Opened 16 months ago

Closed 16 months ago

#15453 closed defect (can't reproduce)

Crash after "surface dust"

Reported by: kananya@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.5.0-41-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x00007134994a7740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/OpenGL/arrays/lists.py", line 167 in dimensions
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/OpenGL/arrays/lists.py", line 155 in asArray
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 367 in drawing_lineage
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 367 in drawing_lineage
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 532 in _scene_positions_changed
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 980 in bounds
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 968 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1061 in first_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1077 in first_intercept_children
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 795 in _positive_closure
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 160 in _model_list_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 514 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 466 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 139 in _as_term_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 514 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 466 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 106 in _atom_specifier_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 514 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 466 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 208 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 217 in _parse_unquoted
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 110 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1266 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2492 in _parse_arg
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2673 in _process_positional_arguments
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2871 in _log_surface_change
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2839 in set_threshold_parameters_from_gui
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 1671 in use_gui_settings
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 362 in show_using_dialog_settings
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 326 in redisplay_needed
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 294 in redisplay_needed_cb
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2216 in select_data_cb
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/histogram.py", line 416 in move_marker_cb
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2159 in _drag
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2162 in mouseReleaseEvent
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 477 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 490 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 674 in _option
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 690 in _optional
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 206 in _model_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 514 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 466 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 158 in block0
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 477 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 522 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 325 in _model_parts_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 792 in _positive_closure
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 323 in block0
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 477 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 522 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 362 in _chain_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 430 in _error
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 430 in _error
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 674 in _option
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 690 in _optional
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 477 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 522 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 561 in _zone_selector_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 477 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 522 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 583 in _zone_operator_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 430 in _error
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 674 in _option
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 399 in _residue_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 522 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 477 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 359 in block7
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 792 in _positive_closure
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 792 in _positive_closure
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 396 in block7
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 477 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 522 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 451 in _atom_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 430 in _error
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 674 in _option
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 430 in _error
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 477 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 522 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 146 in _selector_name_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 621 in _pattern
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 430 in _error
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 674 in _option
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 205 in _model_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 522 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 477 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 157 in block0
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 795 in _positive_closure
  ...
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/ananya/Desktop/BceABS/detergent/cryosparc_P16_J85_007_volume_map_sharp(2).mrc

Opened cryosparc_P16_J85_007_volume_map_sharp(2).mrc as #1, grid size
320,320,320, pixel 1.07, shown at level 0.275, step 2, values float32  

> set bgColor white

> lighting soft

> surface dust #1 size 10.7

> volume #1 step 1

> volume #1 level 1.481

> volume #1 level 1.045

> surface dust #1 size 10.7

> volume #1 color #99c1f1

> open
> /home/ananya/Desktop/BceABS/nanodisc/WT/cryosparc_P16_J393_006_volume_map_sharp.mrc

Opened cryosparc_P16_J393_006_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.07, shown at level 0.281, step 2, values float32  

> volume all step 1 level 1

> surface dust #1 size 10.7

> surface dust #2 size 10.7

> tile

2 models tiled  

> lighting soft

> reset

Unknown command: reset  

> open /home/ananya/Downloads/cryosparc_P16_J783_007_volume_map_sharp.mrc

Opened cryosparc_P16_J783_007_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 1.07, shown at level 0.284, step 2, values float32  

> select add #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.82828,-0.090893,0.55289,-44.073,0.088838,0.99558,0.030582,-21.051,-0.55322,0.023788,0.83269,127.89

> view matrix models
> #3,-0.24013,-0.029354,0.9703,76.5,0.029322,0.99887,0.037475,-11.579,-0.9703,0.03745,-0.239,382.97

> view matrix models
> #3,-0.86326,0.31673,0.39301,229.47,0.27032,0.94765,-0.16996,-13.305,-0.42627,-0.040483,-0.90369,405.27

> view matrix models
> #3,-0.11541,0.99307,0.022235,31.97,0.97718,0.11752,-0.17696,0.48182,-0.17834,0.0013056,-0.98397,364.68

> view matrix models
> #3,-0.31413,0.94181,-0.11966,102.06,0.44868,0.25835,0.85554,-97.199,0.83667,0.21506,-0.50372,55.939

> view matrix models
> #3,-0.27129,0.90711,-0.3218,133.85,-0.52529,0.14062,0.83923,109.49,0.80652,0.39671,0.43835,-127.59

> view matrix models
> #3,0.026939,0.93693,-0.34847,76.94,-0.85223,-0.16067,-0.49789,447.2,-0.52248,0.31038,0.79415,78.254

> view matrix models
> #3,-0.24447,0.90517,-0.34771,133.47,-0.66461,0.1047,0.73982,158.61,0.70606,0.41195,0.57599,-134.35

> view matrix models
> #3,-0.30855,0.94546,-0.10445,97.832,0.51601,0.25861,0.81661,-103.42,0.79908,0.19807,-0.56766,76.671

> view matrix models
> #3,-0.27304,0.96083,-0.047476,78.936,0.75823,0.24531,0.60408,-111.17,0.59207,0.12894,-0.79551,165.82

> view matrix models
> #3,-0.31146,0.94365,-0.1119,99.941,0.48312,0.25865,0.83648,-100.55,0.81829,0.20646,-0.53645,66.373

> view matrix models
> #3,-0.21469,0.97668,-0.0017472,57.536,0.93241,0.20549,0.2973,-85.733,0.29073,0.062197,-0.95478,260.84

> view matrix models
> #3,-0.036429,0.99931,0.0067582,18.595,0.85126,0.034573,-0.5236,96.627,-0.52347,-0.013321,-0.85194,410.15

> view matrix models
> #3,-0.51959,0.7828,0.34242,91.458,0.59903,0.61952,-0.50731,38.745,-0.60926,-0.058473,-0.79081,424.01

> view matrix models
> #3,-0.7844,-0.14395,0.60332,260.33,-0.30616,0.9358,-0.17478,98.077,-0.53942,-0.32181,-0.77811,454.95

> view matrix models
> #3,-0.092847,-0.80551,0.58526,249.27,-0.89078,0.32981,0.31261,233.03,-0.44484,-0.49232,-0.74816,462.06

> view matrix models
> #3,0.40622,-0.76222,0.50399,161.32,-0.8485,-0.10991,0.51766,267.98,-0.33917,-0.63792,-0.69139,458.24

> view matrix models
> #3,0.47343,-0.77576,0.41721,165.54,-0.52447,0.13227,0.84109,110.49,-0.70767,-0.61701,-0.34424,465.95

> view matrix models
> #3,0.3908,-0.76261,0.51546,162.37,-0.88251,-0.15125,0.44531,293.72,-0.26163,-0.62893,-0.73212,448.88

> view matrix models
> #3,0.41275,-0.7623,0.49853,161.02,-0.83119,-0.091389,0.54842,256.34,-0.37251,-0.64074,-0.67134,461.66

> view matrix models
> #3,0.47412,-0.77617,0.41565,165.74,-0.51795,0.13588,0.84455,108.05,-0.71199,-0.6157,-0.3376,465.43

> view matrix models
> #3,0.46467,-0.77141,0.43474,163.5,-0.59641,0.090237,0.79759,138.67,-0.6545,-0.6299,-0.41815,470.55

> view matrix models
> #3,0.49155,-0.80086,0.34206,179.08,-0.18992,0.28475,0.9396,4.3164,-0.84989,-0.52683,-0.012128,421.43

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.49155,-0.80086,0.34206,197.37,-0.18992,0.28475,0.9396,-229.08,-0.84989,-0.52683,-0.012128,376.94

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.402,-0.89764,0.18064,258.16,0.70158,0.42874,0.56919,-360.26,-0.58838,-0.10208,0.80212,117.21

> view matrix models
> #3,0.21923,-0.95894,0.17991,303.44,0.95111,0.16894,-0.25856,-223.4,0.21755,0.2278,0.94909,-116.9

> view matrix models
> #3,0.40072,-0.89835,0.17997,258.64,0.70654,0.42805,0.56354,-360.13,-0.58329,-0.098668,0.80625,114.97

> view matrix models
> #3,0.18262,-0.96242,0.201,307.41,0.89964,0.081107,-0.42903,-169.83,0.3966,0.25918,0.88064,-144.67

> view matrix models
> #3,0.090723,-0.93956,0.33015,299.13,0.40651,-0.2677,-0.87355,58.421,0.90913,0.21346,0.35765,-145.76

> view matrix models
> #3,0.099512,-0.88473,0.45535,266.95,-0.2033,-0.46604,-0.86109,205.91,0.97405,-0.0068815,-0.22624,-21.801

> view matrix models
> #3,0.19194,-0.81766,0.54277,223.18,-0.74524,-0.48129,-0.4615,243.84,0.63858,-0.31591,-0.70173,174.97

> view matrix models
> #3,0.35108,-0.76677,0.53741,185.2,-0.93386,-0.24496,0.26057,117.29,-0.068153,-0.59334,-0.80206,373.41

> view matrix models
> #3,0.45306,-0.76752,0.45349,180.15,-0.67033,0.042057,0.74087,-62.889,-0.5877,-0.63965,-0.49544,428.11

> view matrix models
> #3,0.34068,-0.76849,0.54162,186.75,-0.93999,-0.26691,0.21255,130.31,-0.01878,-0.58153,-0.81331,363.93

> view matrix models
> #3,0.39843,-0.76232,0.51003,180.08,-0.86683,-0.13121,0.48104,47.89,-0.29978,-0.63376,-0.71307,409.24

> view matrix models
> #3,0.18392,-0.82175,0.53936,225.98,-0.71817,-0.48699,-0.49707,245.69,0.67113,-0.29592,-0.67972,161.66

> view matrix models
> #3,0.40245,-0.76224,0.50697,179.82,-0.85766,-0.12032,0.49994,41.097,-0.32007,-0.63601,-0.70217,411.63

> view matrix models
> #3,0.086576,-0.93298,0.34937,295.55,0.32031,-0.306,-0.89653,85.202,0.94335,0.18952,0.27235,-133.75

> view matrix models
> #3,0.17548,-0.82627,0.53525,229.05,-0.68717,-0.49213,-0.53442,247,0.70499,-0.27403,-0.65414,147.18

> view matrix models
> #3,0.40305,-0.76223,0.50651,179.78,-0.85626,-0.11869,0.50273,40.08,-0.32308,-0.63633,-0.7005,411.97

> view matrix models
> #3,0.859,-0.47209,0.19813,94.565,-0.47979,-0.60721,0.63332,33.131,-0.17868,-0.63908,-0.74809,393.23

> view matrix models
> #3,0.89274,-0.45016,-0.019346,120.69,0.10808,0.17226,0.9791,-272.02,-0.43742,-0.87618,0.20243,324.78

> view matrix models
> #3,0.83298,-0.53697,-0.13341,166.22,0.50395,0.63677,0.58358,-361.97,-0.22841,-0.55334,0.80102,128.82

> close #3

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.98181,-0.030138,-0.18746,39.19,0.026649,0.99942,-0.021104,-3.7761,0.18798,0.015725,0.98205,-27.494

> fitmap #2 inMap #1

Fit map cryosparc_P16_J393_006_volume_map_sharp.mrc in map
cryosparc_P16_J85_007_volume_map_sharp(2).mrc using 54746 points  
correlation = 0.9423, correlation about mean = 0.8245, overlap = 2.615e+05  
steps = 52, shift = 3.25, angle = 2.18 degrees  
  
Position of cryosparc_P16_J393_006_volume_map_sharp.mrc (#2) relative to
cryosparc_P16_J85_007_volume_map_sharp(2).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99960194 0.02813970 0.00203170 -4.68263121  
-0.02807893 0.99928142 -0.02546026 9.29498996  
-0.00274668 0.02539308 0.99967377 -0.21647789  
Axis 0.66950386 0.06290926 -0.74013985  
Axis point 333.46159258 114.25873030 0.00000000  
Rotation angle (degrees) 2.17652423  
Shift along axis -2.39007487  
  

> select subtract #2

Nothing selected  

> open
> /home/ananya/Desktop/BceABS/nanodisc/E169Q/cryosparc_P16_J783_007_volume_map_sharp.mrc

Opened cryosparc_P16_J783_007_volume_map_sharp.mrc as #3, grid size
320,320,320, pixel 1.07, shown at level 0.284, step 2, values float32  

> select add #3

2 models selected  

> view matrix models #3,1,0,0,4.1666,0,1,0,0.73395,0,0,1,-19.488

> volume #3 step 1

> volume #3 level -0.1884

> volume #3 level 0.3173

> volume #3 level 0.4859

> volume #3 level 0.958

> surface dust #3 size 10.7

> view matrix models #3,1,0,0,11.837,0,1,0,-2.8893,0,0,1,-54.502

> view matrix models #3,1,0,0,10.982,0,1,0,-147.28,0,0,1,-25.486

> view matrix models #3,1,0,0,13.506,0,1,0,-141.72,0,0,1,-38.178

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.30557,-0.052404,0.95073,-28.094,0.00024837,0.99849,0.054957,-151.42,-0.95217,-0.016557,0.30512,255.71

> view matrix models
> #3,-0.7286,-0.23291,0.64412,239.15,-0.1241,0.96973,0.21027,-152.72,-0.6736,0.073271,-0.73546,379.16

> view matrix models
> #3,-0.97036,-0.2382,0.040854,391.01,-0.22519,0.95252,0.20495,-131.13,-0.087732,0.18967,-0.97792,300.37

> view matrix models
> #3,-0.43255,0.85161,0.29606,57.442,0.89356,0.36113,0.26672,-231.45,0.12022,0.37992,-0.91717,219.39

> view matrix models
> #3,0.86683,0.40561,0.28997,-87.907,0.4011,-0.91273,0.077684,115.07,0.29618,0.048969,-0.95388,254.35

> view matrix models
> #3,0.95251,-0.10368,0.28631,-11.467,-0.11974,-0.99204,0.039099,226.68,0.27998,-0.071524,-0.95734,279.24

> view matrix models
> #3,0.87377,-0.47384,0.10955,100.03,-0.48025,-0.87619,0.040688,268.43,0.076703,-0.088162,-0.99315,324

> view matrix models
> #3,0.84168,-0.27489,0.46478,6.0593,-0.34417,-0.93633,0.069475,250.29,0.41609,-0.21844,-0.8827,268.27

> view matrix models
> #3,0.84095,-0.41659,0.34534,52.975,-0.45611,-0.88911,0.03813,266.99,0.29116,-0.18958,-0.9377,294.77

> view matrix models
> #3,0.76552,-0.58099,0.27646,107.79,-0.608,-0.79378,0.015405,280.53,0.2105,-0.17988,-0.9609,311.25

> volume #3 level 0.9074

> volume #3 level 0.7725

> volume #3 level 0.4522

> volume #3 level 0.8231

> volume #3 level 0.8062

> view matrix models
> #3,0.84943,-0.35123,0.39384,31.243,-0.40227,-0.91402,0.052481,259.62,0.34154,-0.20301,-0.91768,284.89

> view matrix models
> #3,0.86934,-0.13368,0.4758,-25.669,-0.20763,-0.97243,0.10616,226.64,0.44849,-0.19108,-0.87312,256.23

> view matrix models
> #3,0.81484,0.35365,0.45931,-99.996,0.2633,-0.93169,0.25026,111.89,0.51643,-0.082986,-0.8523,221.47

> view matrix models
> #3,0.93431,0.023841,0.35567,-43.347,-0.041369,-0.98377,0.17462,187.54,0.35406,-0.17786,-0.91815,278.33

> view matrix models
> #3,0.91746,-0.14597,0.37008,-12.799,-0.21277,-0.96607,0.14644,219.15,0.33614,-0.2131,-0.91739,287.57

> view matrix models
> #3,0.81786,-0.55163,0.16372,113.78,-0.57126,-0.81252,0.11608,259.39,0.068997,-0.18846,-0.97965,340.67

> volume #3 level 0.7725

> volume #3 level 0.6714

> view matrix models
> #3,0.95428,0.15195,0.2574,-45.293,0.11949,-0.98327,0.13745,167.9,0.27398,-0.10041,-0.95648,286.99

> view matrix models
> #3,0.89544,0.33865,0.28898,-72.611,0.30635,-0.93971,0.15197,126.37,0.32302,-0.047552,-0.9452,267.74

> view matrix models
> #3,0.97216,0.11362,0.20492,-32.62,0.085962,-0.98653,0.13918,173.82,0.21798,-0.11769,-0.96883,301.56

> view matrix models
> #3,0.9706,-0.14191,0.19441,12.928,-0.1706,-0.97538,0.13977,215.2,0.16979,-0.16883,-0.97091,318.76

> surface dust #3 size 10.7

> select subtract #3

Nothing selected  

> select add #3

2 models selected  

> view matrix models
> #3,0.96438,0.13024,0.23025,-38.558,0.098338,-0.98453,0.145,170.37,0.24557,-0.11719,-0.96227,295.66

> view matrix models
> #3,0.96623,-0.11742,0.22935,3.3922,-0.15131,-0.97906,0.13622,213.18,0.20855,-0.16632,-0.96376,310.53

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.96623,-0.11742,0.22935,-5.7704,-0.15131,-0.97906,0.13622,348.3,0.20855,-0.16632,-0.96376,329.67

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.  

> select subtract #3

Nothing selected  

> hide #!1 models

> fitmap #2 inMap #3

Fit map cryosparc_P16_J393_006_volume_map_sharp.mrc in map
cryosparc_P16_J783_007_volume_map_sharp.mrc using 54746 points  
correlation = 0.4305, correlation about mean = 0.06778, overlap = 4.564e+04  
steps = 104, shift = 4.63, angle = 3.03 degrees  
  
Position of cryosparc_P16_J393_006_volume_map_sharp.mrc (#2) relative to
cryosparc_P16_J783_007_volume_map_sharp.mrc (#3) coordinates:  
Matrix rotation and translation  
0.90284630 -0.42444012 -0.06869574 97.75152122  
-0.42876713 -0.90067864 -0.07026144 414.76249043  
-0.03205101 0.09288975 -0.99516037 322.68739812  
Axis 0.97536552 -0.21907291 -0.02586813  
Axis point 0.00000000 211.43156783 171.52866017  
Rotation angle (degrees) 175.20241015  
Shift along axis -3.86707960  
  

> select add #3

2 models selected  

> view matrix models
> #3,0.96623,-0.11742,0.22935,-6.5882,-0.15131,-0.97906,0.13622,350.27,0.20855,-0.16632,-0.96376,333.13

> fitmap #3 inMap #2

Fit map cryosparc_P16_J783_007_volume_map_sharp.mrc in map
cryosparc_P16_J393_006_volume_map_sharp.mrc using 81187 points  
correlation = 0.3612, correlation about mean = 0.0857, overlap = 4.255e+04  
steps = 124, shift = 3.23, angle = 10.1 degrees  
  
Position of cryosparc_P16_J783_007_volume_map_sharp.mrc (#3) relative to
cryosparc_P16_J393_006_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.93092912 -0.32658173 -0.16344843 98.12606849  
-0.32617155 -0.94483088 0.03011291 391.28917270  
-0.16426544 0.02527924 -0.98609223 357.46656754  
Axis -0.98258067 0.16608073 0.08338118  
Axis point 0.00000000 204.16126268 182.65169560  
Rotation angle (degrees) 179.85907052  
Shift along axis -1.62520321  
  

> select subtract #3

Nothing selected  

> show #!1 models

> reset

Unknown command: reset  

> tile

3 models tiled  

> lighting soft

> select add #1

2 models selected  

> view matrix models
> #1,0.89383,-0.34888,-0.28169,109.21,0.35386,0.93465,-0.034744,49.783,0.2754,-0.068623,0.95888,30.402

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> view matrix models
> #2,0.91536,-0.28304,-0.28637,108.56,0.27881,0.95869,-0.056373,-115.21,0.29049,-0.02824,0.95646,-11.299

> select subtract #2

Nothing selected  

> select add #3

2 models selected  

> view matrix models
> #3,0.99149,-0.038749,0.12425,-3.3428,-0.043888,-0.99828,0.038887,120.21,0.12253,-0.044009,-0.99149,321.37

> select subtract #3

Nothing selected  

> select add #2

2 models selected  

> view matrix models
> #2,0.94208,-0.20243,-0.26741,86.046,0.19856,0.9792,-0.041721,-98.872,0.2703,-0.013794,0.96268,-8.1491

> select subtract #2

Nothing selected  

> save /home/ananya/Desktop/BceABS/detvsnano.jpg width 5000 height 3168
> supersample 4

> close #1

> close #2

> close #3

> open
> /home/ananya/Desktop/BceABS/nanodisc/E169Q/cryosparc_P16_J692_002_volume_map_sharp.mrc
> /home/ananya/Desktop/BceABS/nanodisc/E169Q/cryosparc_P16_J691_003_volume_map_sharp.mrc

Opened cryosparc_P16_J692_002_volume_map_sharp.mrc as #1.1, grid size
320,320,320, pixel 1.07, shown at level 0.196, step 2, values float32  
Opened cryosparc_P16_J691_003_volume_map_sharp.mrc as #1.2, grid size
320,320,320, pixel 1.07, shown at level 0.236, step 2, values float32  

> volume all step 1 level 0.5

> surface dust #1.1 size 10.7

> surface dust #1.2 size 10.7

> tile

2 models tiled  

> select add #1.2

2 models selected  

> color #1.2 #8ff0a4ff models

> color #1.2 #ffbe6fff models

> lighting soft

> select add #1.1

4 models selected  

> select subtract #1.2

2 models selected  

> view matrix models
> #1.1,-0.93605,-0.3205,-0.14523,415.31,0.32149,-0.94676,0.017262,273.38,-0.14303,-0.030532,0.98925,-11.111

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1,-0.41015,-0.22767,-0.88314,439.18,-0.018401,-0.96608,0.25759,292.8,-0.91183,0.1219,0.39205,200.78

> view matrix models
> #1.1,0.40598,-0.48576,-0.77409,323.88,-0.35801,-0.86387,0.35434,316.51,-0.84084,0.13327,-0.52462,348.87

> view matrix models
> #1.1,0.77009,-0.46855,-0.43293,197.69,-0.45249,-0.87956,0.14705,372.23,-0.44969,0.082651,-0.88935,354.78

> view matrix models
> #1.1,0.8515,-0.5002,0.15729,84.635,-0.49095,-0.8659,-0.095822,419.5,0.18413,0.0043703,-0.98289,275.61

> view matrix models
> #1.1,0.99599,-0.0078976,0.089139,-13.575,-0.0058927,-0.99972,-0.022732,346.11,0.089294,0.022116,-0.99576,291.16

> view matrix models
> #1.1,0.74598,-0.65173,0.13696,132.71,-0.63935,-0.75842,-0.12664,431.91,0.18641,0.0069086,-0.98245,274.7

> select subtract #1.1

Nothing selected  

> select add #1.1

2 models selected  

> view matrix models
> #1.1,-0.99532,0.072535,-0.06387,342.98,0.090053,0.93595,-0.34041,50.18,0.035087,-0.34457,-0.9381,353.88

> view matrix models
> #1.1,0.81394,0.57724,-0.065527,-56.253,0.58077,-0.80575,0.1161,186.72,0.014219,-0.13255,-0.99107,330.1

> view matrix models
> #1.1,0.99129,0.083234,0.10208,-30.857,0.074615,-0.99354,0.085536,311.98,0.10853,-0.077174,-0.99109,304.24

> hide #!1.1 models

> open
> /home/ananya/Desktop/BceABS/nanodisc/E169Q/19424/cryosparc_P16_J643_005_volume_map_sharp.mrc

Opened cryosparc_P16_J643_005_volume_map_sharp.mrc as #2, grid size
320,320,320, pixel 1.07, shown at level 0.277, step 2, values float32  

> select add #2

4 models selected  

> view matrix models
> #1.1,0.91204,0.23478,0.33624,-75.861,-0.07465,-0.71116,0.69906,201.95,0.40325,-0.66267,-0.63108,291.31,#2,0.95796,-0.13645,-0.25237,73.051,-0.061836,0.76078,-0.64605,159.25,0.28016,0.6345,0.72036,-117.16

> ui mousemode right "translate selected models"

> view matrix models
> #1.1,0.91204,0.23478,0.33624,2.681,-0.07465,-0.71116,0.69906,385.46,0.40325,-0.66267,-0.63108,253.07,#2,0.95796,-0.13645,-0.25237,151.59,-0.061836,0.76078,-0.64605,342.75,0.28016,0.6345,0.72036,-155.4

> view matrix models
> #1.1,0.91204,0.23478,0.33624,17.865,-0.07465,-0.71116,0.69906,421.9,0.40325,-0.66267,-0.63108,252.6,#2,0.95796,-0.13645,-0.25237,166.78,-0.061836,0.76078,-0.64605,379.2,0.28016,0.6345,0.72036,-155.87

> view matrix models
> #1.1,0.91204,0.23478,0.33624,29.549,-0.07465,-0.71116,0.69906,448.88,0.40325,-0.66267,-0.63108,244.59,#2,0.95796,-0.13645,-0.25237,178.46,-0.061836,0.76078,-0.64605,406.17,0.28016,0.6345,0.72036,-163.88

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1,0.023132,0.40356,0.91466,80.428,0.29604,-0.87664,0.37929,454.9,0.9549,0.262,-0.13975,-81.904,#2,0.14988,-0.32099,-0.93515,469.7,0.25921,0.92551,-0.27613,258.17,0.95412,-0.20101,0.22192,-57.268

> view matrix models
> #1.1,-0.29432,-0.7568,0.58363,377.99,0.85938,-0.47676,-0.18484,369.5,0.41814,0.44716,0.7907,-151.57,#2,-0.29517,0.77987,-0.55197,293.51,0.79334,0.52199,0.31326,135.83,0.53243,-0.34544,-0.77278,207.73

> view matrix models
> #1.1,-0.71622,-0.69492,-0.064158,542.89,0.66033,-0.70456,0.25991,377.13,-0.22582,0.14379,0.9635,-8.5097,#2,-0.77437,0.6315,0.039481,309.96,0.62246,0.77151,-0.13155,195.66,-0.11354,-0.077296,-0.99052,313.45

> view matrix models
> #1.1,-0.408,-0.5731,-0.7107,562.45,0.37488,-0.81495,0.44196,420.86,-0.83247,-0.086107,0.54734,203.63,#2,-0.52469,0.47817,0.70432,182.8,0.34889,0.87546,-0.33444,260.25,-0.77652,0.070252,-0.62617,348.25

> view matrix models
> #1.1,-0.94024,-0.15343,-0.30399,531.93,0.16832,-0.98546,-0.023209,556.46,-0.29601,-0.072988,0.95239,41.519,#2,-0.97585,0.056284,0.21107,420.04,0.082457,0.98966,0.11732,214.55,-0.20229,0.13189,-0.9704,289.36

> view matrix models
> #1.1,-0.7229,-0.16722,-0.67041,548.62,0.097669,-0.98526,0.14043,545.08,-0.68401,0.036042,0.72858,129.11,#2,-0.79896,0.054854,0.59888,324.65,0.029145,0.99819,-0.052546,250.55,-0.60068,-0.024528,-0.79911,361.34

> view matrix models
> #1.1,-0.9151,-0.39975,0.052896,514.13,0.39211,-0.91276,-0.11457,516.75,0.09408,-0.084099,0.99201,-34.912,#2,-0.935,0.33341,-0.12089,418.04,0.30103,0.92632,0.22655,168.13,0.18752,0.17543,-0.96647,210.18

> volume #2 step 1

> volume #2 level 0.01718

> surface dust #2 size 10.7


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) HD Graphics 2000 (SNB GT1)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_IN.ISO8859-1
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: LENOVO
Model: 5030AR8
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
Cache Size: 6144 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       2.2Gi       9.8Gi       603Mi       3.4Gi        12Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation 2nd Generation Core Processor Family Integrated Graphics Controller [8086:0102] (rev 09)	
	DeviceName:  Onboard IGD	
	Subsystem: Lenovo 2nd Generation Core Processor Family Integrated Graphics Controller [17aa:3077]

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 16 months ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash after "surface dust"

Reported by Ananya Kundu

comment:2 by Tom Goddard, 16 months ago

Resolution: → can't reproduce
Status: assigned → closed

I don't see any clues about what caused this ChimeraX crash. I would bet it is a Python garbage collection crash which is probably fixed in the current ChimeraX 1.8.

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