![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17258 closed defect (can't reproduce)
Crash running open/save dialog
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.3-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00000001ef630840 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 50 in display
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138 in show_save_file_dialog
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55)
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"captureTime" : "2025-04-01 14:56:53.9643 +0800",
"codeSigningMonitor" : 1,
"incident" : "1D871B8A-1DE7-4D43-9C4B-D4BCE1895CB6",
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"translated" : false,
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"procLaunch" : "2025-04-01 14:31:22.6640 +0800",
"procStartAbsTime" : 26589341273712,
"procExitAbsTime" : 26626092642704,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
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"wakeTime" : 1789,
"sleepWakeUUID" : "49429E98-9771-4CBF-8F34-E04822A00189",
"sip" : "enabled",
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"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":86195},
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex
> 结构预测/AlphaFold3/fold_2025_02_06_16_38_model_0.cif"
Chain information for fold_2025_02_06_16_38_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> color bychain
> open "/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex
> 结构预测/cryosparc_P19_J325_005_volume_map-3.23A.mrc"
Opened cryosparc_P19_J325_005_volume_map-3.23A.mrc as #2, grid size
320,320,320, pixel 0.86, shown at level 0.0315, step 2, values float32
> ui mousemode right zoom
> volume #2 step 1
> volume #2 level 0.1296
> open /Volumes/data-4T/Projects/校外合作/SunLitao/4-BrxC/PDB-
> models/RealSpaceRefine_8/N550-dimer-inimod-
> coot-8_real_space_refined_008-coot_pro-addAGS-addto564.pdb
Chain information for N550-dimer-inimod-
coot-8_real_space_refined_008-coot_pro-addAGS-addto564.pdb #3
---
Chain | Description
A | No description available
B | No description available
> ui mousemode right "translate selected models"
> select add #3
9157 atoms, 9331 bonds, 1125 residues, 1 model selected
> view matrix models #3,1,0,0,-5.7909,0,1,0,-39.132,0,0,1,-10.593
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.37223,0.2285,-0.89958,308.7,0.29219,0.94879,0.12009,-94.233,0.88095,-0.21815,-0.41993,119.16
> view matrix models
> #3,-0.69676,0.67663,-0.23809,178.45,-0.47376,-0.68333,-0.55553,397.55,-0.53859,-0.27427,0.79668,148.52
> view matrix models
> #3,0.26591,-0.94816,0.17404,232.95,-0.88546,-0.16885,0.43296,217.25,-0.38113,-0.26923,-0.88445,393.11
> view matrix models
> #3,0.70404,-0.69021,0.16712,125.41,-0.71007,-0.6804,0.1813,314.84,-0.011425,-0.24631,-0.96912,346.91
> view matrix models
> #3,0.68216,-0.54078,0.49215,52.17,-0.66615,-0.73716,0.11335,328.38,0.30149,-0.40517,-0.8631,308.57
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.68216,-0.54078,0.49215,54.747,-0.66615,-0.73716,0.11335,334.85,0.30149,-0.40517,-0.8631,305.14
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.8152,-0.57431,-0.075013,130.94,-0.54279,-0.80272,0.24702,305.5,-0.20208,-0.16065,-0.9661,357.83
> fitmap #3 inMap #2
Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
using 9157 atoms
average map value = 0.05333, steps = 280
shifted from previous position = 13.4
rotated from previous position = 20 degrees
atoms outside contour = 7710, contour level = 0.12961
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
coordinates:
Matrix rotation and translation
0.95267151 -0.26822987 -0.14307249 59.01134143
-0.24610664 -0.95676971 0.15499437 304.33632268
-0.17846154 -0.11244763 -0.97750039 345.25794382
Axis -0.98804169 0.13074185 0.08173239
Axis point 0.00000000 167.92297449 164.64340021
Rotation angle (degrees) 172.22175202
Shift along axis 9.70258351
> fitmap #3 inMap #2
Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
using 9157 atoms
average map value = 0.05333, steps = 64
shifted from previous position = 0.0138
rotated from previous position = 0.0186 degrees
atoms outside contour = 7705, contour level = 0.12961
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
coordinates:
Matrix rotation and translation
0.95270424 -0.26800051 -0.14328418 59.01005925
-0.24587294 -0.95684849 0.15487886 304.32077469
-0.17860886 -0.11232404 -0.97748769 345.25507278
Axis -0.98805011 0.13062193 0.08182227
Axis point 0.00000000 167.90049672 164.65462415
Rotation angle (degrees) 172.22881560
Shift along axis 9.69562337
> volume #2 level 0.03023
> volume #2 level 0.122
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.9527,-0.268,-0.14328,85.71,-0.24587,-0.95685,0.15488,336.7,-0.17861,-0.11232,-0.97749,274.93
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.52241,-0.82135,-0.22909,255.34,-0.71934,-0.56877,0.39881,305.73,-0.45786,-0.043543,-0.88796,291.62
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.52241,-0.82135,-0.22909,227.62,-0.71934,-0.56877,0.39881,271.38,-0.45786,-0.043543,-0.88796,355.98
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.77538,-0.29852,0.55648,212.67,0.10871,-0.93116,-0.34803,324.98,0.62207,-0.20936,0.75446,-43.495
> view matrix models
> #3,-0.99016,0.0070287,-0.13976,306.64,-0.026244,-0.99034,0.13613,277.57,-0.13745,0.13846,0.98078,-21.713
> fitmap #3 inMap #2
Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
using 9157 atoms
average map value = 0.1503, steps = 272
shifted from previous position = 9.25
rotated from previous position = 44.5 degrees
atoms outside contour = 3491, contour level = 0.12197
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
coordinates:
Matrix rotation and translation
-0.72711438 0.68159229 0.08207695 125.62170437
-0.67472361 -0.73156312 0.09779287 348.46591547
0.12669934 0.01572735 0.99181648 -42.95845621
Axis -0.06036321 -0.03282195 -0.99763671
Axis point 132.75151949 149.96721374 0.00000000
Rotation angle (degrees) 137.17476244
Shift along axis 23.83667299
> fitmap #3 inMap #2
Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
using 9157 atoms
average map value = 0.1503, steps = 40
shifted from previous position = 0.0197
rotated from previous position = 0.0112 degrees
atoms outside contour = 3493, contour level = 0.12197
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
coordinates:
Matrix rotation and translation
-0.72708409 0.68161930 0.08212096 125.60753256
-0.67472618 -0.73153573 0.09797989 348.41603670
0.12685940 0.01583045 0.99179438 -42.98471289
Axis -0.06042322 -0.03290638 -0.99763029
Axis point 132.74015013 149.94601340 0.00000000
Rotation angle (degrees) 137.17326283
Shift along axis 23.82812955
> fitmap #3 inMap #2
Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
using 9157 atoms
average map value = 0.1503, steps = 36
shifted from previous position = 0.00746
rotated from previous position = 0.00342 degrees
atoms outside contour = 3488, contour level = 0.12197
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
coordinates:
Matrix rotation and translation
-0.72707260 0.68163570 0.08208661 125.61463200
-0.67474863 -0.73152068 0.09793766 348.42808464
0.12680585 0.01581996 0.99180139 -42.97611343
Axis -0.06039827 -0.03289139 -0.99763230
Axis point 132.74754586 149.94944732 0.00000000
Rotation angle (degrees) 137.17184823
Shift along axis 23.82716884
> fitmap #3 inMap #2
Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
using 9157 atoms
average map value = 0.1503, steps = 36
shifted from previous position = 0.0155
rotated from previous position = 0.018 degrees
atoms outside contour = 3492, contour level = 0.12197
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
coordinates:
Matrix rotation and translation
-0.72716677 0.68151934 0.08221848 125.61787410
-0.67466186 -0.73163460 0.09768416 348.48555827
0.12672753 0.01556300 0.99181547 -42.92958410
Axis -0.06041012 -0.03274183 -0.99763650
Axis point 132.74391807 149.97882401 0.00000000
Rotation angle (degrees) 137.18002525
Shift along axis 23.82947626
> fitmap #3 inMap #2
Fit molecule N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) to map cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
using 9157 atoms
average map value = 0.1503, steps = 40
shifted from previous position = 0.012
rotated from previous position = 0.0126 degrees
atoms outside contour = 3491, contour level = 0.12197
Position of N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb (#3) relative to cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2)
coordinates:
Matrix rotation and translation
-0.72710741 0.68159166 0.08214399 125.61400717
-0.67471142 -0.73156339 0.09787495 348.44120658
0.12680428 0.01574211 0.99180283 -42.96369464
Axis -0.06041305 -0.03285001 -0.99763277
Axis point 132.74387602 149.95703592 0.00000000
Rotation angle (degrees) 137.17505489
Shift along axis 23.82696649
> select subtract #3
Nothing selected
> volume #2 color #b2b2b289
> ui tool show Matchmaker
> ui mousemode right zoom
> matchmaker #1/A to #3/B pairing ss
Computing secondary structure
Parameters
---
Chain pairing | ss
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 N550-dimer-inimod-coot-8_real_space_refined_008-coot_pro-addAGS-
addto564.pdb, chain B (#3) with fold_2025_02_06_16_38_model_0.cif, chain A
(#1), sequence alignment score = 2634.1
RMSD between 274 pruned atom pairs is 1.035 angstroms; (across all 559 pairs:
7.850)
> hide #!2 models
> show #!2 models
> open "/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex
> 结构预测/AF-brxB.pdb"
Summary of feedback from opening
/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex 结构预测/AF-
brxB.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 17 ILE A 20 1 4
Start residue of secondary structure not found: HELIX 2 2 ASP A 40 GLU A 49 1
10
Start residue of secondary structure not found: HELIX 3 3 ARG A 54 THR A 71 1
18
Start residue of secondary structure not found: HELIX 4 4 ARG A 75 MET A 78 1
4
Start residue of secondary structure not found: HELIX 5 5 LYS A 94 LEU A 105 1
12
99 messages similar to the above omitted
Chain information for AF-brxB.pdb #4
---
Chain | Description
B | No description available
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 1 maps.
> hide #3 models
> show #3 models
> hide #1 models
> hide #4 models
> show #4 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> ui mousemode right "rotate selected models"
> hide #4 models
> show #4 models
> ui mousemode right "translate selected models"
> select #4/B:50
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
183 atoms, 185 bonds, 21 residues, 1 model selected
> select up
1669 atoms, 1711 bonds, 206 residues, 1 model selected
> view matrix models #4,1,0,0,0.84142,0,1,0,0.9042,0,0,1,-2.3685
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.87437,0.45992,-0.15476,-4.6382,-0.47243,0.87965,-0.054976,83.52,0.11085,0.12118,0.98642,-26.939
> view matrix models
> #4,0.99046,0.12409,-0.059896,-1.2675,-0.12351,0.99225,0.013368,16.2,0.061091,-0.0058429,0.99812,-9.679
> view matrix models
> #4,0.97777,0.15678,-0.13926,8.7132,-0.15747,0.9875,0.0061251,22.236,0.13848,0.015941,0.99024,-20.976
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.97777,0.15678,-0.13926,9.6312,-0.15747,0.9875,0.0061251,24.555,0.13848,0.015941,0.99024,-23.486
> fitmap #4 inMap #2
Fit molecule AF-brxB.pdb (#4) to map
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 1669 atoms
average map value = 0.1168, steps = 88
shifted from previous position = 5.29
rotated from previous position = 10.1 degrees
atoms outside contour = 870, contour level = 0.12197
Position of AF-brxB.pdb (#4) relative to
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates:
Matrix rotation and translation
0.99428376 0.09169075 -0.05470478 -2.93318254
-0.09851074 0.98540277 -0.13884166 37.65032173
0.04117574 0.14343701 0.98880250 -22.87973986
Axis 0.79824205 -0.27113584 -0.53786149
Axis point 0.00000000 180.07848216 251.76610812
Rotation angle (degrees) 10.18416361
Shift along axis -0.24361031
> fitmap #4 inMap #2
Fit molecule AF-brxB.pdb (#4) to map
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 1669 atoms
average map value = 0.1168, steps = 28
shifted from previous position = 0.0238
rotated from previous position = 0.0135 degrees
atoms outside contour = 865, contour level = 0.12197
Position of AF-brxB.pdb (#4) relative to
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates:
Matrix rotation and translation
0.99425898 0.09188852 -0.05482315 -2.94335710
-0.09872141 0.98538960 -0.13878553 37.68675605
0.04126937 0.14340098 0.98880382 -22.90478918
Axis 0.79752170 -0.27157878 -0.53870596
Axis point 0.00000000 180.32170649 252.08745033
Rotation angle (degrees) 10.19009676
Shift along axis -0.24336796
> fitmap #4 inMap #2
Fit molecule AF-brxB.pdb (#4) to map
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 1669 atoms
average map value = 0.1168, steps = 28
shifted from previous position = 0.0193
rotated from previous position = 0.00917 degrees
atoms outside contour = 868, contour level = 0.12197
Position of AF-brxB.pdb (#4) relative to
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates:
Matrix rotation and translation
0.99427095 0.09184760 -0.05467439 -2.95232204
-0.09865794 0.98540116 -0.13874859 37.66272739
0.04113249 0.14334776 0.98881724 -22.86844927
Axis 0.79773048 -0.27092896 -0.53872403
Axis point 0.00000000 180.09177056 252.02967958
Rotation angle (degrees) 10.18411182
Shift along axis -0.23929770
> fitmap #4 inMap #2
Fit molecule AF-brxB.pdb (#4) to map
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 1669 atoms
average map value = 0.1168, steps = 40
shifted from previous position = 0.00407
rotated from previous position = 0.0123 degrees
atoms outside contour = 868, contour level = 0.12197
Position of AF-brxB.pdb (#4) relative to
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates:
Matrix rotation and translation
0.99426586 0.09178151 -0.05487762 -2.91335159
-0.09862102 0.98540695 -0.13873367 37.65380769
0.04134361 0.14335024 0.98880808 -22.89851145
Axis 0.79758908 -0.27206444 -0.53836102
Axis point 0.00000000 180.31302577 251.97290682
Rotation angle (degrees) 10.18548275
Shift along axis -0.24025353
> show #1 models
> hide #1 models
> select subtract #4
Nothing selected
> ui mousemode right zoom
> show #1 models
> ui tool show Matchmaker
> matchmaker #4/B to #1/B pairing ss
Computing secondary structure
Parameters
---
Chain pairing | ss
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_06_16_38_model_0.cif, chain B (#1) with AF-brxB.pdb,
chain B (#4), sequence alignment score = 1092.9
RMSD between 206 pruned atom pairs is 0.000 angstroms; (across all 206 pairs:
0.000)
> undo
> show #1 models
> open "/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex
> 结构预测/AF-BrxZ.pdb"
Summary of feedback from opening
/Volumes/data-4T/Projects/校外合作/SunLitao/5-BCZ-complex/C550BZ complex 结构预测/AF-
BrxZ.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 17 ILE A 20 1 4
Start residue of secondary structure not found: HELIX 2 2 ASP A 40 GLU A 49 1
10
Start residue of secondary structure not found: HELIX 3 3 ARG A 54 THR A 71 1
18
Start residue of secondary structure not found: HELIX 4 4 ARG A 75 MET A 78 1
4
Start residue of secondary structure not found: HELIX 5 5 LYS A 94 LEU A 105 1
12
51 messages similar to the above omitted
Chain information for AF-BrxZ.pdb #5
---
Chain | Description
C | No description available
> hide #4 models
> hide #3 models
> hide #!2 models
> hide #1 models
> show #!2 models
> show #3 models
> show #4 models
> hide #5 models
> show #5 models
> select #5/C:8
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
118 atoms, 119 bonds, 15 residues, 1 model selected
> select up
7133 atoms, 7292 bonds, 871 residues, 1 model selected
> volume #2 level 0.06315
> volume #2 level 0.07593
> fitmap #5 inMap #2
Fit molecule AF-BrxZ.pdb (#5) to map
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) using 7133 atoms
average map value = 0.04619, steps = 484
shifted from previous position = 37.8
rotated from previous position = 19 degrees
atoms outside contour = 5410, contour level = 0.075935
Position of AF-BrxZ.pdb (#5) relative to
cryosparc_P19_J325_005_volume_map-3.23A.mrc (#2) coordinates:
Matrix rotation and translation
0.98166123 -0.05374970 -0.18289943 69.15628069
0.10063652 0.96096034 0.25773534 -49.75606256
0.16190591 -0.27141516 0.94874669 35.23366351
Axis -0.81385997 -0.53032788 0.23745374
Axis point 0.00000000 100.94248704 252.64231618
Rotation angle (degrees) 18.97084245
Shift along axis -21.53013615
> hide #5 models
> hide #4 models
> show #4 models
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/Li/Downloads/cryosparc_P22_J202_008_volume_map.mrc
Opened cryosparc_P22_J202_008_volume_map.mrc as #1, grid size 360,360,360,
pixel 0.86, shown at level 0.00785, step 2, values float32
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: MacBookAir10,1
Model Number: Z1250003LCH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.81.2
OS Loader Version: 11881.81.2
Software:
System Software Overview:
System Version: macOS 15.3 (24D60)
Kernel Version: Darwin 24.3.0
Time since boot: 31 days, 5 hours, 18 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
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
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash running open/save dialog |
comment:2 by , 7 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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