 | SC6B1_YEAST 1-82
C | Protein transport protein SSS1 | SC61G_YEAST 1-80
D | Protein translocation protein SEC63 | SEC63_YEAST 2-663
E | Translocation protein SEC66 | SEC66_YEAST 1-206
F | Translocation protein SEC72 | SEC72_YEAST 1-193
G | Protein transport protein Sec62 |
> rename #8 "7kai Sc, WT, wtSec62, (C1)"
> open 7kaj
7kaj title:
Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with
Sec62, conformation 2 (C2) [more info...]
Chain information for 7kaj #9
---
Chain | Description | UniProt
A | Protein transport protein SEC61 | SC61A_YEAST 1-480
B | Protein transport protein SBH1 | SC6B1_YEAST 1-82
C | Protein transport protein SSS1 | SC61G_YEAST 1-80
D | Protein translocation protein SEC63 | SEC63_YEAST 2-663
E | Translocation protein SEC66 | SEC66_YEAST 1-206
F | Translocation protein SEC72 | SEC72_YEAST 1-193
G | Protein transport protein Sec62 |
> rename #9 "7kaj Sc, WT, wtSec62, (C2)"
> show sel cartoons
> hide sel atoms
> select add #6
10916 atoms, 11157 bonds, 9 pseudobonds, 1445 residues, 2 models selected
> select subtract #6
Nothing selected
> hide #2#!6,8-9 atoms
> show #2#!6,8-9 cartoons
> select add #8
10718 atoms, 10924 bonds, 6 pseudobonds, 1399 residues, 2 models selected
> select add #9
21430 atoms, 21842 bonds, 12 pseudobonds, 2798 residues, 4 models selected
> view matrix models
> #8,1,0,0,86.197,0,1,0,19.771,0,0,1,25.38,#9,1,0,0,86.197,0,1,0,19.771,0,0,1,25.38
> ui mousemode right "rotate selected models"
> view matrix models
> #8,0.84265,0.50523,-0.18624,55.887,0.4946,-0.86297,-0.10324,257.07,-0.21288,-0.0051208,-0.97707,341.88,#9,0.84265,0.50523,-0.18624,55.887,0.4946,-0.86297,-0.10324,257.07,-0.21288,-0.0051208,-0.97707,341.88
> view matrix models
> #8,0.82869,0.55371,-0.081747,35.268,0.50771,-0.80512,-0.30661,275.05,-0.23559,0.21258,-0.94832,306.48,#9,0.82869,0.55371,-0.081747,35.268,0.50771,-0.80512,-0.30661,275.05,-0.23559,0.21258,-0.94832,306.48
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.82869,0.55371,-0.081747,-84.359,0.50771,-0.80512,-0.30661,236.11,-0.23559,0.21258,-0.94832,274.38,#9,0.82869,0.55371,-0.081747,-84.359,0.50771,-0.80512,-0.30661,236.11,-0.23559,0.21258,-0.94832,274.38
> view matrix models
> #8,0.82869,0.55371,-0.081747,-67.287,0.50771,-0.80512,-0.30661,223.18,-0.23559,0.21258,-0.94832,272.07,#9,0.82869,0.55371,-0.081747,-67.287,0.50771,-0.80512,-0.30661,223.18,-0.23559,0.21258,-0.94832,272.07
> mmaker #8 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7aft Tsai, chain D (#5) with 7kai Sc, WT, wtSec62, (C1), chain D
(#8), sequence alignment score = 3040.5
RMSD between 431 pruned atom pairs is 1.014 angstroms; (across all 486 pairs:
1.292)
> mmaker #9 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7aft Tsai, chain D (#5) with 7kaj Sc, WT, wtSec62, (C2), chain D
(#9), sequence alignment score = 3037.5
RMSD between 451 pruned atom pairs is 0.985 angstroms; (across all 486 pairs:
1.187)
> select subtract #8
10712 atoms, 10918 bonds, 6 pseudobonds, 1399 residues, 2 models selected
> select subtract #9
Nothing selected
> hide #!8 models
> show #!8 models
> hide #2 models
> hide #!6 models
> hide #!8 models
> show #!8 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> mmaker #8/A to #9/A
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 7kaj Sc, WT, wtSec62, (C2), chain A (#9) with 7kai Sc, WT, wtSec62,
(C1), chain A (#8), sequence alignment score = 2348.5
RMSD between 386 pruned atom pairs is 0.512 angstroms; (across all 436 pairs:
1.651)
> show #2 models
> hide #2 models
> select #9/B
229 atoms, 233 bonds, 32 residues, 1 model selected
> show #2 models
> hide #2 models
> clip off
===== 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 - 89.4
OpenGL renderer: Apple M2
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: Mac14,7
Model Number: Z16U000NJD/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 50 days, 20 hours, 32 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P3223QE:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 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 , 4 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 , 4 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
The ChimeraX bug report panel explained 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 ChimeraX daily build is using a newer Qt version 6.9.1 while the ChimeraX 1.10.1 release you are using has Qt 6.8.2. So you might try the daily build to see if it has fixed these multi-display Mac Qt crashes.
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Reported by Ahn Nguyen