![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15790 closed defect (can't reproduce)
Unknown crash
| 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
The following bug report has been submitted:
Platform: macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.9.dev202406122300 (2024-06-12 23:00:04 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 0x00000001e5d4a500 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 55)
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"pid" : 45773,
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"procLaunch" : "2024-08-20 16:00:56.1012 +0900",
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"crashReporterKey" : "BAD2AE41-161A-1B52-2311-32EA41EAEBF4",
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}
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"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.9.dev202406122300 (2024-06-12)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/uijin/Downloads/cryosparc_P9_J214_map_sharp.mrc
Opened cryosparc_P9_J214_map_sharp.mrc as #1, grid size 240,240,240, pixel
0.901, shown at level 8.4e-05, step 1, values float32
> open /Users/uijin/Downloads/cryosparc_P9_J211_map_sharp.mrc
Opened cryosparc_P9_J211_map_sharp.mrc as #2, grid size 320,320,320, pixel
0.705, shown at level 9.36e-05, step 2, values float32
> open /Users/uijin/Downloads/cryosparc_P3_J1394_008_volume_map_sharp.mrc
Opened cryosparc_P3_J1394_008_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 0.705, shown at level 0.0486, step 2, values float32
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume level 0.5
> hide #!2 models
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map cryosparc_P3_J1394_008_volume_map_sharp.mrc in map
cryosparc_P9_J214_map_sharp.mrc using 1354 points
correlation = 0.4596, correlation about mean = 0.06927, overlap = 85.6
steps = 112, shift = 0.765, angle = 5.44 degrees
Position of cryosparc_P3_J1394_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P9_J214_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99661480 -0.00651889 0.08195391 -7.92418870
0.01039274 0.99884405 -0.04693129 4.73821863
-0.08155324 0.04762414 0.99553052 5.02205267
Axis 0.49861880 0.86222167 0.08918002
Axis point 55.32507105 0.00000000 102.51770518
Rotation angle (degrees) 5.44080744
Shift along axis 0.58211208
> volume level 0.3
> select add #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.99661,-0.0065189,0.081954,-11.541,0.010393,0.99884,-0.046931,2.6864,-0.081553,0.047624,0.99553,-0.65721
> fitmap #3 inMap #1
Fit map cryosparc_P3_J1394_008_volume_map_sharp.mrc in map
cryosparc_P9_J214_map_sharp.mrc using 3755 points
correlation = 0.5523, correlation about mean = 0.1135, overlap = 263.3
steps = 104, shift = 3.4, angle = 3.86 degrees
Position of cryosparc_P3_J1394_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P9_J214_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99963779 0.01818816 0.01983655 -4.59989748
-0.01706680 0.99832366 -0.05530462 5.34700337
-0.02080918 0.05494604 0.99827246 -8.73445506
Axis 0.89869045 0.33131710 -0.28737513
Axis point 0.00000000 161.05001485 90.91611559
Rotation angle (degrees) 3.51670897
Shift along axis 0.14773486
> view matrix models
> #3,0.99964,0.018188,0.019837,-8.5419,-0.017067,0.99832,-0.055305,3.0918,-0.020809,0.054946,0.99827,-8.5002
> fitmap #3 inMap #1
Fit map cryosparc_P3_J1394_008_volume_map_sharp.mrc in map
cryosparc_P9_J214_map_sharp.mrc using 3755 points
correlation = 0.9133, correlation about mean = 0.6228, overlap = 789.5
steps = 52, shift = 1.11, angle = 2.58 degrees
Position of cryosparc_P3_J1394_008_volume_map_sharp.mrc (#3) relative to
cryosparc_P9_J214_map_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99971353 0.02269228 0.00761047 -8.68927063
-0.02259718 0.99966828 -0.01235723 -0.78749182
-0.00788836 0.01218171 0.99989468 -5.24822930
Axis 0.45618740 0.28812880 -0.84194706
Axis point -43.43529210 386.95054957 0.00000000
Rotation angle (degrees) 1.54119443
Shift along axis 0.22789636
> select clear
> open
> /Users/uijin/Desktop/Phenix/GTR1_I3M/RealSpaceRefine_27/1279-coot-9_real_space_refined_027.pdb
Chain information for 1279-coot-9_real_space_refined_027.pdb #4
---
Chain | Description
B | No description available
> rename #4 GTR1_I3M
> rename #3 GTR1_I3M
> rename #1 GTR1_4MTB
> open
> /Users/uijin/Desktop/Phenix/GTR1_4MTB/RealSpaceRefine_81/4MTB_1403-coot-1_real_space_refined_081.pdb
Chain information for 4MTB_1403-coot-1_real_space_refined_081.pdb #5
---
Chain | Description
B | No description available
> fitmap #5 inMap #1
Fit molecule 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) to map GTR1_4MTB
(#1) using 4279 atoms
average map value = 0.3419, steps = 40
shifted from previous position = 0.00846
rotated from previous position = 0.0178 degrees
atoms outside contour = 2253, contour level = 0.3
Position of 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) relative to
GTR1_4MTB (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00006738 -0.00005690 0.00695491
0.00006736 0.99999995 -0.00029796 0.01930624
0.00005692 0.00029795 0.99999995 -0.03758873
Axis 0.95888242 -0.18313496 0.21680887
Axis point 0.00000000 122.51519116 61.69268913
Rotation angle (degrees) 0.01780371
Shift along axis -0.00501628
> fitmap #5 inMap #1
Fit molecule 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) to map GTR1_4MTB
(#1) using 4279 atoms
average map value = 0.3419, steps = 40
shifted from previous position = 0.00187
rotated from previous position = 0.00345 degrees
atoms outside contour = 2253, contour level = 0.3
Position of 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) relative to
GTR1_4MTB (#1) coordinates:
Matrix rotation and translation
1.00000000 -0.00008408 -0.00001375 0.00311433
0.00008408 0.99999996 -0.00025949 0.01453845
0.00001377 0.00025949 0.99999997 -0.03019469
Axis 0.95009914 -0.05038224 0.30785264
Axis point 0.00000000 107.98123295 54.63826711
Rotation angle (degrees) 0.01564873
Shift along axis -0.00706907
> fitmap #5 inMap #1
Fit molecule 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) to map GTR1_4MTB
(#1) using 4279 atoms
average map value = 0.3418, steps = 28
shifted from previous position = 0.0171
rotated from previous position = 0.0152 degrees
atoms outside contour = 2252, contour level = 0.3
Position of 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) relative to
GTR1_4MTB (#1) coordinates:
Matrix rotation and translation
0.99999999 0.00005306 -0.00010675 -0.00471675
-0.00005311 0.99999989 -0.00046564 0.06287255
0.00010673 0.00046565 0.99999989 -0.07348019
Axis 0.96875605 -0.22206955 -0.11043930
Axis point 0.00000000 160.30495253 130.01829084
Rotation angle (degrees) 0.02753986
Shift along axis -0.01041635
> fitmap #5 inMap #1
Fit molecule 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) to map GTR1_4MTB
(#1) using 4279 atoms
average map value = 0.3418, steps = 40
shifted from previous position = 0.00552
rotated from previous position = 0.00689 degrees
atoms outside contour = 2255, contour level = 0.3
Position of 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) relative to
GTR1_4MTB (#1) coordinates:
Matrix rotation and translation
0.99999998 0.00001034 -0.00021471 0.01328375
-0.00001043 0.99999991 -0.00043438 0.05005478
0.00021471 0.00043439 0.99999988 -0.08009326
Axis 0.89626092 -0.44300896 -0.02143402
Axis point 0.00000000 184.83309491 106.46920718
Rotation angle (degrees) 0.02776922
Shift along axis -0.00855229
> fitmap #5 inMap #1
Fit molecule 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) to map GTR1_4MTB
(#1) using 4279 atoms
average map value = 0.3419, steps = 40
shifted from previous position = 0.00302
rotated from previous position = 0.0133 degrees
atoms outside contour = 2257, contour level = 0.3
Position of 4MTB_1403-coot-1_real_space_refined_081.pdb (#5) relative to
GTR1_4MTB (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00002440 -0.00002853 -0.00666211
-0.00002441 0.99999996 -0.00029617 0.03424570
0.00002852 0.00029618 0.99999996 -0.04514688
Axis 0.99206200 -0.09554692 -0.08175438
Axis point 0.00000000 154.15875178 113.60674880
Rotation angle (degrees) 0.01710535
Shift along axis -0.00619034
> rename #5 GTR1_4MTB
> close #2
> rename #3 I3M_map
> rename #4 I3M_model
> rename #5 4MTB_model
> rename #1 4MTB_map
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> fitmap #4 inMap #3
Fit molecule I3M_model (#4) to map I3M_map (#3) using 4567 atoms
average map value = 0.03086, steps = 76
shifted from previous position = 1.22
rotated from previous position = 5.04 degrees
atoms outside contour = 4245, contour level = 0.3
Position of I3M_model (#4) relative to I3M_map (#3) coordinates:
Matrix rotation and translation
0.99687574 -0.02101553 0.07613870 -0.46519254
0.02210901 0.99966377 -0.01354730 4.97232827
-0.07582839 0.01518832 0.99700520 12.49583890
Axis 0.17897143 0.94648265 0.26858858
Axis point 135.32684774 0.00000000 30.41867616
Rotation angle (degrees) 4.60465535
Shift along axis 7.97920593
> select add #4
4567 atoms, 4682 bonds, 548 residues, 1 model selected
> view matrix models
> #4,0.99651,0.0017907,0.083397,-8.1072,0.00051212,0.99962,-0.027584,4.2884,-0.083415,0.02753,0.99613,3.1736
> view matrix models
> #4,0.99651,0.0017907,0.083397,-11.061,0.00051212,0.99962,-0.027584,3.063,-0.083415,0.02753,0.99613,3.0719
> view matrix models
> #4,0.99651,0.0017907,0.083397,-11.562,0.00051212,0.99962,-0.027584,-0.15603,-0.083415,0.02753,0.99613,2.4692
> fitmap #4 inMap #3
Fit molecule I3M_model (#4) to map I3M_map (#3) using 4567 atoms
average map value = 0.06295, steps = 76
shifted from previous position = 2.48
rotated from previous position = 4.5 degrees
atoms outside contour = 4052, contour level = 0.3
Position of I3M_model (#4) relative to I3M_map (#3) coordinates:
Matrix rotation and translation
0.99995045 -0.00993957 0.00055029 5.99936727
0.00995207 0.99944078 -0.03192299 4.10500349
-0.00023268 0.03192688 0.99949018 -4.25000081
Axis 0.95467579 0.01170681 0.29741736
Axis point 0.00000000 177.12117070 123.83361811
Rotation angle (degrees) 1.91636285
Shift along axis 4.51148320
> fitmap #4 inMap #3
Fit molecule I3M_model (#4) to map I3M_map (#3) using 4567 atoms
average map value = 0.06296, steps = 44
shifted from previous position = 0.0134
rotated from previous position = 0.0162 degrees
atoms outside contour = 4055, contour level = 0.3
Position of I3M_model (#4) relative to I3M_map (#3) coordinates:
Matrix rotation and translation
0.99995246 -0.00972362 0.00073233 5.94177326
0.00974205 0.99944235 -0.03193863 4.12734619
-0.00042137 0.03194425 0.99948956 -4.22975465
Axis 0.95643493 0.01727282 0.29143417
Axis point 0.00000000 175.63812215 123.71546863
Rotation angle (degrees) 1.91382599
Shift along axis 4.52151534
> fitmap #4 inMap #3
Fit molecule I3M_model (#4) to map I3M_map (#3) using 4567 atoms
average map value = 0.06295, steps = 48
shifted from previous position = 0.0143
rotated from previous position = 0.0152 degrees
atoms outside contour = 4053, contour level = 0.3
Position of I3M_model (#4) relative to I3M_map (#3) coordinates:
Matrix rotation and translation
0.99995038 -0.00994478 0.00058496 5.99690603
0.00995838 0.99944058 -0.03192746 4.10477877
-0.00026713 0.03193170 0.99949002 -4.24713419
Axis 0.95462710 0.01273784 0.29753126
Axis point 0.00000000 177.03690994 123.66310632
Rotation angle (degrees) 1.91673950
Shift along axis 4.51343985
> fitmap #4 inMap #3
Fit molecule I3M_model (#4) to map I3M_map (#3) using 4567 atoms
average map value = 0.06296, steps = 44
shifted from previous position = 0.0146
rotated from previous position = 0.015 degrees
atoms outside contour = 4054, contour level = 0.3
Position of I3M_model (#4) relative to I3M_map (#3) coordinates:
Matrix rotation and translation
0.99995246 -0.00972350 0.00072381 5.94238377
0.00974166 0.99944238 -0.03193795 4.12731647
-0.00041286 0.03194348 0.99948959 -4.23043780
Axis 0.95643939 0.01701844 0.29143448
Axis point 0.00000000 175.65842598 123.75332961
Rotation angle (degrees) 1.91377355
Shift along axis 4.52087495
> view matrix models
> #4,0.99988,0.013202,0.0076055,-6.8258,-0.012853,0.99894,-0.044295,1.6111,-0.0081821,0.044192,0.99899,-8.178
> fitmap #4 inMap #3
Fit molecule I3M_model (#4) to map I3M_map (#3) using 4567 atoms
average map value = 0.326, steps = 72
shifted from previous position = 0.976
rotated from previous position = 1.92 degrees
atoms outside contour = 2860, contour level = 0.3
Position of I3M_model (#4) relative to I3M_map (#3) coordinates:
Matrix rotation and translation
0.99999998 0.00009931 0.00018637 -0.02839605
-0.00009931 0.99999999 0.00001591 0.01530320
-0.00018637 -0.00001592 0.99999998 0.01997159
Axis -0.07515117 0.88002912 -0.46893609
Axis point 122.83911484 0.00000000 149.86493257
Rotation angle (degrees) 0.01213381
Shift along axis 0.00623586
> fitmap #4 inMap #3
Fit molecule I3M_model (#4) to map I3M_map (#3) using 4567 atoms
average map value = 0.326, steps = 40
shifted from previous position = 0.00638
rotated from previous position = 0.00881 degrees
atoms outside contour = 2863, contour level = 0.3
Position of I3M_model (#4) relative to I3M_map (#3) coordinates:
Matrix rotation and translation
0.99999999 -0.00000166 0.00010895 -0.00929113
0.00000167 1.00000000 -0.00007033 0.00758422
-0.00010895 0.00007033 0.99999999 0.00242287
Axis 0.54228636 0.84009606 0.01281039
Axis point 22.07011593 0.00000000 92.06610260
Rotation angle (degrees) 0.00743082
Shift along axis 0.00136406
> fitmap #4 inMap #3
Fit molecule I3M_model (#4) to map I3M_map (#3) using 4567 atoms
average map value = 0.326, steps = 44
shifted from previous position = 0.00372
rotated from previous position = 0.00685 degrees
atoms outside contour = 2863, contour level = 0.3
Position of I3M_model (#4) relative to I3M_map (#3) coordinates:
Matrix rotation and translation
1.00000000 -0.00005734 0.00003209 0.00510126
0.00005735 0.99999999 -0.00014313 0.01048687
-0.00003209 0.00014314 0.99999999 -0.01765579
Axis 0.90880281 0.20374747 0.36409396
Axis point 0.00000000 124.23147943 72.76575182
Rotation angle (degrees) 0.00902397
Shift along axis 0.00034434
> select clear
> hide #4 models
> hide #5 models
> volume #3 level 0.1338
> volume #1 level 0.2549
> open /Users/uijin/Downloads/cryosparc_P3_J1403_008_volume_map_sharp.mrc
Opened cryosparc_P3_J1403_008_volume_map_sharp.mrc as #2, grid size
240,240,240, pixel 0.901, shown at level 0.0983, step 1, values float32
> rename #2 4MTB_map_1403
> fitmap #2 inMap #1
Fit map 4MTB_map_1403 in map 4MTB_map using 137597 points
correlation = 0.8366, correlation about mean = 0.9228, overlap = 6980
steps = 44, shift = 0.0545, angle = 0.00369 degrees
Position of 4MTB_map_1403 (#2) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00000532 0.00004652 0.01899701
-0.00000532 1.00000000 -0.00004427 0.03810896
-0.00004652 0.00004427 1.00000000 0.03612486
Axis 0.68698629 0.72197117 -0.08250735
Axis point 843.15475994 0.00000000 146.67010538
Rotation angle (degrees) 0.00369201
Shift along axis 0.03758368
> volume #2 level 0.2
> volume #2 level 0.3995
> hide #!1 models
> hide #!2 models
> volume #3 level 0.1374
> show #4 models
> volume #2 level 0.3596
> volume #2 level 0.3311
> surface dust #3 size 7.05
> surface dust #2 size 9.01
> surface dust #1-5 size 5
> surface dust #1-5 size 4
> surface dust #1-5 size 3
Drag select of 3 I3M_map , 5 residues, 2 4MTB_map_1403
> select add #4
4567 atoms, 4682 bonds, 548 residues, 5 models selected
> select subtract #3
4567 atoms, 4682 bonds, 548 residues, 3 models selected
> select subtract #2
4567 atoms, 4682 bonds, 548 residues, 1 model selected
> select subtract #4
Nothing selected
> hide #!2 models
> hide #!3 models
> show #5 models
Mismatch between Cocoa '\x0' and Carbon '\u3134' for virtual key 1 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\u3134' for virtual key 1 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> show atoms
> hide H
> hide #5 models
Mismatch between Cocoa '\x0' and Carbon '\u314a' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\u314a' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color #4 cyan
> color byhetero
> select clear
> rainbow
> color byhetero
> select clear
> color #4 cyan
> color #5 salmon
> color byhetero
> show #5 models
> show #!2 models
> show #!1 models
> hide #!2 models
> volume #1 level 0.3085
> show #!2 models
> hide #!1 models
> volume #1 level 0.3299
> hide #!2 models
> volume #3 level 0.1738
> volume #3 level 0.192
> hide #!3 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> volume #1 level 0.1085
> volume #1 level 0.3871
> volume #1 level 0.2406
> hide #5 models
> show #5 models
> volume #3 level 0.2649
> hide #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> save 4MTB_map.mrc #2
> save I3M_map.mrc #3
> save 4MTB_model.mrc #5
Specified models are not volumes (#5)
> save 4MTB_model.pdb #5
> save I3M_model.pdb #4
> show #!3 models
> show #!1 models
> hide #!3 models
> show #!3 models
> save I3M-map.mrc #3
> volume #3 level 0.1265
> hide #!3 models
> volume #1 level 0.1227
> volume #1 level 0.07631
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> ui tool show "Side View"
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and Models/Pontous
> Gourdon/GTR3_I3M_IF_6.5 /Gtr3_pH6.5_map.mrc"
No such file/path: /Users/uijin/Library/Mobile
Documents/com~apple~CloudDocs/Lab Archive/Project/GTR1 (2024.02~)/Map and
Models/Pontous Gourdon/GTR3_I3M_IF_6.5 /Gtr3_pH6.5_map.mrc
> ui tool show "Side View"
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and Models/Pontous
> Gourdon/GTR3_I3M_IF_6.5 /Gtr3_pH6.5_map.mrc"
Opened Gtr3_pH6.5_map.mrc as #6, grid size 320,320,320, pixel 0.725, shown at
level 0.0933, step 2, values float32
> volume #6 level 0.1327
> select add #6
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.97689,0.21132,-0.032133,208.98,-0.1967,-0.82991,0.52207,184.27,0.083658,0.51633,0.8523,-55.235
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.97689,0.21132,-0.032133,198.97,-0.1967,-0.82991,0.52207,176.24,0.083658,0.51633,0.8523,-62.338
> view matrix models
> #6,-0.97689,0.21132,-0.032133,202.47,-0.1967,-0.82991,0.52207,168.45,0.083658,0.51633,0.8523,-62.314
> view matrix models
> #6,-0.97689,0.21132,-0.032133,200.98,-0.1967,-0.82991,0.52207,169.13,0.083658,0.51633,0.8523,-56.456
> fitmap #6 inMap #1
Fit map Gtr3_pH6.5_map.mrc in map 4MTB_map using 12275 points
correlation = 0.6389, correlation about mean = 0.4107, overlap = 521.6
steps = 136, shift = 5.5, angle = 28.7 degrees
Position of Gtr3_pH6.5_map.mrc (#6) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
-0.99782265 0.00780904 0.06549031 214.25941581
-0.00135229 -0.99517948 0.09806108 213.54484943
0.06594038 0.09775901 0.99302318 -25.58402183
Axis -0.03291525 -0.04904090 -0.99825426
Axis point 107.79734965 107.15432766 0.00000000
Rotation angle (degrees) 179.73708756
Shift along axis 8.01452553
> volume #6 step 1
> volume #6 level 0.306
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> hide #4 models
> hide #5 models
> show #5 models
> view matrix models
> #6,-0.99782,0.007809,0.06549,214.32,-0.0013523,-0.99518,0.098061,212.44,0.06594,0.097759,0.99302,-25.31
> fitmap #6 inMap #1
Fit map Gtr3_pH6.5_map.mrc in map 4MTB_map using 25326 points
correlation = 0.7234, correlation about mean = 0.1889, overlap = 2633
steps = 52, shift = 1.16, angle = 0.416 degrees
Position of Gtr3_pH6.5_map.mrc (#6) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
-0.99756067 0.00427535 0.06967382 214.11827045
0.00289651 -0.99472776 0.10250994 212.51114004
0.06974475 0.10246170 0.99228891 -26.45784443
Axis -0.03492166 -0.05134201 -0.99807038
Axis point 107.55884458 106.89898702 0.00000000
Rotation angle (degrees) 179.96042281
Shift along axis 8.01867679
> hide #!1 models
> hide #5 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #4 models
> show #!3 models
> view matrix models
> #6,-0.99756,0.0042754,0.069674,213.85,0.0028965,-0.99473,0.10251,213.65,0.069745,0.10246,0.99229,-26.204
> fitmap #6 inMap #1
Fit map Gtr3_pH6.5_map.mrc in map 4MTB_map using 25326 points
correlation = 0.7233, correlation about mean = 0.1884, overlap = 2633
steps = 28, shift = 0.0106, angle = 0.0244 degrees
Position of Gtr3_pH6.5_map.mrc (#6) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
-0.99758729 0.00443239 0.06928173 214.15770340
0.00269676 -0.99473245 0.10246994 212.54322068
0.06937097 0.10240955 0.99232049 -26.41120011
Axis -0.03472962 -0.05131852 -0.99807828
Axis point 107.58473954 106.90390513 0.00000000
Rotation angle (degrees) 179.95018223
Shift along axis 8.01542479
> fitmap #6 inMap #1
Fit map Gtr3_pH6.5_map.mrc in map 4MTB_map using 25326 points
correlation = 0.7235, correlation about mean = 0.1891, overlap = 2633
steps = 48, shift = 0.0173, angle = 0.0282 degrees
Position of Gtr3_pH6.5_map.mrc (#6) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
-0.99755917 0.00417687 0.06970117 214.12016970
0.00299351 -0.99473337 0.10245269 212.50480306
0.06976201 0.10241127 0.99229290 -26.45441812
Axis -0.03493273 -0.05131499 -0.99807138
Axis point 107.55465658 106.90063054 0.00000000
Rotation angle (degrees) 179.96603378
Shift along axis 8.01891326
> fitmap #6 inMap #1
Fit map Gtr3_pH6.5_map.mrc in map 4MTB_map using 25326 points
correlation = 0.7233, correlation about mean = 0.1884, overlap = 2633
steps = 28, shift = 0.0226, angle = 0.0252 degrees
Position of Gtr3_pH6.5_map.mrc (#6) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
-0.99757779 0.00450445 0.06941377 214.13763464
0.00264256 -0.99472662 0.10252791 212.54504028
0.06950956 0.10246300 0.99230527 -26.43253716
Axis -0.03479756 -0.05134663 -0.99807447
Axis point 107.57935273 106.90234483 0.00000000
Rotation angle (degrees) 179.94655780
Shift along axis 8.01670201
> hide #!3 models
> volume #6 level 0.1159
> volume #6 level 0.08058
> show #!3 models
> hide #!6 models
> select subtract #6
Nothing selected
> show #!6 models
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Map and Models/Pontous
> Gourdon/GTR3_I3M_IF_6.5 /Gtr3_pH6.5.pdb"
Chain information for Gtr3_pH6.5.pdb #7
---
Chain | Description
A | No description available
> hide #!7 models
> hide #4 models
> hide #!3 models
> volume #6 level 0.2236
> show #4 models
> show #!7 models
> select add #7
4231 atoms, 4336 bonds, 2 pseudobonds, 542 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.92117,0.38912,0.0063769,172.8,-0.385,-0.91357,0.13099,265.55,0.056795,0.1182,0.99136,-20.148
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.92117,0.38912,0.0063769,164.67,-0.385,-0.91357,0.13099,247.62,0.056795,0.1182,0.99136,-29.015
> fitmap #7 inMap #1
Fit molecule Gtr3_pH6.5.pdb (#7) to map 4MTB_map (#1) using 4231 atoms
average map value = 0.2319, steps = 136
shifted from previous position = 3.37
rotated from previous position = 22.6 degrees
atoms outside contour = 1762, contour level = 0.07631
Position of Gtr3_pH6.5.pdb (#7) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
-0.99776036 0.00903266 0.06627728 214.01069415
-0.00233292 -0.99493682 0.10047522 213.32755364
0.06684926 0.10009557 0.99272960 -26.00212089
Axis -0.03334265 -0.05023443 -0.99818073
Axis point 107.74438943 107.01252652 0.00000000
Rotation angle (degrees) 179.67380494
Shift along axis 8.10274587
> select subtract #7
Nothing selected
> close #7
> open "/Users/uijin/Library/Mobile Documents/com~apple~CloudDocs/Lab
> Archive/Project/GTR1 (2024.02~)/Manuscript/Manuscript_Yonsei/Analysis
> Data/gtr3_i3m_added.pdb"
Chain information for gtr3_i3m_added.pdb #7
---
Chain | Description
A | No description available
> select add #7
4279 atoms, 4386 bonds, 2 pseudobonds, 543 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.99697,-0.064851,0.042938,233.37,0.057456,-0.98618,-0.15539,256.83,0.052422,-0.15246,0.98692,14.31
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.99697,-0.064851,0.042938,235.75,0.057456,-0.98618,-0.15539,237.03,0.052422,-0.15246,0.98692,6.3247
> fitmap #7 inMap #1
Fit molecule gtr3_i3m_added.pdb (#7) to map 4MTB_map (#1) using 4279 atoms
average map value = 0.08326, steps = 80
shifted from previous position = 2.42
rotated from previous position = 3.14 degrees
atoms outside contour = 3288, contour level = 0.07631
Position of gtr3_i3m_added.pdb (#7) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
-0.99818256 -0.03233911 0.05085023 229.72707951
0.02653253 -0.99346795 -0.11098399 235.11444091
0.05410720 -0.10943310 0.99252043 -1.16475551
Axis 0.02629429 -0.05521962 0.99812795
Axis point 113.14511793 119.22384352 0.00000000
Rotation angle (degrees) 178.31004374
Shift along axis -8.10499511
> view matrix models
> #7,-0.99818,-0.032339,0.05085,223.59,0.026533,-0.99347,-0.11098,232.47,0.054107,-0.10943,0.99252,-1.4065
> fitmap #7 inMap #1
Fit molecule gtr3_i3m_added.pdb (#7) to map 4MTB_map (#1) using 4279 atoms
average map value = 0.1107, steps = 96
shifted from previous position = 3.95
rotated from previous position = 8.55 degrees
atoms outside contour = 2969, contour level = 0.07631
Position of gtr3_i3m_added.pdb (#7) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
-0.99638782 0.01330800 0.08387022 216.45655129
-0.01083442 -0.99949479 0.02987932 223.93403979
0.08422548 0.02886271 0.99602862 -20.00704546
Axis -0.04206725 -0.01470063 -0.99900663
Axis point 109.32701024 111.45871197 0.00000000
Rotation angle (degrees) 179.30766601
Shift along axis 7.58946846
> view matrix models
> #7,-0.99639,0.013308,0.08387,212.49,-0.010834,-0.99949,0.029879,222.6,0.084225,0.028863,0.99603,-21.904
> fitmap #7 inMap #1
Fit molecule gtr3_i3m_added.pdb (#7) to map 4MTB_map (#1) using 4279 atoms
average map value = 0.2295, steps = 76
shifted from previous position = 2.35
rotated from previous position = 4.21 degrees
atoms outside contour = 1811, contour level = 0.07631
Position of gtr3_i3m_added.pdb (#7) relative to 4MTB_map (#1) coordinates:
Matrix rotation and translation
-0.99777294 0.00930557 0.06604967 214.00595175
-0.00262774 -0.99493578 0.10047829 213.35508708
0.06665018 0.10008096 0.99274445 -25.99245821
Axis -0.03323561 -0.05023142 -0.99818445
Axis point 107.75572508 107.01075602 0.00000000
Rotation angle (degrees) 179.65751199
Shift along axis 8.11552120
> select clear
Mismatch between Cocoa '\x0' and Carbon '\u3157' for virtual key 4 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\u3157' for virtual key 4 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'H' for virtual key 4 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'h' for virtual key 4 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 4 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide H
> select add #6
3 models selected
> select subtract #6
Nothing selected
> volume #6 level 0.1025
> ui tool show "Side View"
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> show #!6 models
> show #!3 models
> volume #2 level 0.2684
> hide #!2 models
> volume #6 level 0.09236
> hide #!3 models
> show #!3 models
> hide #!6 models
> hide #4 models
> show #4 models
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> hide #4 models
> show #4 models
> hide #4 models
> show atoms
> show #4 models
> hide H
> show #!6 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> ui tool show Distances
> hide #!6 models
> hide #!3 models
> show #!6 models
> show #!3 models
> volume #6 level 0.05198
> volume #2 level 0.2114
> hide #!6 models
> hide #!3 models
> volume #6 level 0.09404
> hide #!2 models
> select #7/A:I3M
48 atoms, 50 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.99777,0.0093056,0.06605,214.06,-0.0026277,-0.99494,0.10048,212.02,0.06665,0.10008,0.99274,-26.359
> view matrix models
> #7,-0.99777,0.0093056,0.06605,214.24,-0.0026277,-0.99494,0.10048,211.67,0.06665,0.10008,0.99274,-26.562
> hide #4 models
> show #!3 models
> hide #!6 models
> hide #!7 models
> show #!7 models
> select add #7
4279 atoms, 4386 bonds, 2 pseudobonds, 543 residues, 2 models selected
> select subtract #7
Nothing selected
> hide #!3 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> volume #6 level 0.07385
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #4 models
> hide #!7 models
> show #!3 models
> show #!6 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!7 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9.dev202406122300 (2024-06-12)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/uijin/Downloads/cryosparc_P3_J888_007_volume_map_sharp.mrc
Opened cryosparc_P3_J888_007_volume_map_sharp.mrc as #1, grid size
240,240,240, pixel 0.901, shown at level 0.0623, step 1, values float32
> open /Users/uijin/Downloads/cryosparc_P3_J900_009_volume_map_sharp.mrc
Opened cryosparc_P3_J900_009_volume_map_sharp.mrc as #2, grid size
240,240,240, pixel 0.901, shown at level 0.0626, step 1, values float32
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11C001DKKH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.41.10
OS Loader Version: 8419.41.10
Software:
System Software Overview:
System Version: macOS 13.0 (22A380)
Kernel Version: Darwin 22.1.0
Time since boot: 21일 13시간 40분
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:
LG FULL HD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.13
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.2
ChimeraX-AtomicLibrary: 14.1.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-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.dev202406122300
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepMutationalScan: 1.0
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.4
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.6
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.1.5
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.12.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.6
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.32.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 14 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Unknown crash |
comment:2 by , 14 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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