![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 21 months ago
Closed 21 months ago
#14450 closed defect (can't reproduce)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: macOS-14.0-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x0000000204993240 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 1382 in
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 1382 in get_tangents
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 1189 in __init__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 156 in _make_ribbon_graphics
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/ribbon.py", line 600 in compute_ribbons
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 667 in _create_ribbon_graphics
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 357 in update_graphics_if_needed
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1891 in _update_graphics_if_needed
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 294 in check_for_drawing_change
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, lxml._elementpath, lxml.etree, 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, chimerax.mmcif.mmcif_write, lxml.builder (total: 56)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
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"modelCode" : "Mac14,2",
"coalitionID" : 3361,
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"captureTime" : "2024-01-22 16:56:08.3731 -0800",
"codeSigningMonitor" : 1,
"incident" : "3482E60E-BBCD-4EA2-9CA7-0558FF7125F2",
"pid" : 10048,
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"cpuType" : "X86-64",
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"procLaunch" : "2024-01-22 15:43:05.7844 -0800",
"procStartAbsTime" : 1300750641894,
"procExitAbsTime" : 1405932330349,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"DC33E73C-FA52-5625-BB1C-E16B2534C308","thirdParty":true},
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"parentPid" : 1,
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"crashReporterKey" : "D90B7D68-427E-98ED-CD16-515C91CC8B65",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 8891,
"sleepWakeUUID" : "EDE8CA60-DD36-425C-80A2-C1E200AB93A8",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140723131826007\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca848c000-7ffccdbac000 [599.1M] r-x\/r-x SM=COW ...t_id=a97e7b63",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":10048},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140723131826007\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffca848c000-7ffccdbac000 [599.1M] r-x\/r-x SM=COW ...t_id=a97e7b63",
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"faultingThread" : 0,
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Atom #1/A:583@C 207.812 138.330 162.063
Atom #1/A:583@O 207.647 138.198 163.281
Atom #1/A:583@CB 206.643 140.355 161.085
Atom #1/A:583@CG1 205.616 140.108 162.176
Atom #1/A:583@CG2 206.807 141.843 160.833
Atom #1/A:584@N 207.844 137.280 161.241
Atom #1/A:584@CA 207.628 135.934 161.760
Atom #1/A:584@C 208.835 135.425 162.536
Atom #1/A:584@O 208.674 134.678 163.507
Atom #1/A:584@CB 207.287 134.976 160.619
Atom #1/A:584@CG 206.024 135.341 159.857
Atom #1/A:584@CD 204.872 135.723 160.771
Atom #1/A:584@OE1 204.201 136.740 160.492
Atom #1/A:584@OE2 204.636 135.008 161.767
Atom #1/A:585@N 210.044 135.809 162.130
Atom #1/A:585@CA 211.230 135.424 162.886
Atom #1/A:585@C 211.375 136.278 164.139
Atom #1/A:585@O 211.918 135.820 165.150
Atom #1/A:585@CB 212.478 135.512 161.991
Atom #1/A:585@CG1 212.535 134.313 161.046
Atom #1/A:585@CG2 213.741 135.602 162.832
Atom #1/A:585@CD1 213.430 134.522 159.854
Atom #1/A:586@N 210.883 137.516 164.105
Atom #1/A:586@CA 210.960 138.401 165.258
Atom #1/A:586@C 209.956 138.036 166.344
Atom #1/A:586@O 210.163 138.399 167.506
Atom #1/A:586@CB 210.742 139.848 164.808
Atom #1/A:586@CG 211.215 140.999 165.696
Atom #1/A:586@CD1 212.703 140.903 165.979
Atom #1/A:586@CD2 210.880 142.321 165.030
Atom #1/A:587@N 208.880 137.332 165.995
Atom #1/A:587@CA 207.875 136.905 166.960
Atom #1/A:587@C 208.242 135.612 167.668
Atom #1/A:587@O 207.454 135.127 168.486
Atom #1/A:587@CB 206.518 136.738 166.273
Atom #1/A:587@CG 205.782 138.006 165.847
Atom #1/A:587@CD1 204.500 137.644 165.128
Atom #1/A:587@CD2 205.503 138.899 167.042
Atom #1/A:588@N 209.410 135.044 167.375
Atom #1/A:588@CA 209.831 133.791 167.980
Atom #1/A:588@C 211.205 133.852 168.627
Atom #1/A:588@O 211.565 132.915 169.347
Atom #1/A:588@CB 209.809 132.661 166.939
Atom #1/A:588@CG 210.777 132.849 165.787
Atom #1/A:588@CD 210.645 131.762 164.738
Atom #1/A:588@OE1 209.786 130.873 164.907
Atom #1/A:588@OE2 211.398 131.797 163.741
Atom #1/A:589@N 211.980 134.911 168.399
Atom #1/A:589@CA 213.267 135.089 169.059
Atom #1/A:589@C 213.385 136.388 169.839
Atom #1/A:589@O 214.228 136.463 170.739
Atom #1/A:589@CB 214.409 135.020 168.035
Atom #1/A:589@CG 214.266 133.880 167.046
Atom #1/A:589@CD 215.249 134.008 165.901
Atom #1/A:589@CE 216.642 133.578 166.315
Atom #1/A:589@NZ 217.507 133.341 165.130
Atom #1/A:590@N 212.586 137.406 169.529
Atom #1/A:590@CA 212.458 138.678 170.230
Atom #1/A:590@C 213.646 139.611 169.963
Atom #1/A:590@O 213.553 140.798 170.273
Atom #1/A:590@CB 212.283 138.494 171.753
Atom #1/A:590@CG 212.160 139.765 172.584
Atom #1/A:590@CD 212.041 139.480 174.074
Atom #1/A:590@OE1 210.905 139.322 174.564
Atom #1/A:590@OE2 213.085 139.410 174.753
Atom #1/A:591@N 214.721 139.142 169.332
Atom #1/A:591@CA 215.885 139.977 169.066
Atom #1/A:591@C 216.756 139.298 168.019
Atom #1/A:591@O 216.958 138.084 168.068
Atom #1/A:591@CB 216.708 140.235 170.336
Atom #1/A:591@CG2 217.954 141.038 170.008
Atom #1/A:591@OG1 215.923 140.962 171.288
Atom #1/A:592@N 217.270 140.091 167.082
Atom #1/A:592@CA 218.189 139.622 166.052
Atom #1/A:592@C 219.352 140.601 165.980
Atom #1/A:592@O 219.140 141.818 165.962
Atom #1/A:592@CB 217.502 139.498 164.678
Atom #1/A:592@CG1 216.135 138.830 164.816
Atom #1/A:592@CG2 218.370 138.705 163.723
Atom #1/A:592@CD1 215.212 139.090 163.646
Atom #1/A:593@N 220.576 140.077 165.931
Atom #1/A:593@CA 221.744 140.949 165.967
Atom #1/A:593@C 222.821 140.525 164.973
Atom #1/A:593@O 222.570 139.698 164.091
Atom #1/A:593@CB 222.306 141.021 167.388
Atom #1/A:593@CG 222.830 139.718 167.936
Atom #1/A:593@CD 223.258 139.844 169.382
Atom #1/A:593@OE1 223.107 140.946 169.949
Atom #1/A:593@OE2 223.742 138.845 169.954
Atom #1/A:594@N 224.028 141.065 165.143
Atom #1/A:594@CA 224.986 141.307 164.074
Atom #1/A:594@C 225.190 140.298 162.960
Atom #1/A:594@O 224.837 140.584 161.812
Atom #1/A:595@N 225.748 139.124 163.259
Atom #1/A:595@CA 226.068 138.199 162.175
Atom #1/A:595@C 224.848 137.404 161.731
Atom #1/A:595@O 224.684 137.132 160.537
Atom #1/A:595@CB 227.205 137.265 162.588
Atom #1/A:595@CG 228.550 137.966 162.611
Atom #1/A:595@OD1 228.730 138.929 161.834
Atom #1/A:595@OD2 229.425 137.555 163.401
Atom #1/A:596@N 223.977 137.033 162.669
Atom #1/A:596@CA 222.734 136.372 162.292
Atom #1/A:596@C 221.825 137.301 161.495
Atom #1/A:596@O 221.026 136.831 160.677
Atom #1/A:596@CB 222.017 135.861 163.539
Atom #1/A:596@CG 220.660 135.254 163.266
Atom #1/A:596@CD 220.387 134.040 164.126
Atom #1/A:596@OE1 219.499 133.243 163.759
Atom #1/A:596@OE2 221.057 133.880 165.168
Atom #1/A:597@N 221.932 138.613 161.715
Atom #1/A:597@CA 221.096 139.564 160.991
Atom #1/A:597@C 221.629 139.850 159.592
Atom #1/A:597@O 220.842 140.120 158.680
Atom #1/A:597@CB 220.974 140.869 161.782
Atom #1/A:597@CG 220.131 141.971 161.139
Atom #1/A:597@CD1 218.734 141.465 160.822
Atom #1/A:597@CD2 220.070 143.198 162.030
Atom #1/A:598@N 222.951 139.801 159.403
Atom #1/A:598@CA 223.518 140.019 158.076
Atom #1/A:598@C 223.081 138.932 157.103
Atom #1/A:598@O 222.745 139.218 155.948
Atom #1/A:598@CB 225.042 140.077 158.159
Atom #1/A:598@CG 225.609 141.483 158.206
Atom #1/A:598@CD 227.121 141.458 158.323
Atom #1/A:598@NE 227.556 141.274 159.703
Atom #1/A:598@CZ 227.875 142.269 160.523
Atom #1/A:598@NH1 227.808 143.524 160.099
Atom #1/A:598@NH2 228.261 142.014 161.765
Atom #1/A:599@N 223.081 137.677 157.554
Atom #1/A:599@CA 222.692 136.575 156.681
Atom #1/A:599@C 221.227 136.677 156.276
Atom #1/A:599@O 220.879 136.441 155.113
Atom #1/A:599@CB 222.970 135.243 157.374
Atom #1/A:599@CG 222.601 134.022 156.552
Atom #1/A:599@CD 222.880 132.742 157.319
Atom #1/A:599@NE 222.249 132.743 158.635
Atom #1/A:599@CZ 220.944 132.599 158.838
Atom #1/A:599@NH1 220.123 132.444 157.808
Atom #1/A:599@NH2 220.456 132.612 160.071
Atom #1/A:600@N 220.352 137.026 157.221
Atom #1/A:600@CA 218.926 137.115 156.920
Atom #1/A:600@C 218.653 138.240 155.930
Atom #1/A:600@O 217.864 138.080 154.991
Atom #1/A:600@CB 218.117 137.292 158.218
Atom #1/A:600@CG1 218.121 135.997 159.029
Atom #1/A:600@CG2 216.694 137.727 157.907
Atom #1/A:600@CD1 217.568 136.153 160.426
Atom #1/A:601@N 219.299 139.392 156.117
Atom #1/A:601@CA 219.095 140.518 155.215
Atom #1/A:601@C 219.702 140.289 153.837
Atom #1/A:601@O 219.390 141.045 152.911
Atom #1/A:601@CB 219.673 141.797 155.826
Atom #1/A:601@CG 218.843 142.469 156.922
Atom #1/A:601@CD1 219.516 143.742 157.404
Atom #1/A:601@CD2 217.436 142.760 156.433
Atom #1/A:602@N 220.556 139.279 153.678
Atom #1/A:602@CA 221.105 138.943 152.371
Atom #1/A:602@C 220.240 137.931 151.631
Atom #1/A:602@O 220.109 138.010 150.406
Atom #1/A:602@CB 222.530 138.403 152.516
Atom #1/A:602@OG 223.399 139.393 153.034
Atom #1/A:603@N 219.651 136.975 152.353
Atom #1/A:603@CA 218.702 136.059 151.728
Atom #1/A:603@C 217.511 136.816 151.154
Atom #1/A:603@O 217.035 136.498 150.058
Atom #1/A:603@CB 218.240 135.012 152.738
Atom #1/A:603@CG 219.370 134.363 153.516
Atom #1/A:603@CD 218.924 133.844 154.870
Atom #1/A:603@OE1 217.730 133.998 155.203
Atom #1/A:603@OE2 219.768 133.284 155.602
Atom #1/A:604@N 217.017 137.810 151.879
Atom #1/A:604@CA 216.028 138.736 151.354
Atom #1/A:604@C 216.731 139.887 150.642
Atom #1/A:604@O 217.938 140.092 150.784
Atom #1/A:604@CB 215.137 139.269 152.477
Atom #1/A:604@CG 213.870 138.462 152.714
Atom #1/A:604@CD 214.131 137.147 153.420
Atom #1/A:604@OE1 215.016 137.107 154.300
Atom #1/A:604@OE2 213.450 136.152 153.096
Atom #1/A:605@N 215.959 140.637 149.863
Atom #1/A:605@CA 216.491 141.790 149.139
Atom #1/A:605@C 217.571 141.384 148.141
Atom #1/A:605@O 217.751 140.202 147.848
Atom #1/A:605@CB 217.052 142.827 150.117
Atom #1/A:605@CG 216.019 143.418 151.030
Atom #1/A:605@CD1 215.036 144.254 150.535
Atom #1/A:605@CD2 216.028 143.131 152.383
Atom #1/A:605@CE1 214.087 144.795 151.372
Atom #1/A:605@CE2 215.082 143.669 153.223
Atom #1/A:605@CZ 214.111 144.503 152.718
Atom #1/A:800@MG 215.753 154.838 193.412
Atom #1/A:800@ZN 209.382 154.659 164.824
Atom #1/A:801@PA 216.413 150.494 192.485
Atom #1/A:801@PB 215.484 152.570 190.821
Atom #1/A:801@PG 213.280 154.344 191.040
Atom #1/A:801@C5' 214.629 148.660 193.123
Atom #1/A:801@O5' 215.921 148.976 192.619
Atom #1/A:801@C4' 214.494 147.161 193.368
Atom #1/A:801@O4' 214.448 146.457 192.129
Atom #1/A:801@C3' 215.630 146.577 194.195
Atom #1/A:801@O3' 215.139 146.174 195.476
Atom #1/A:801@C2' 216.147 145.394 193.403
Atom #1/A:801@O2' 215.973 144.192 194.151
Atom #1/A:801@C1' 215.337 145.341 192.115
Atom #1/A:801@N1 219.167 143.201 189.203
Atom #1/A:801@O1A 217.868 150.442 192.111
Atom #1/A:801@O1B 215.863 152.672 189.373
Atom #1/A:801@O1G 213.314 154.901 189.643
Atom #1/A:801@C2 218.612 142.760 190.345
Atom #1/A:801@O2A 216.001 151.261 193.715
Atom #1/A:801@O2B 216.231 153.382 191.845
Atom #1/A:801@O2G 211.893 154.080 191.559
Atom #1/A:801@N3 217.630 143.410 190.993
Atom #1/A:801@O3A 215.561 151.018 191.224
Atom #1/A:801@O3B 213.906 152.864 190.927
Atom #1/A:801@O3G 214.172 155.063 192.020
Atom #1/A:801@C4 217.128 144.572 190.518
Atom #1/A:801@C5 217.687 145.113 189.279
Atom #1/A:801@C6 218.761 144.348 188.624
Atom #1/A:801@N6 219.300 144.811 187.481
Atom #1/A:801@N7 217.040 146.250 189.023
Atom #1/A:801@C8 216.142 146.436 190.010
Atom #1/A:801@N9 216.198 145.440 190.910
Atom #1/A:801@HN61 220.033 144.301 187.025
Atom #1/A:801@HN62 218.964 145.671 187.087
Atom #1/A:801@HO2' 216.594 144.190 194.888
Atom #1/A:801@HO3' 215.879 146.088 196.092
Atom #1/A:801@H2 218.974 141.838 190.768
Atom #1/A:801@H8 215.478 147.284 190.060
Atom #1/A:801@H1' 214.770 144.405 192.092
Atom #1/A:801@H2' 217.209 145.545 193.182
Atom #1/A:801@H3' 216.441 147.301 194.322
Atom #1/A:801@H4' 213.559 146.989 193.910
Atom #1/A:801@H5'1 214.457 149.203 194.050
Atom #1/A:801@H5'2 213.876 148.978 192.406
> getcrd #3 screen
No atoms specified
> getcrd #3 scene
No atoms specified
> ui tool show "Volume Viewer"
> show #!3 models
> close #2
> view orient
> sym #1 c1*h,9.1,157.5,5 coordinateSystem #3 addMmcifAssembly true
Made 5 copies for FtsH_fresh_group1_segi.cif symmetry c1*h,9.1,157.5,5
> hide #!3 models
> show #!3 models
> view
> hide #!2 models
> show #!1 models
> view orient
> move [223.5,223.5,0] models #1
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> move x 223.5 1 y 223.5 1 models #1
Expected a keyword
> move x 223.5 1, y 223.5 1 models #1
Expected an integer >= 1 or a keyword
> move x 223.5 1 models #1
> view
> move x 223.5 1 models #1
> view
> move x 223.5 1 models #1
> view
> move x -223.5 1 models #1
> move y 223.5 1 models #1
> move y -223.5 1 models #1
> view orient
> select add #1
3176 atoms, 3218 bonds, 406 residues, 1 model selected
> close #3
> close #1
> close #2
> open /Users/yiyingli/Desktop/FtsH_fresh_group1_segi.cif
Summary of feedback from opening
/Users/yiyingli/Desktop/FtsH_fresh_group1_segi.cif
---
warnings | Unknown polymer entity '1' near line 37
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for FtsH_fresh_group1_segi.cif #1
---
Chain | Description
A | No description available
> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA
> W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc" format mrc
Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #2, grid size
448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32
> volume #2 step 1
> volume #2 level 1.5
> view orient
> view #2 clip false
> move y 20 1 coordinateSystem #2 models #1
> hide #!2 models
> move y -20 1 coordinateSystem #2 models #1
> show #!2 models
> hide #!2 models
> move y -20 1 models #1
> show #!2 models
> hide #!2 models
> open /Users/yiyingli/Desktop/FtsH_fresh_group1_segi.cif
Summary of feedback from opening
/Users/yiyingli/Desktop/FtsH_fresh_group1_segi.cif
---
warnings | Unknown polymer entity '1' near line 37
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for FtsH_fresh_group1_segi.cif #3
---
Chain | Description
A | No description available
> move y -20 1 models #1
> show #!2 models
> hide #!2 models
> move y 20 1 models #1
> move y 20 1 coordinateSystem #2 models #3
> show #!2 models
> hide #!2 models
> move y -20 1 coordinateSystem #2 models #3
> move y -20 1 models #1
> sym #1 h,9.1,157.5,5 coordinateSystem #2
Made 5 copies for FtsH_fresh_group1_segi.cif symmetry h,9.1,157.5,5
> sym #3 h,9.1,157.5,5
Made 5 copies for FtsH_fresh_group1_segi.cif symmetry h,9.1,157.5,5
> view
> hide #!4 models
> show #!4 models
> view position #2
Missing required "same_as_models" argument
> view matrix models #2
Invalid "models" argument: Expected model id and 12 comma-separated numbers
> view matrix models #1
Invalid "models" argument: Expected model id and 12 comma-separated numbers
> view matrix models
Missing "models" keyword's argument
> view matrix models #2
Invalid "models" argument: Expected model id and 12 comma-separated numbers
> view matrix
view matrix camera 1,0,0,3.2827,0,1,0,-31.654,0,0,1,1457
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.2,-0.92388,-0.38268,0,0,0.38268,-0.92388,0,0,0,0,1,9.1,#4.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.3,0.70711,0.70711,0,0,-0.70711,0.70711,0,0,0,0,1,18.2,#4.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.4,-0.38268,-0.92388,0,0,0.92388,-0.38268,0,0,0,0,1,27.3,#4.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#4.5,-4.4409e-16,1,0,0,-1,-4.4409e-16,0,0,0,0,1,36.4,#4.5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.1.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.2,-0.92388,-0.38268,0,0,0.38268,-0.92388,0,0,0,0,1,9.1,#5.2.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.3,0.70711,0.70711,0,0,-0.70711,0.70711,0,0,0,0,1,18.2,#5.3.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.4,-0.38268,-0.92388,0,0,0.92388,-0.38268,0,0,0,0,1,27.3,#5.4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5.5,-4.4409e-16,1,0,0,-1,-4.4409e-16,0,0,0,0,1,36.4,#5.5.1,1,0,0,0,0,1,0,0,0,0,1,0
> close #4
> close #5
> view matrix
view matrix camera 1,0,0,3.2827,0,1,0,-31.654,0,0,1,1457
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0
> hide #2.1 models
> show #!2 models
> show #!3 models
> sym #3 h,9.1,157.5,5
Made 5 copies for FtsH_fresh_group1_segi.cif symmetry h,9.1,157.5,5
> combine #4
Remapping chain ID 'A' in FtsH_fresh_group1_segi.cif #4.2 to 'B'
Remapping chain ID 'A' in FtsH_fresh_group1_segi.cif #4.3 to 'C'
Remapping chain ID 'A' in FtsH_fresh_group1_segi.cif #4.4 to 'D'
Remapping chain ID 'A' in FtsH_fresh_group1_segi.cif #4.5 to 'E'
> save "/Users/yiyingli/Desktop/try pdb.pdb"
> sym #3 h,9.1,157.5,5 addMmcifAssembly true
Made 5 copies for FtsH_fresh_group1_segi.cif symmetry h,9.1,157.5,5
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M2
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: Mac
Model Identifier: Mac14,2
Model Number: FLY13LL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 3 days, 8 hours, 53 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2414H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 50.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
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: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
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: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
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: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 21 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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