Crash in event loop

[sudipag@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x80000003

Thread 0x00004528 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 316 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 574 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 1284 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004e54 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00005798 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000538c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000048b8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000187c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00000bec (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x000021d0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002930 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002878 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00002360 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x0000392c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap

Thread 0x00004518 (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 301 in event_loop
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 867 in init
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in 
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Updating list of available bundles failed: Internal Server Error  

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/Maps for
> Chimera/cryosparc_P39_J431_009_volume_map_sharp (1).mrc"

Opened cryosparc_P39_J431_009_volume_map_sharp (1).mrc as #1, grid size
400,400,400, pixel 0.813, shown at level 0.0432, step 2, values float32  

> surface dust #1 size 8.13

> volume #1 step 1

> volume #1 level 0.05

> volume #1 level 0.06

> open "Y:\sudipag\Sudipa\Projects\2023\CRBN-DDB1-HPK1\Reanalysis of older
> datasets in cryosparc\Maps for
> Chimera\cryosparc_P39_J431_009_volume_map_sharp (1).mrc" format mrc

Opened cryosparc_P39_J431_009_volume_map_sharp (1).mrc as #2, grid size
400,400,400, pixel 0.813, shown at level 0.0432, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.06

> surface dust #1 size 8.13

> surface dust #2 size 8.13

> hide #!1 models

> show #!1 models

> hide #!1 models

> close #2

> show #!1 models

> close

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/Maps for Chimera/With models fitting in volume.cxs"

Opened cryosparc_P39_J435_008_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.813, shown at level 0.08, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.813, shown at level 0.05, step 1, values float32  
opened ChimeraX session  

> close

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/Maps for Chimera/Model fitting with individual
> components .cxs"

Opened cryosparc_P39_J435_008_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.813, shown at level 0.08, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.813, shown at level 0.05, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc z flip as #5, grid size
400,400,400, pixel 0.813, shown at level 0.05, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc z flip as #6, grid size
400,400,400, pixel 0.813, shown at level 0.05, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc z flip as #7, grid size
400,400,400, pixel 0.813, shown at level 0.05, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc z flip as #8, grid size
400,400,400, pixel 0.813, shown at level 3, step 1, values float32  
opened ChimeraX session  

> open "Y:\sudipag\Sudipa\Projects\2023\CRBN-DDB1-HPK1\Reanalysis of older
> datasets in cryosparc\Maps for Chimera\Model fitting with individual
> components .cxs" format session

Opened cryosparc_P39_J435_008_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 0.813, shown at level 0.08, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 0.813, shown at level 0.05, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc z flip as #5, grid size
400,400,400, pixel 0.813, shown at level 0.05, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc z flip as #6, grid size
400,400,400, pixel 0.813, shown at level 0.05, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc z flip as #7, grid size
400,400,400, pixel 0.813, shown at level 0.05, step 1, values float32  
Opened cryosparc_P39_J433_008_volume_map_sharp.mrc z flip as #8, grid size
400,400,400, pixel 0.813, shown at level 3, step 1, values float32  
opened ChimeraX session  

> hide #!4 models

> hide #!7 models

> hide #11 models

> hide #!12 models

> hide #13 models

> hide #!14 models

> open C:/Users/sudipag/Downloads/emd_27241.map.gz

File reader requires uncompressed file;
'C:/Users/sudipag/Downloads/emd_27241.map.gz' is compressed  

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/Published Cryo-EM MRC maps/emd_27012.map"

Opened emd_27012.map as #15, grid size 224,224,224, pixel 1.15, shown at level
0.094, step 1, values float32  

> close #15

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/Published Cryo-EM MRC maps/emd_27241.map"

Opened emd_27241.map as #15, grid size 224,224,224, pixel 1.15, shown at level
0.106, step 1, values float32  

> open "Y:/sudipag/Sudipa/Projects/2023/CRBN-DDB1-HPK1/Reanalysis of older
> datasets in cryosparc/Maps for Chimera/PDB models/8D80.pdb"

Chain information for 8D80.pdb #16  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> ~select #14

Nothing selected  

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!15 models

> transparency #15.1 50

> show #!7 models

> select #7

3 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.85125,0.12848,0.5088,-88.805,0.51583,-0.0267,-0.85627,187.63,-0.096426,0.99135,-0.089,51.713

> view matrix models
> #7,0.77081,0.36589,0.52151,-114.19,0.62681,-0.58186,-0.51821,200.28,0.11384,0.72633,-0.67785,153.04

> view matrix models
> #7,0.87676,0.071878,0.47552,-78.912,0.46191,0.14941,-0.87425,172.28,-0.13389,0.98616,0.097791,28.51

> view matrix models
> #7,0.25639,-0.66735,0.69922,102.66,0.36824,-0.60141,-0.70902,277.31,0.89368,0.43926,0.091551,-57.148

> view matrix models
> #7,0.077834,-0.71464,0.69515,140.4,0.32548,-0.64085,-0.69526,288.31,0.94234,0.28037,0.18272,-55.439

> view matrix models
> #7,0.41034,-0.54836,0.72864,53.818,-0.55137,-0.78561,-0.28073,389.74,0.72637,-0.28656,-0.62472,199.05

> view matrix models
> #7,-0.9101,0.069296,0.40855,230.2,-0.33479,0.45802,-0.82349,249.11,-0.24419,-0.88623,-0.39365,416.21

> view matrix models
> #7,-0.90727,0.25905,0.3313,212.88,-0.16909,0.49659,-0.85136,220.04,-0.38506,-0.82843,-0.40673,432.87

> view matrix models
> #7,-0.90385,0.15922,0.39711,217.1,-0.28616,0.46501,-0.83778,242.24,-0.31805,-0.87087,-0.37474,423.08

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.90385,0.15922,0.39711,214.24,-0.28616,0.46501,-0.83778,267.2,-0.31805,-0.87087,-0.37474,397.71

> view matrix models
> #7,-0.90385,0.15922,0.39711,186.86,-0.28616,0.46501,-0.83778,257.67,-0.31805,-0.87087,-0.37474,374.07

> view matrix models
> #7,-0.90385,0.15922,0.39711,183.51,-0.28616,0.46501,-0.83778,258.79,-0.31805,-0.87087,-0.37474,387.02

> view matrix models
> #7,-0.90385,0.15922,0.39711,185.36,-0.28616,0.46501,-0.83778,250.61,-0.31805,-0.87087,-0.37474,389.98

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.8801,0.25456,0.40079,166.05,-0.23914,0.49157,-0.83736,238.6,-0.41017,-0.8328,-0.37175,398.96

> view matrix models
> #7,-0.94096,0.19175,0.27898,205.64,-0.18942,0.38477,-0.90337,257.52,-0.28056,-0.90288,-0.32573,380.75

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.94096,0.19175,0.27898,204.97,-0.18942,0.38477,-0.90337,260.99,-0.28056,-0.90288,-0.32573,379.02

> view matrix models
> #7,-0.94096,0.19175,0.27898,205.39,-0.18942,0.38477,-0.90337,261.9,-0.28056,-0.90288,-0.32573,375.96

> view matrix models
> #7,-0.94096,0.19175,0.27898,201.89,-0.18942,0.38477,-0.90337,260.08,-0.28056,-0.90288,-0.32573,374.96

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.  

> hide #!16 models

> fitmap #7 inMap #15

Fit map cryosparc_P39_J433_008_volume_map_sharp.mrc z flip in map
emd_27241.map using 313827 points  
correlation = 0.7246, correlation about mean = 0.4572, overlap = 1.053e+04  
steps = 156, shift = 2.86, angle = 11.1 degrees  
  
Position of cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) relative
to emd_27241.map (#15) coordinates:  
Matrix rotation and translation  
-0.90223903 0.10823206 0.41743328 185.06287894  
-0.36640260 0.31805775 -0.87440745 297.53448667  
-0.22740681 -0.94187318 -0.24730761 358.96249290  
Axis -0.08396246 0.80251652 -0.59069242  
Axis point 155.86305670 0.00000000 264.67798297  
Rotation angle (degrees) 156.31167066  
Shift along axis 11.20158272  
  

> show #!16 models

> hide #!15 models

> fitmap #16 inMap #7

Fit molecule 8D80.pdb (#16) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 10970 atoms  
average map value = 0.1538, steps = 52  
shifted from previous position = 0.0868  
rotated from previous position = 0.483 degrees  
atoms outside contour = 3721, contour level = 0.05  
  
Position of 8D80.pdb (#16) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.90077344 -0.37300072 -0.22243583 357.76741833  
0.10191296 0.31633126 -0.94315868 224.60138707  
0.42216227 -0.87224137 -0.24692919 270.76530663  
Axis 0.08822861 -0.80194801 0.59084271  
Axis point 156.70538119 0.00000000 264.78584982  
Rotation angle (degrees) 156.30329063  
Shift along axis 11.42639362  
  

> ~select #7

Nothing selected  

> fitmap #16 inMap #7

Fit molecule 8D80.pdb (#16) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 10970 atoms  
average map value = 0.1537, steps = 28  
shifted from previous position = 0.0199  
rotated from previous position = 0.0127 degrees  
atoms outside contour = 3721, contour level = 0.05  
  
Position of 8D80.pdb (#16) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.90073775 -0.37307538 -0.22245510 357.77392636  
0.10199757 0.31615245 -0.94320949 224.61527667  
0.42221796 -0.87227427 -0.24671767 270.71681179  
Axis 0.08823379 -0.80188584 0.59092631  
Axis point 156.70750397 0.00000000 264.79919363  
Rotation angle (degrees) 156.29841582  
Shift along axis 11.42562546  
  

> fitmap #16 inMap #7

Fit molecule 8D80.pdb (#16) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 10970 atoms  
average map value = 0.1538, steps = 28  
shifted from previous position = 0.0164  
rotated from previous position = 0.0139 degrees  
atoms outside contour = 3721, contour level = 0.05  
  
Position of 8D80.pdb (#16) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.90078379 -0.37297734 -0.22243310 357.76375660  
0.10191176 0.31634215 -0.94315516 224.59572288  
0.42214046 -0.87224742 -0.24694511 270.76827734  
Axis 0.08822055 -0.80195245 0.59083789  
Axis point 156.70354201 0.00000000 264.78115987  
Rotation angle (degrees) 156.30438701  
Shift along axis 11.42718235  
  

> show #!15 models

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 2 maps.  

> hide #!15 models

> fitmap #16 inMap #7

Fit molecule 8D80.pdb (#16) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 10970 atoms  
average map value = 0.1538, steps = 40  
shifted from previous position = 0.00557  
rotated from previous position = 0.00201 degrees  
atoms outside contour = 3718, contour level = 0.05  
  
Position of 8D80.pdb (#16) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.90077332 -0.37300087 -0.22243603 357.76753977  
0.10191851 0.31632016 -0.94316180 224.60369069  
0.42216117 -0.87224533 -0.24691707 270.75995016  
Axis 0.08822729 -0.80194433 0.59084790  
Axis point 156.70561834 0.00000000 264.78555950  
Rotation angle (degrees) 156.30321010  
Shift along axis 11.42315042  
  

> select #16

10970 atoms, 11184 bonds, 1 pseudobond, 1513 residues, 2 models selected  

> view matrix models
> #16,0.99997,0.0066677,-0.0044613,-2.5649,-0.0066792,0.99997,-0.0025727,6.269,0.004444,0.0026024,0.99999,0.25294

> fitmap #16 inMap #7

Fit molecule 8D80.pdb (#16) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 10970 atoms  
average map value = 0.06942, steps = 72  
shifted from previous position = 1.18  
rotated from previous position = 3.04 degrees  
atoms outside contour = 5790, contour level = 0.05  
  
Position of 8D80.pdb (#16) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.89328528 -0.35759441 -0.27233739 361.46334181  
0.14692611 0.34030380 -0.92876588 213.90379328  
0.42479893 -0.86966636 -0.25144842 265.96863508  
Axis 0.06851535 -0.80820527 0.58490160  
Axis point 153.10339501 0.00000000 261.01552579  
Rotation angle (degrees) 154.45075690  
Shift along axis 7.45309594  
  

> view matrix models
> #16,0.99918,-0.0035603,0.040228,-5.0315,0.0025857,0.9997,0.024252,-3.9143,-0.040303,-0.024129,0.9989,6.7753

> fitmap #16 inMap #7

Fit molecule 8D80.pdb (#16) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 10970 atoms  
average map value = 0.1538, steps = 76  
shifted from previous position = 1.91  
rotated from previous position = 3.04 degrees  
atoms outside contour = 3716, contour level = 0.05  
  
Position of 8D80.pdb (#16) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.90077084 -0.37300640 -0.22243679 357.76749940  
0.10191462 0.31632643 -0.94316012 224.60117903  
0.42216739 -0.87224069 -0.24692282 270.75794773  
Axis 0.08823021 -0.80194620 0.59084493  
Axis point 156.70590880 0.00000000 264.78333212  
Rotation angle (degrees) 156.30299624  
Shift along axis 11.42380212  
  

> ~select #16

Nothing selected  

> show #11 models

> select #11

1742 atoms, 1770 bonds, 316 residues, 1 model selected  

> view matrix models
> #11,0.78829,0.21024,0.57828,-76.056,-0.18518,0.9773,-0.10289,68.48,-0.58678,-0.025976,0.80933,54.072

> view matrix models
> #11,0.78829,0.21024,0.57828,-42.577,-0.18518,0.9773,-0.10289,59.127,-0.58678,-0.025976,0.80933,76.661

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.56409,0.33072,-0.75659,112.2,-0.76866,0.54501,-0.33486,203.69,0.30161,0.77045,0.56164,-95.588

> view matrix models
> #11,0.60997,0.47706,-0.63273,79.652,-0.71115,0.68181,-0.17149,166.43,0.34959,0.55457,0.75514,-101.63

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.60997,0.47706,-0.63273,89.997,-0.71115,0.68181,-0.17149,162.53,0.34959,0.55457,0.75514,-95.412

> view matrix models
> #11,0.60997,0.47706,-0.63273,93.375,-0.71115,0.68181,-0.17149,156.57,0.34959,0.55457,0.75514,-81.05

> view matrix models
> #11,0.60997,0.47706,-0.63273,83.232,-0.71115,0.68181,-0.17149,156.98,0.34959,0.55457,0.75514,-87.283

> volume #7 level 0.07

> volume #7 change image level -0.007323,0 level 0.02609,0.8 level 1.779,1

> view matrix models
> #11,0.60997,0.47706,-0.63273,80.257,-0.71115,0.68181,-0.17149,156.92,0.34959,0.55457,0.75514,-89.25

> view matrix models
> #11,0.60997,0.47706,-0.63273,83.038,-0.71115,0.68181,-0.17149,151.5,0.34959,0.55457,0.75514,-76.704

> view matrix models
> #11,0.60997,0.47706,-0.63273,76.691,-0.71115,0.68181,-0.17149,150.59,0.34959,0.55457,0.75514,-81.258

> fitmap #11 inMap #7

Fit molecule BPB.pdb (#11) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 1742 atoms  
average map value = 0.05809, steps = 144  
shifted from previous position = 2.05  
rotated from previous position = 29.6 degrees  
atoms outside contour = 1172, contour level = 0.07  
  
Position of BPB.pdb (#11) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.27139853 -0.62144961 0.73494438 194.54428684  
-0.83690678 -0.22473456 -0.49908058 366.33736351  
0.47532083 -0.75052967 -0.45910276 272.27898683  
Axis -0.59758354 0.61701064 -0.51204665  
Axis point 296.83821102 0.00000000 272.90353657  
Rotation angle (degrees) 167.85489563  
Shift along axis -29.64195517  
  

> view matrix models
> #11,0.3527,0.22308,-0.90876,162.7,-0.58237,0.81249,-0.026579,104.48,0.73243,0.53861,0.41648,-97.88

> fitmap #11 inMap #7

Fit molecule BPB.pdb (#11) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 1742 atoms  
average map value = 0.05809, steps = 60  
shifted from previous position = 0.349  
rotated from previous position = 0.027 degrees  
atoms outside contour = 1173, contour level = 0.07  
  
Position of BPB.pdb (#11) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.27137661 -0.62180159 0.73465470 194.59781318  
-0.83679523 -0.22469501 -0.49928540 366.33226428  
0.47552969 -0.75024993 -0.45934363 272.23278007  
Axis -0.59761721 0.61704961 -0.51196039  
Axis point 296.81205100 0.00000000 272.86946359  
Rotation angle (degrees) 167.87934902  
Shift along axis -29.62222158  
  

> show #!12 models

> ~select #11

Nothing selected  

> select #12

2990 atoms, 3039 bonds, 1 pseudobond, 393 residues, 2 models selected  

> view matrix models
> #12,0.1324,0.62224,0.77155,-25.553,-0.75636,0.56651,-0.32709,272.07,-0.64062,-0.54026,0.54564,141.23

> view matrix models
> #12,0.1324,0.62224,0.77155,-26.467,-0.75636,0.56651,-0.32709,267.24,-0.64062,-0.54026,0.54564,146.6

> hide #!7 models

> view matrix models
> #12,0.1324,0.62224,0.77155,-21.684,-0.75636,0.56651,-0.32709,282.11,-0.64062,-0.54026,0.54564,130.2

> view matrix models
> #12,0.1324,0.62224,0.77155,-37.46,-0.75636,0.56651,-0.32709,271,-0.64062,-0.54026,0.54564,143.21

> view matrix models
> #12,0.1324,0.62224,0.77155,-37.891,-0.75636,0.56651,-0.32709,202.56,-0.64062,-0.54026,0.54564,231.79

> ui mousemode right "rotate selected models"

> view matrix models
> #12,-0.92,-0.20399,-0.33466,354.44,0.33841,0.017266,-0.94084,209.73,0.1977,-0.97882,0.053148,242.58

> view matrix models
> #12,-0.83169,0.24229,0.49958,173.05,-0.55415,-0.41844,-0.7196,349.59,0.034693,-0.87533,0.48228,192.04

> view matrix models
> #12,0.039638,0.71738,0.69556,-26.634,-0.51393,0.61161,-0.60151,203.17,-0.85691,-0.33363,0.39293,256.48

> view matrix models
> #12,0.0014852,0.57316,0.81944,-21.314,-0.56441,0.67693,-0.47245,184.02,-0.8255,-0.4618,0.3245,277.35

> show #!7 models

> view matrix models
> #12,-0.83087,-0.28444,-0.47828,372.33,0.44742,0.16955,-0.8781,168.21,0.33086,-0.94358,-0.013613,230

> view matrix models
> #12,-0.8634,0.057404,0.50125,199.39,-0.46717,-0.46613,-0.75132,348.29,0.19052,-0.88285,0.42927,179.75

> view matrix models
> #12,-0.14103,0.83394,0.53353,5.558,-0.9716,-0.013152,-0.23627,288.57,-0.19002,-0.55169,0.81211,136.76

> view matrix models
> #12,0.57954,0.64228,0.50161,-61.884,-0.80591,0.54307,0.23577,133.89,-0.12098,-0.54089,0.83235,123.54

> view matrix models
> #12,0.59618,0.70435,0.38531,-55.469,-0.79998,0.56172,0.21095,134.29,-0.06786,-0.434,0.89835,94.431

> view matrix models
> #12,0.66577,0.49317,0.55993,-63.293,-0.72842,0.59221,0.34451,102.63,-0.1617,-0.63724,0.75352,151.51

> view matrix models
> #12,0.32334,0.79903,0.50696,-47.803,-0.9342,0.35489,0.036495,201.24,-0.15075,-0.4854,0.8612,116.75

> fitmap #12 inMap #7

Fit molecule BPA.pdb (#12) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 2990 atoms  
average map value = 0.01345, steps = 2000  
shifted from previous position = 6.3  
rotated from previous position = 4.99 degrees  
atoms outside contour = 2705, contour level = 0.07  
  
Position of BPA.pdb (#12) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
0.06337520 -0.78695553 -0.61374635 306.74361128  
-0.16115357 0.59884205 -0.78448565 187.48545415  
0.98489244 0.14862434 -0.08886896 56.00464835  
Axis 0.47754762 -0.81815235 0.32027332  
Axis point 182.26753610 0.00000000 213.05227834  
Rotation angle (degrees) 102.31732762  
Shift along axis 11.02980906  
  

> view matrix models
> #12,0.21899,0.84389,0.4898,-41.416,-0.97441,0.2152,0.064884,215.46,-0.050649,-0.49147,0.86942,104.17

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.21899,0.84389,0.4898,-56.026,-0.97441,0.2152,0.064884,220.13,-0.050649,-0.49147,0.86942,82.341

> fitmap #12 inMap #7

Fit molecule BPA.pdb (#12) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 2990 atoms  
average map value = 0.04759, steps = 104  
shifted from previous position = 2.16  
rotated from previous position = 4.33 degrees  
atoms outside contour = 2028, contour level = 0.07  
  
Position of BPA.pdb (#12) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
0.20869560 -0.76291702 -0.61188542 302.79375409  
-0.20534230 0.57753245 -0.79012075 217.86591129  
0.95618026 0.29054069 -0.03613066 30.01690646  
Axis 0.54459881 -0.79022594 0.28098951  
Axis point 209.90311524 0.00000000 222.35876068  
Rotation angle (degrees) 97.17794362  
Shift along axis 1.17225899  
  

> hide #!7 models

> view matrix models
> #12,0.18862,0.87212,0.45147,-52.287,-0.97787,0.20917,0.0044853,199.36,-0.090523,-0.44232,0.89228,140.81

> view matrix models
> #12,0.18862,0.87212,0.45147,-52.346,-0.97787,0.20917,0.0044853,187.54,-0.090523,-0.44232,0.89228,129.63

> view matrix models
> #12,0.18862,0.87212,0.45147,-52.225,-0.97787,0.20917,0.0044853,188.67,-0.090523,-0.44232,0.89228,131.3

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.80343,0.59151,0.067945,-46.181,-0.59152,0.80599,-0.022164,69.105,-0.067873,-0.022384,0.99744,62.867

> view matrix models
> #12,0.73851,0.67409,-0.014512,-36.181,-0.67424,0.73826,-0.019008,87.785,-0.0020991,0.023822,0.99971,48.277

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.73851,0.67409,-0.014512,-57.889,-0.67424,0.73826,-0.019008,115.69,-0.0020991,0.023822,0.99971,5.1573

> view matrix models
> #12,0.73851,0.67409,-0.014512,-57.198,-0.67424,0.73826,-0.019008,118.19,-0.0020991,0.023822,0.99971,1.2794

> select #16

10970 atoms, 11184 bonds, 1 pseudobond, 1513 residues, 2 models selected  

> ~select #16

Nothing selected  

> show #!15 models

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

> hide #!16 models

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.  

> select #12

2990 atoms, 3039 bonds, 1 pseudobond, 393 residues, 2 models selected  

> fitmap #12 inMap #15

Fit molecule BPA.pdb (#12) to map emd_27241.map (#15) using 2990 atoms  
average map value = 0.4214, steps = 192  
shifted from previous position = 12.1  
rotated from previous position = 42.4 degrees  
atoms outside contour = 44, contour level = 0.10581  
  
Position of BPA.pdb (#12) relative to emd_27241.map (#15) coordinates:  
Matrix rotation and translation  
0.99999977 0.00028891 -0.00059163 0.04410953  
-0.00028757 0.99999737 0.00227389 -0.28301297  
0.00059229 -0.00227372 0.99999723 0.19386795  
Axis -0.96054174 -0.25006590 -0.12176459  
Axis point 0.00000000 85.37101907 124.03321812  
Rotation angle (degrees) 0.13563124  
Shift along axis 0.00479659  
  

> show #!7 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> volume #7 level 0.06

> volume #7 level 0.05

> volume #7 level 0.08

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> hide #!12 models

> hide #11 models

> ~select #12

Nothing selected  

> show #13 models

> select #13

2942 atoms, 3012 bonds, 381 residues, 1 model selected  

> view matrix models
> #13,0.62636,0.50771,-0.59152,68.078,0.31597,0.52833,0.78805,-64.18,0.71262,-0.68051,0.1705,214.52

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.8145,0.40098,-0.4193,40.39,-0.57747,0.49063,-0.65254,242.95,-0.055938,0.77362,0.63117,-0.76969

> view matrix models
> #13,0.75255,0.38547,-0.53393,65.846,-0.43995,0.89759,0.027923,66.285,0.49001,0.21389,0.84507,-0.47515

> hide #!7 models

> show #!15 models

> hide #!15 models

> show #!16 models

> view matrix models
> #13,0.7798,0.37565,-0.5008,59.777,-0.42168,0.90644,0.023332,63.375,0.46271,0.19298,0.86525,3.2982

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.7798,0.37565,-0.5008,64.336,-0.42168,0.90644,0.023332,67.511,0.46271,0.19298,0.86525,-63.55

> view matrix models
> #13,0.7798,0.37565,-0.5008,41.378,-0.42168,0.90644,0.023332,67.095,0.46271,0.19298,0.86525,-79.615

> view matrix models
> #13,0.7798,0.37565,-0.5008,40.303,-0.42168,0.90644,0.023332,65.093,0.46271,0.19298,0.86525,-68.98

> view matrix models
> #13,0.7798,0.37565,-0.5008,39.108,-0.42168,0.90644,0.023332,64.372,0.46271,0.19298,0.86525,-65.395

> show #!15 models

> fitmap #13 inMap #15

Fit molecule CRBN.pdb (#13) to map emd_27241.map (#15) using 2942 atoms  
average map value = 0.2727, steps = 172  
shifted from previous position = 8.62  
rotated from previous position = 39.1 degrees  
atoms outside contour = 205, contour level = 0.10581  
  
Position of CRBN.pdb (#13) relative to emd_27241.map (#15) coordinates:  
Matrix rotation and translation  
0.99999974 -0.00029043 -0.00066192 0.12905861  
0.00029079 0.99999981 0.00054840 -0.10156818  
0.00066176 -0.00054859 0.99999963 0.03339441  
Axis -0.60448090 -0.72940042 0.32027781  
Axis point -47.07591329 0.00000000 201.17261493  
Rotation angle (degrees) 0.05198904  
Shift along axis 0.00676590  
  

> hide #!15 models

> show #!7 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #11 models

> show #!12 models

> hide #13 models

> hide #!12 models

> hide #11 models

> show #!14 models

> show #!15 models

> hide #!15 models

> show #!16 models

> ~select #13

Nothing selected  

> select #14

3296 atoms, 3360 bonds, 1 pseudobond, 423 residues, 2 models selected  

> hide #!7 models

> view matrix models
> #14,-0.81485,0.12613,-0.56579,321.02,0.56077,-0.07573,-0.8245,156.55,-0.14684,-0.98912,-0.0090201,368.68

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.60447,0.66494,0.43872,102.7,0.049482,0.58099,-0.8124,134.87,-0.79509,-0.46936,-0.38409,429.07

> view matrix models
> #14,-0.59177,0.80573,0.024474,131.44,0.67482,0.47856,0.56178,-96.459,0.44093,0.34896,-0.82693,210.7

> view matrix models
> #14,-0.60769,0.79412,0.0094644,136.85,0.65456,0.49407,0.57223,-97.102,0.44975,0.35393,-0.82004,208.06

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.60769,0.79412,0.0094644,87.103,0.65456,0.49407,0.57223,-82.621,0.44975,0.35393,-0.82004,104.82

> view matrix models
> #14,-0.60769,0.79412,0.0094644,90.535,0.65456,0.49407,0.57223,-86.188,0.44975,0.35393,-0.82004,98.756

> ~select #14

Nothing selected  

> show #!15 models

> hide #!14 models

> show #!14 models

> hide #!16 models

> fitmap #14 inMap #15

Fit molecule BPC.pdb (#14) to map emd_27241.map (#15) using 3296 atoms  
average map value = 0.1331, steps = 100  
shifted from previous position = 6.15  
rotated from previous position = 13.6 degrees  
atoms outside contour = 1877, contour level = 0.10581  
  
Position of BPC.pdb (#14) relative to emd_27241.map (#15) coordinates:  
Matrix rotation and translation  
-0.53628461 0.84259527 0.04931556 70.00193583  
0.79063130 0.48103970 0.37881785 -78.71287836  
0.29546739 0.24214461 -0.92415638 152.66007493  
Axis -0.47736939 -0.85975386 -0.18149868  
Axis point 50.41596112 0.00000000 87.69819412  
Rotation angle (degrees) 171.76969102  
Shift along axis 6.54931681  
  

> show #!16 models

> hide #!16 models

> hide #!15 models

> show #!7 models

> select #14

3296 atoms, 3360 bonds, 1 pseudobond, 423 residues, 2 models selected  

> view matrix models
> #14,-0.53628,0.8426,0.049316,71.231,0.79063,0.48104,0.37882,-75.089,0.29547,0.24214,-0.92416,143.76

> view matrix models
> #14,-0.53628,0.8426,0.049316,73.103,0.79063,0.48104,0.37882,-79.627,0.29547,0.24214,-0.92416,145.96

> fitmap #14 inMap #7

Fit molecule BPC.pdb (#14) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 3296 atoms  
average map value = 0.05408, steps = 52  
shifted from previous position = 1.12  
rotated from previous position = 1.86 degrees  
atoms outside contour = 2273, contour level = 0.08  
  
Position of BPC.pdb (#14) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
0.12967479 -0.99106742 0.03114218 285.87055471  
-0.11693908 0.01590255 0.99301177 72.58610187  
-0.98463685 -0.13241034 -0.11383235 339.02982832  
Axis -0.64310020 0.58044683 0.49950335  
Axis point 0.00000000 314.38045156 254.61514554  
Rotation angle (degrees) 118.95532416  
Shift along axis 27.63549760  
  

> view matrix models
> #14,-0.54067,0.84063,0.031861,71.988,0.77627,0.48397,0.40396,-68.428,0.32416,0.24314,-0.91422,140.18

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.1002,0.99416,-0.040187,-23.926,0.72027,-0.044614,0.69226,-25.003,0.68642,-0.098312,-0.72053,115.1

> view matrix models
> #14,-0.40597,0.90013,0.15796,31.461,0.82879,0.28979,0.47867,-58.363,0.38509,0.32524,-0.86367,115.29

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.40597,0.90013,0.15796,31.452,0.82879,0.28979,0.47867,-59.125,0.38509,0.32524,-0.86367,116.98

> view matrix models
> #14,-0.40597,0.90013,0.15796,55.458,0.82879,0.28979,0.47867,-39.942,0.38509,0.32524,-0.86367,80.002

> show #!16 models

> hide #!7 models

> view matrix models
> #14,-0.40597,0.90013,0.15796,-42.798,0.82879,0.28979,0.47867,-131.74,0.38509,0.32524,-0.86367,208.76

> view matrix models
> #14,-0.40597,0.90013,0.15796,-22.235,0.82879,0.28979,0.47867,-111,0.38509,0.32524,-0.86367,185.43

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.22564,0.95379,0.19841,-57.814,0.95881,0.18134,0.21865,-82.806,0.17257,0.23957,-0.95542,235.56

> view matrix models
> #14,0.088167,-0.19827,-0.97617,193.44,0.78059,0.62253,-0.055937,-85.524,0.61879,-0.75706,0.20965,171.39

> view matrix models
> #14,0.22528,-0.55254,-0.80247,201.96,0.73616,0.63606,-0.23129,-60.704,0.63822,-0.53864,0.55005,99.442

> view matrix models
> #14,0.45956,-0.41665,-0.78435,151.02,0.81684,0.54498,0.1891,-109.02,0.34867,-0.72759,0.59079,157.7

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.45956,-0.41665,-0.78435,207.82,0.81684,0.54498,0.1891,-67.647,0.34867,-0.72759,0.59079,90.826

> hide #!16 models

> show #!15 models

> fitmap #14 inMap #15

Fit molecule BPC.pdb (#14) to map emd_27241.map (#15) using 3296 atoms  
average map value = 0.1322, steps = 148  
shifted from previous position = 7.95  
rotated from previous position = 18.7 degrees  
atoms outside contour = 1814, contour level = 0.10581  
  
Position of BPC.pdb (#14) relative to emd_27241.map (#15) coordinates:  
Matrix rotation and translation  
0.40163425 -0.66747854 -0.62702659 235.75131760  
0.84884010 0.52831923 -0.01868899 -49.40701641  
0.34374470 -0.52473917 0.77877364 47.33806584  
Axis -0.27058389 -0.51906922 0.81077216  
Axis point 169.79561381 201.07788074 0.00000000  
Rotation angle (degrees) 69.24555667  
Shift along axis 0.23553832  
  

> view matrix models
> #14,0.40163,-0.66748,-0.62703,161.44,0.84884,0.52832,-0.018689,-79.688,0.34374,-0.52474,0.77877,112.6

> show #!16 models

> view matrix models
> #14,0.40163,-0.66748,-0.62703,233.74,0.84884,0.52832,-0.018689,-41.672,0.34374,-0.52474,0.77877,42.213

> view matrix models
> #14,0.40163,-0.66748,-0.62703,289.56,0.84884,0.52832,-0.018689,-8.4396,0.34374,-0.52474,0.77877,21.655

> show #!12 models

> show #11 models

> show #13 models

> hide #!15 models

> view matrix models
> #14,0.40163,-0.66748,-0.62703,288.6,0.84884,0.52832,-0.018689,-9.9459,0.34374,-0.52474,0.77877,21.986

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.1508,-0.89732,-0.41482,366.44,0.8809,0.068459,-0.46833,100.29,0.44864,-0.43604,0.78012,-3.721

> view matrix models
> #14,0.133,-0.81799,-0.55965,335.85,0.91102,0.32327,-0.25599,37.293,0.39031,-0.47581,0.7882,8.2555

> view matrix models
> #14,-0.41181,-0.88781,-0.20542,374.58,0.75403,-0.2054,-0.6239,171.78,0.51172,-0.41182,0.75402,-12.118

> view matrix models
> #14,0.19334,-0.79073,-0.58083,326.82,0.90493,0.37246,-0.20584,25.606,0.3791,-0.48582,0.78757,11.132

> view matrix models
> #14,-0.30348,-0.90336,-0.30306,374.02,0.82064,-0.086173,-0.56492,140.2,0.48421,-0.42014,0.76748,-9.0011

> view matrix models
> #14,-0.065058,-0.88206,-0.46663,359.31,0.90047,0.14962,-0.40837,79.827,0.43002,-0.44675,0.78454,-0.37889

> view matrix models
> #14,0.37946,-0.6829,-0.62423,293.23,0.85757,0.51283,-0.039719,-6.5382,0.34725,-0.52025,0.78023,20.757

> view matrix models
> #14,0.59646,0.66282,0.45267,-41.804,-0.66477,0.091895,0.74137,156.45,0.4498,-0.74312,0.49543,70.701

> view matrix models
> #14,0.18729,-0.79363,-0.57886,327.77,0.90574,0.36761,-0.21095,26.751,0.38021,-0.48479,0.78767,10.838

> view matrix models
> #14,-0.36461,-0.89694,-0.25014,374.9,0.78588,-0.15232,-0.59933,157.63,0.49946,-0.4151,0.76042,-10.834

> view matrix models
> #14,-0.27559,-0.90781,-0.31611,372.5,0.84558,-0.072526,-0.5289,130.85,0.45722,-0.41306,0.78761,-8.7899

> view matrix models
> #14,0.049268,-0.88139,-0.46982,344.61,0.9504,0.18601,-0.24929,49.58,0.30711,-0.43424,0.84683,6.6901

> view matrix models
> #14,0.57094,-0.73348,0.36884,157.09,0.80951,0.57782,-0.104,-1.2525,-0.13684,0.35796,0.92366,-49.503

> view matrix models
> #14,0.5063,-0.69217,0.51435,142.83,0.83866,0.53407,-0.10681,1.0724,-0.20077,0.48545,0.8509,-49.439

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.38244,-0.22573,0.89598,152.13,0.68135,0.58608,0.43848,-49.865,-0.6241,0.77817,-0.07034,76.397

> view matrix models
> #14,-0.99805,-0.0035875,-0.062367,316.96,-0.029638,0.90603,0.42218,2.7815,0.054991,0.4232,-0.90436,133.41

> view matrix models
> #14,-0.98658,-0.028926,-0.16069,330.48,-0.084905,0.93154,0.35359,14.771,0.13946,0.36249,-0.92149,132.44

> view matrix models
> #14,-0.93403,-0.074778,-0.34929,352.05,-0.16833,0.9546,0.24577,35.431,0.31505,0.28835,-0.90421,117.21

> view matrix models
> #14,-0.15968,0.86464,-0.47634,140.68,0.92272,0.30223,0.23927,-20.166,0.35084,-0.40132,-0.84608,197.31

> view matrix models
> #14,-0.16403,0.97383,-0.15734,88.916,0.95058,0.19866,0.23858,-9.9724,0.2636,-0.11043,-0.95829,183.38

> view matrix models
> #14,-0.20391,0.97449,-0.093777,86.522,0.968,0.215,0.12943,-1.4865,0.14629,-0.064384,-0.98714,196.07

> view matrix models
> #14,-0.33496,0.93989,-0.066415,105.06,0.92249,0.34148,0.18,-18.327,0.19186,-0.00097492,-0.98142,180.99

> view matrix models
> #14,-0.34597,0.93603,-0.064398,106.78,0.91769,0.35188,0.18446,-19.608,0.19532,0.004719,-0.98073,179.69

> view matrix models
> #14,0.56184,0.017927,0.82705,4.071,0.64674,0.61386,-0.45266,56.643,-0.51581,0.78921,0.3333,12.869

> hide #13 models

> show #13 models

> view matrix models
> #14,0.56007,-0.044014,0.82728,12.511,0.59715,0.71361,-0.3663,39.649,-0.57423,0.69916,0.42595,21.515

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.56007,-0.044014,0.82728,-34.841,0.59715,0.71361,-0.3663,1.6458,-0.57423,0.69916,0.42595,38.434

> view matrix models
> #14,0.56007,-0.044014,0.82728,-32.714,0.59715,0.71361,-0.3663,6.6038,-0.57423,0.69916,0.42595,43.789

> color #14 #ff55ff transparency 0

> view matrix models
> #14,0.56007,-0.044014,0.82728,-35.747,0.59715,0.71361,-0.3663,-1.2402,-0.57423,0.69916,0.42595,42.049

> view matrix models
> #14,0.56007,-0.044014,0.82728,-33.902,0.59715,0.71361,-0.3663,3.1599,-0.57423,0.69916,0.42595,50.245

> view matrix models
> #14,0.56007,-0.044014,0.82728,-31.134,0.59715,0.71361,-0.3663,0.43304,-0.57423,0.69916,0.42595,45.246

> show #!15 models

> fitmap #14 inMap #15

Fit molecule BPC.pdb (#14) to map emd_27241.map (#15) using 3296 atoms  
average map value = 0.172, steps = 72  
shifted from previous position = 5.4  
rotated from previous position = 6.12 degrees  
atoms outside contour = 1510, contour level = 0.10581  
  
Position of BPC.pdb (#14) relative to emd_27241.map (#15) coordinates:  
Matrix rotation and translation  
0.61372277 -0.12326940 0.77983909 -21.52042970  
0.60031644 0.71440110 -0.35951529 -0.59298217  
-0.51280067 0.68879295 0.51244487 33.96168434  
Axis 0.57764876 0.71228264 0.39871714  
Axis point 26.49436092 0.00000000 41.22866274  
Rotation angle (degrees) 65.14745785  
Shift along axis 0.68748534  
  

> hide #!16 models

> hide #!15 models

> show #!7 models

> view matrix models
> #14,0.61372,-0.12327,0.77984,-22.07,0.60032,0.7144,-0.35952,5.7161,-0.5128,0.68879,0.51244,28.364

> view matrix models
> #14,0.61372,-0.12327,0.77984,-21.452,0.60032,0.7144,-0.35952,3.7585,-0.5128,0.68879,0.51244,26.922

> fitmap #14 inMap #7

Fit molecule BPC.pdb (#14) to map cryosparc_P39_J433_008_volume_map_sharp.mrc
z flip (#7) using 3296 atoms  
average map value = 0.06133, steps = 72  
shifted from previous position = 2.25  
rotated from previous position = 7.18 degrees  
atoms outside contour = 2164, contour level = 0.08  
  
Position of BPC.pdb (#14) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
-0.65047098 -0.26818483 -0.71060848 365.91891519  
0.75485365 -0.33193432 -0.56569920 186.71333557  
-0.08416340 -0.90437631 0.41835394 266.44703730  
Axis -0.27170411 -0.50256629 0.82073382  
Axis point 184.55848687 254.37104493 0.00000000  
Rotation angle (degrees) 141.44642072  
Shift along axis 25.42459036  
  

> show #!4 models

> ~select #14

Nothing selected  

> color #4 blue transparency 0

> select #4

2215 atoms, 2264 bonds, 1 pseudobond, 283 residues, 2 models selected  

> view matrix models
> #4,0.99206,0.12534,0.0103,-146.73,-0.11819,0.95723,-0.2641,7.8605,-0.042961,0.26079,0.96444,11.861

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.55739,-0.5779,-0.59611,128.74,-0.37471,-0.81581,0.44051,324.7,-0.74088,-0.022162,-0.67127,358.04

> view matrix models
> #4,-0.8222,0.48386,0.2998,63.558,-0.39479,-0.86417,0.31201,351.06,0.41004,0.13818,0.90154,-35.159

> view matrix models
> #4,-0.88163,0.28493,0.37623,104.63,-0.16613,-0.93353,0.31769,324.86,0.44174,0.21758,0.87036,-52.849

> view matrix models
> #4,-0.88054,0.013005,0.4738,147.4,0.145,-0.94431,0.2954,276.02,0.45125,0.32881,0.82961,-71.96

> view matrix models
> #4,-0.85567,0.3948,0.33459,83.062,-0.2923,-0.90224,0.31706,340.42,0.42706,0.1735,0.88742,-43.502

> view matrix models
> #4,-0.75742,0.27479,0.59229,62.71,-0.35434,-0.93492,-0.019374,392.67,0.54842,-0.22455,0.80549,22.132

> view matrix models
> #4,-0.58337,0.57427,0.57436,-23.782,-0.66446,-0.74412,0.069115,399.21,0.46709,-0.34132,0.81568,57.83

> view matrix models
> #4,-0.35369,0.55047,0.75623,-77.514,-0.56195,-0.77137,0.29867,362.94,0.74774,-0.31932,0.58216,29.92

> view matrix models
> #4,-0.055218,-0.89947,0.43347,188.71,0.74299,-0.32703,-0.58396,145.01,0.66702,0.28982,0.68636,-86.285

> view matrix models
> #4,0.031529,-0.9275,0.3725,185.72,0.61994,-0.27419,-0.73519,171.59,0.78402,0.2541,0.56635,-86.768

> view matrix models
> #4,0.12224,-0.89773,0.42324,159.05,0.60777,-0.26942,-0.74701,173.98,0.78465,0.34855,0.51268,-99.724

> view matrix models
> #4,0.016258,-0.83772,0.54586,152.62,0.56243,-0.44371,-0.69771,210.66,0.82668,0.31835,0.46395,-95.914

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.016258,-0.83772,0.54586,200.22,0.56243,-0.44371,-0.69771,262.4,0.82668,0.31835,0.46395,-110.14

> view matrix models
> #4,0.016258,-0.83772,0.54586,173.85,0.56243,-0.44371,-0.69771,276.36,0.82668,0.31835,0.46395,-155.72

> view matrix models
> #4,0.016258,-0.83772,0.54586,169.35,0.56243,-0.44371,-0.69771,277.33,0.82668,0.31835,0.46395,-161.81

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.58406,-0.79706,-0.15353,337.46,0.26767,-0.01056,-0.96345,270.95,0.76631,-0.60381,0.21952,54.455

> view matrix models
> #4,-0.71035,-0.69946,-0.078511,332.15,0.32311,-0.22496,-0.91923,298.75,0.6253,-0.67834,0.3858,75.762

> view matrix models
> #4,-0.76485,-0.5949,-0.24719,338.71,0.38733,-0.11805,-0.91435,266.34,0.51477,-0.79508,0.32071,124.34

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.76485,-0.5949,-0.24719,370,0.38733,-0.11805,-0.91435,252.7,0.51477,-0.79508,0.32071,159.39

> fitmap #4 inMap #7

Fit molecule HPK1_docking_model.pdb (#4) to map
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) using 2215 atoms  
average map value = 0.04637, steps = 216  
shifted from previous position = 14.6  
rotated from previous position = 25.6 degrees  
atoms outside contour = 1780, contour level = 0.08  
  
Position of HPK1_docking_model.pdb (#4) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
0.52339130 0.43404667 0.73325647 -88.09149265  
-0.35582523 0.89324748 -0.27476780 83.43483423  
-0.77424154 -0.11710008 0.62196271 203.75282047  
Axis 0.09224741 0.88199911 -0.46213416  
Axis point 143.57303001 0.00000000 209.84791690  
Rotation angle (degrees) 58.71464158  
Shift along axis -28.69789983  
  

> view matrix models
> #4,-0.83393,-0.34382,-0.43168,354.03,0.37206,0.22746,-0.89991,183.46,0.4076,-0.91107,-0.061767,245.32

> fitmap #4 inMap #7

Fit molecule HPK1_docking_model.pdb (#4) to map
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) using 2215 atoms  
average map value = 0.04604, steps = 84  
shifted from previous position = 5.28  
rotated from previous position = 5.26 degrees  
atoms outside contour = 1782, contour level = 0.08  
  
Position of HPK1_docking_model.pdb (#4) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
0.51561304 0.43922441 0.73568004 -87.13278455  
-0.42876393 0.87564404 -0.22228137 96.90184451  
-0.74182524 -0.20082189 0.63981707 210.65701040  
Axis 0.01252205 0.86215527 -0.50648937  
Axis point 159.21487777 0.00000000 222.85616805  
Rotation angle (degrees) 58.96663934  
Shift along axis -24.24218265  
  

> volume #7 level 0.05

> view matrix models
> #4,-0.82127,-0.38534,-0.42074,356.14,0.32336,0.29317,-0.89971,185.21,0.47005,-0.87496,-0.11617,234.81

> fitmap #4 inMap #7

Fit molecule HPK1_docking_model.pdb (#4) to map
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) using 2215 atoms  
average map value = 0.05273, steps = 344  
shifted from previous position = 19.3  
rotated from previous position = 21.8 degrees  
atoms outside contour = 1206, contour level = 0.05  
  
Position of HPK1_docking_model.pdb (#4) relative to
cryosparc_P39_J433_008_volume_map_sharp.mrc z flip (#7) coordinates:  
Matrix rotation and translation  
0.63790938 0.41149714 0.65095448 -92.58117569  
-0.59738330 0.79784906 0.08105606 105.77970985  
-0.48600908 -0.44057576 0.75477691 207.74341758  
Axis -0.32458866 0.70748269 -0.62778216  
Axis point 246.97131117 0.00000000 292.33035919  
Rotation angle (degrees) 53.46828401  
Shift along axis -25.52949775  
  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 - Build 27.20.100.9168
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 20XXS0KR00
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,868,499,456
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1185G7 @ 3.00GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

Happened after a "fitmap" command.

Reported by Sudipa Rijal

[Tom Goddard]

This ChimeraX crash was in the Qt window toolkit event loop, not in any ChimeraX code. There is no information about what caused it. It could have been a graphics driver crash or out of memory or a Qt bug.