Crash in QFileDialog.__init__

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.2.6-76060206-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

Current thread 0x00007f497eca1b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/open_save.py", line 39 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 22 in display
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 27 in _file_save
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/toolbar/providers.py", line 45 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/toolbar/__init__.py", line 37 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py", line 1289 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 386 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/toolbar/tool.py", line 165 in callback
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
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/azinas/projects/ClpP-C-A-Z/J163_aligned_refined.pdb format pdb

J163_aligned_refined.pdb title:  
\--- [more info...]  
  
Chain information for J163_aligned_refined.pdb #1  
---  
Chain | Description  
A | No description available  
B J K | No description available  
C E | No description available  
D | No description available  
F | No description available  
G H M | No description available  
I | No description available  
L | No description available  
N | No description available  
O | No description available  
P R S T U V | No description available  
Q W X Y Z g | No description available  
a b c d | No description available  
e | No description available  
f | No description available  
h i j k l n | No description available  
  
Non-standard residues in J163_aligned_refined.pdb #1  
---  
ATP — (ATP)  
  

> close

> open /home/azinas/Downloads/Lon-LarA.cif

Summary of feedback from opening /home/azinas/Downloads/Lon-LarA.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Lon-LarA.cif #1  
---  
Chain | Description  
A | No description available  
  

> open /home/azinas/projects/Lon-LarA/doubletrouble.mrc

Opened doubletrouble.mrc as #2, grid size 256,256,256, pixel 1.7, shown at
level 0.0519, step 1, values float32  

> close #2

> close

> open /home/azinas/Downloads/cryosparc_P7_J120_007_volume_map_sharp.mrc
> /home/azinas/Downloads/cryosparc_P7_J121_map_sharp.mrc
> /home/azinas/Downloads/cryosparc_P7_J67_map_sharp.mrc
> /home/azinas/Downloads/assembly.cif

Summary of feedback from opening /home/azinas/Downloads/assembly.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Opened cryosparc_P7_J120_007_volume_map_sharp.mrc as #1, grid size
400,400,400, pixel 1.63, shown at level 0.0644, step 2, values float32  
Opened cryosparc_P7_J121_map_sharp.mrc as #2, grid size 400,400,400, pixel
1.63, shown at level 3.37e-05, step 2, values float32  
Opened cryosparc_P7_J67_map_sharp.mrc as #3, grid size 400,400,400, pixel
0.85, shown at level 0.00205, step 2, values float32  
Chain information for assembly.cif  
---  
Chain | Description  
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A | No description available  
  

> close #4

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> close #2

> volume #3 level 0.1691

> volume #1 level 0.1431

> hide #!3 models

> show #!3 models

> select add #3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.28142,0.45452,-0.84511,182.87,0.48398,-0.82771,-0.284,272.64,-0.82859,-0.32909,-0.45291,432.8

> select up

4 models selected  

> select up

4 models selected  

> select up

4 models selected  

> select up

4 models selected  

> vop flip #1

Opened cryosparc_P7_J120_007_volume_map_sharp.mrc z flip as #2, grid size
400,400,400, pixel 1.63, shown at step 1, values float32  

> view matrix models
> #1,-0.98921,0.14326,-0.030546,301.29,0.10948,0.58456,-0.80393,186.78,-0.097317,-0.7986,-0.59394,416.73,#3,-0.18374,-0.55815,0.80914,146.24,0.97986,-0.16952,0.10557,18.231,0.078241,0.81224,0.57805,-75.856

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.98921,0.14326,-0.030546,463.76,0.10948,0.58456,-0.80393,276.49,-0.097317,-0.7986,-0.59394,587.5,#3,-0.18374,-0.55815,0.80914,308.71,0.97986,-0.16952,0.10557,107.94,0.078241,0.81224,0.57805,94.917

> view matrix models
> #1,-0.98921,0.14326,-0.030546,460.95,0.10948,0.58456,-0.80393,347.76,-0.097317,-0.7986,-0.59394,549.79,#3,-0.18374,-0.55815,0.80914,305.89,0.97986,-0.16952,0.10557,179.21,0.078241,0.81224,0.57805,57.209

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.74726,0.46187,0.47779,283.55,0.36127,0.8858,-0.29127,170.92,-0.55776,-0.045044,-0.82878,538.7,#3,-0.38266,-0.87918,0.28394,479.62,0.77172,-0.47313,-0.42496,352.43,0.50796,0.056511,0.85953,65.73

> view matrix models
> #1,-0.89075,0.04012,0.45272,380.67,0.065561,0.99702,0.04064,144.07,-0.44974,0.06588,-0.89073,513.42,#3,-0.60638,-0.58706,0.53635,424.65,0.46731,-0.80882,-0.35697,445.48,0.64337,0.034182,0.76479,63.633

> select subtract #1

2 models selected  

> hide #!2 models

> show #!2 models

> select add #2

4 models selected  

> select subtract #3

2 models selected  

> select add #3

4 models selected  

> select subtract #2

2 models selected  

> select add #2

4 models selected  

> select subtract #3

2 models selected  

> select add #3

4 models selected  

> select subtract #2

2 models selected  

> fitmap #3 inMap #2

Fit map cryosparc_P7_J67_map_sharp.mrc in map
cryosparc_P7_J120_007_volume_map_sharp.mrc z flip using 20310 points  
correlation = 0.889, correlation about mean = 0.3882, overlap = 3914  
steps = 144, shift = 17.5, angle = 23.3 degrees  
  
Position of cryosparc_P7_J67_map_sharp.mrc (#3) relative to
cryosparc_P7_J120_007_volume_map_sharp.mrc z flip (#2) coordinates:  
Matrix rotation and translation  
-0.26427246 -0.80225915 0.53529462 418.94716043  
0.62313592 -0.56565668 -0.54012421 409.70339235  
0.73611256 0.19082135 0.64940397 52.70361005  
Axis 0.45275974 -0.12438995 0.88291322  
Axis point 71.56491450 304.88265592 0.00000000  
Rotation angle (degrees) 126.17564395  
Shift along axis 185.25213883  
  

> open /home/azinas/Downloads/Lon-LarA.cif

Summary of feedback from opening /home/azinas/Downloads/Lon-LarA.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for Lon-LarA.cif #4  
---  
Chain | Description  
A | No description available  
  

> open /home/azinas/Desktop/LonLarA_pred.pdb

Chain information for LonLarA_pred.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close #4

> hide #!2 models

> open 6u5z

6u5z title:  
Cryo-EM structure of E. coli LonA S679A [more info...]  
  
Chain information for 6u5z #4  
---  
Chain | Description | UniProt  
A B C D E F | Lon protease | C3TLS2_ECOLX 1-784  
  

> hide atoms

> show cartoons

> select add #4

24606 atoms, 24972 bonds, 3174 residues, 3 models selected  

> select subtract #3

24606 atoms, 24972 bonds, 3174 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,159.62,0,1,0,27.585,0,0,1,179.97

> view matrix models #4,1,0,0,237.13,0,1,0,158.7,0,0,1,198.57

> view matrix models #4,1,0,0,216.85,0,1,0,179.95,0,0,1,153.74

> view matrix models #4,1,0,0,220.28,0,1,0,193.83,0,0,1,159.76

> fitmap #4 inMap #3

Fit molecule 6u5z (#4) to map cryosparc_P7_J67_map_sharp.mrc (#3) using 24606
atoms  
average map value = 0.06021, steps = 144  
shifted from previous position = 8.89  
rotated from previous position = 8.75 degrees  
atoms outside contour = 21582, contour level = 0.16907  
  
Position of 6u5z (#4) relative to cryosparc_P7_J67_map_sharp.mrc (#3)
coordinates:  
Matrix rotation and translation  
-0.21300320 0.72104507 0.65933575 -4.99087821  
-0.86391845 -0.45419352 0.21760779 296.00668439  
0.45637105 -0.52326117 0.71966882 73.69759410  
Axis -0.42063668 0.11523549 -0.89988086  
Axis point 79.71157147 158.58414698 0.00000000  
Rotation angle (degrees) 118.27890166  
Shift along axis -30.10923193  
  

> hide #5 models

> fitmap #4 inMap #3

Fit molecule 6u5z (#4) to map cryosparc_P7_J67_map_sharp.mrc (#3) using 24606
atoms  
average map value = 0.06021, steps = 80  
shifted from previous position = 0.0126  
rotated from previous position = 0.00781 degrees  
atoms outside contour = 21580, contour level = 0.16907  
  
Position of 6u5z (#4) relative to cryosparc_P7_J67_map_sharp.mrc (#3)
coordinates:  
Matrix rotation and translation  
-0.21299105 0.72097325 0.65941821 -4.98470743  
-0.86387318 -0.45426452 0.21763929 296.01284223  
0.45646240 -0.52329849 0.71958374 73.70279960  
Axis -0.42069425 0.11523551 -0.89985395  
Axis point 79.70652352 158.58645902 0.00000000  
Rotation angle (degrees) 118.28358383  
Shift along axis -30.11352742  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.97649,-0.11117,0.18469,203.57,0.10503,0.99355,0.042739,178.44,-0.18825,-0.022337,0.98187,193.06

> view matrix models
> #4,0.95644,-0.28259,-0.073209,266.23,0.27294,0.95463,-0.11909,185.24,0.10354,0.093925,0.99018,138.58

> fitmap #4 inMap #3

Fit molecule 6u5z (#4) to map cryosparc_P7_J67_map_sharp.mrc (#3) using 24606
atoms  
average map value = 0.1554, steps = 212  
shifted from previous position = 15.1  
rotated from previous position = 15.3 degrees  
atoms outside contour = 17002, contour level = 0.16907  
  
Position of 6u5z (#4) relative to cryosparc_P7_J67_map_sharp.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.02751634 0.82625334 0.56262622 -25.70629997  
-0.97452022 -0.10316558 0.19916622 277.14366235  
0.22260542 -0.55377095 0.80236186 92.94510606  
Axis -0.38003320 0.17162015 -0.90891215  
Axis point 102.82216911 164.61737443 0.00000000  
Rotation angle (degrees) 97.85367747  
Shift along axis -27.14625101  
  

> open /home/azinas/Desktop/LonLarA_pred.pdb format pdb

Chain information for LonLarA_pred.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open /home/azinas/Desktop/LonLarA_pred.pdb format pdb

Chain information for LonLarA_pred.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open /home/azinas/Desktop/LonLarA_pred.pdb format pdb

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

> open /home/azinas/Desktop/LonLarA_pred.pdb format pdb

Chain information for LonLarA_pred.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open /home/azinas/Desktop/LonLarA_pred.pdb format pdb

Chain information for LonLarA_pred.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> changechains #6 A,B C,E

Chain IDs of 888 residues changed  

> changechains #6 E D

Chain IDs of 89 residues changed  

> changechains #7 A,B E,F

Chain IDs of 888 residues changed  

> changechains #8 A,B G,H

Chain IDs of 888 residues changed  

> changechains #9 A,B I,J

Chain IDs of 888 residues changed  

> changechains #10 A,B K,L

Chain IDs of 888 residues changed  

> ui tool show Matchmaker

> matchmaker #5 to #4/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6u5z, chain A (#4) with LonLarA_pred.pdb, chain A (#5), sequence
alignment score = 2320.8  
RMSD between 310 pruned atom pairs is 1.088 angstroms; (across all 528 pairs:
3.066)  
  

> select subtract #4

Nothing selected  

> hide #4 models

> show #5 models

> matchmaker #6 to #4/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6u5z, chain B (#4) with LonLarA_pred.pdb, chain C (#6), sequence
alignment score = 2320.8  
RMSD between 310 pruned atom pairs is 1.088 angstroms; (across all 528 pairs:
3.066)  
  

> matchmaker #7 to #4/C pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6u5z, chain C (#4) with LonLarA_pred.pdb, chain E (#7), sequence
alignment score = 2320.8  
RMSD between 310 pruned atom pairs is 1.088 angstroms; (across all 528 pairs:
3.066)  
  

> matchmaker #8 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6u5z, chain D (#4) with LonLarA_pred.pdb, chain G (#8), sequence
alignment score = 2320.8  
RMSD between 310 pruned atom pairs is 1.088 angstroms; (across all 528 pairs:
3.066)  
  

> matchmaker #9 to #4/E pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6u5z, chain E (#4) with LonLarA_pred.pdb, chain I (#9), sequence
alignment score = 2320.8  
RMSD between 310 pruned atom pairs is 1.088 angstroms; (across all 528 pairs:
3.066)  
  

> matchmaker #10 to #4/F pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6u5z, chain F (#4) with LonLarA_pred.pdb, chain K (#10), sequence
alignment score = 2320.8  
RMSD between 310 pruned atom pairs is 1.088 angstroms; (across all 528 pairs:
3.066)  
  

> hide #!3 models

> show #!3 models

> select add #10

6858 atoms, 6962 bonds, 888 residues, 1 model selected  

> fitmap #10 inMap #3

Fit molecule LonLarA_pred.pdb (#10) to map cryosparc_P7_J67_map_sharp.mrc (#3)
using 6858 atoms  
average map value = 0.09035, steps = 312  
shifted from previous position = 3.92  
rotated from previous position = 3.1 degrees  
atoms outside contour = 5566, contour level = 0.16907  
  
Position of LonLarA_pred.pdb (#10) relative to cryosparc_P7_J67_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.57419492 -0.56350182 0.59394098 124.44225657  
0.65504495 -0.11899232 -0.74616146 191.43927680  
0.49113775 0.81750017 0.30079424 61.39646694  
Axis 0.78771512 0.05178848 0.61385897  
Axis point 0.00000000 107.35020673 85.46857703  
Rotation angle (degrees) 97.00763354  
Shift along axis 145.62816863  
  

> select add #9

13716 atoms, 13924 bonds, 1776 residues, 2 models selected  

> select subtract #10

6858 atoms, 6962 bonds, 888 residues, 1 model selected  

> fitmap #9 inMap #3

Fit molecule LonLarA_pred.pdb (#9) to map cryosparc_P7_J67_map_sharp.mrc (#3)
using 6858 atoms  
average map value = 0.1213, steps = 472  
shifted from previous position = 2.11  
rotated from previous position = 4.22 degrees  
atoms outside contour = 5279, contour level = 0.16907  
  
Position of LonLarA_pred.pdb (#9) relative to cryosparc_P7_J67_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.48146626 -0.17153156 0.85951565 82.40161163  
0.43449815 -0.80496480 -0.40403344 224.88662890  
0.76118434 0.56798643 -0.31303325 100.07610924  
Axis 0.84547006 0.08552931 0.52712912  
Axis point 0.00000000 103.52544186 64.13120414  
Rotation angle (degrees) 144.91157853  
Shift along axis 141.65552479  
  

> select add #8

13716 atoms, 13924 bonds, 1776 residues, 2 models selected  

> select subtract #9

6858 atoms, 6962 bonds, 888 residues, 1 model selected  

> fitmap #8 inMap #3

Fit molecule LonLarA_pred.pdb (#8) to map cryosparc_P7_J67_map_sharp.mrc (#3)
using 6858 atoms  
average map value = 0.1317, steps = 124  
shifted from previous position = 3.13  
rotated from previous position = 5.2 degrees  
atoms outside contour = 5169, contour level = 0.16907  
  
Position of LonLarA_pred.pdb (#8) relative to cryosparc_P7_J67_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.58066549 0.40019827 0.70899148 39.19582686  
0.14205133 -0.90728855 0.39578896 192.83338687  
0.80165391 -0.12910781 -0.58367985 159.05074980  
Axis -0.88629750 -0.15646216 -0.43588569  
Axis point 0.00000000 101.54723113 55.20540246  
Rotation angle (degrees) 162.77542790  
Shift along axis -134.23823692  
  

> select add #7

13716 atoms, 13924 bonds, 1776 residues, 2 models selected  

> select subtract #8

6858 atoms, 6962 bonds, 888 residues, 1 model selected  

> fitmap #7 inMap #3

Fit molecule LonLarA_pred.pdb (#7) to map cryosparc_P7_J67_map_sharp.mrc (#3)
using 6858 atoms  
average map value = 0.1256, steps = 208  
shifted from previous position = 3.88  
rotated from previous position = 4.72 degrees  
atoms outside contour = 5237, contour level = 0.16907  
  
Position of LonLarA_pred.pdb (#7) relative to cryosparc_P7_J67_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.78147532 0.57827403 0.23429780 41.43801951  
-0.06272312 -0.30080250 0.95162159 122.25643435  
0.62077542 -0.75836468 -0.19879858 182.92482750  
Axis -0.91608367 -0.20704602 -0.34339868  
Axis point 0.00000000 108.78003371 47.65680386  
Rotation angle (degrees) 111.04265569  
Shift along axis -126.08954452  
  

> select add #6

13716 atoms, 13924 bonds, 1776 residues, 2 models selected  

> select subtract #7

6858 atoms, 6962 bonds, 888 residues, 1 model selected  

> fitmap #6 inMap #3

Fit molecule LonLarA_pred.pdb (#6) to map cryosparc_P7_J67_map_sharp.mrc (#3)
using 6858 atoms  
average map value = 0.1242, steps = 196  
shifted from previous position = 1.32  
rotated from previous position = 2.54 degrees  
atoms outside contour = 5281, contour level = 0.16907  
  
Position of LonLarA_pred.pdb (#6) relative to cryosparc_P7_J67_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.94191649 0.27059505 -0.19892620 77.03669648  
0.00956696 0.57045295 0.82127456 63.02278291  
0.33571087 -0.77547517 0.53473027 146.88343758  
Axis -0.93706516 -0.31375597 -0.15318639  
Axis point 0.00000000 142.03389634 41.27830445  
Rotation angle (degrees) 58.42932835  
Shift along axis -114.46272262  
  

> select add #5

13716 atoms, 13924 bonds, 1776 residues, 2 models selected  

> select subtract #6

6858 atoms, 6962 bonds, 888 residues, 1 model selected  

> fitmap #5 inMap #3

Fit molecule LonLarA_pred.pdb (#5) to map cryosparc_P7_J67_map_sharp.mrc (#3)
using 6858 atoms  
average map value = 0.08775, steps = 456  
shifted from previous position = 6.9  
rotated from previous position = 10.7 degrees  
atoms outside contour = 5659, contour level = 0.16907  
  
Position of LonLarA_pred.pdb (#5) relative to cryosparc_P7_J67_map_sharp.mrc
(#3) coordinates:  
Matrix rotation and translation  
0.93706482 -0.25584408 -0.23759907 108.92970667  
0.25670143 0.96608879 -0.02787141 74.73776730  
0.23667254 -0.03487470 0.97096336 61.48738911  
Axis -0.01002842 -0.67913670 0.73394330  
Axis point -210.31957193 477.23910489 -0.00000000  
Rotation angle (degrees) 20.43670499  
Shift along axis -6.72129601  
  

> combine #5,6,7,8,9,10'

Expected a keyword  

> combine #5,6,7,8,9,10

> select subtract #5

Nothing selected  

> hide #5 models

> hide #6 models

> hide #8 models

> hide #7 models

> hide #9 models

> hide #10 models

> fitmap #11 inMap #3

Fit molecule combination (#11) to map cryosparc_P7_J67_map_sharp.mrc (#3)
using 41148 atoms  
average map value = 0.1135, steps = 60  
shifted from previous position = 0.00797  
rotated from previous position = 0.00381 degrees  
atoms outside contour = 32187, contour level = 0.16907  
  
Position of combination (#11) relative to cryosparc_P7_J67_map_sharp.mrc (#3)
coordinates:  
Matrix rotation and translation  
0.93704838 -0.25587024 -0.23763576 108.93077874  
0.25671723 0.96608311 -0.02792279 74.73606861  
0.23672050 -0.03484018 0.97095291 61.48097277  
Axis -0.00990417 -0.67917290 0.73391150  
Axis point -210.30661584 477.20831109 0.00000000  
Rotation angle (degrees) 20.43937769  
Shift along axis -6.71598816  
  

> show #!2 models

> hide #!2 models

> show #!2 models

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 11.2 - if installed, please make sure this is
on your library path before starting ChimeraX.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 870 residues in model #11 to IUPAC-IUB
standards.  

> clipper associate #2 toModel #11

Opened cryosparc_P7_J120_007_volume_map_sharp.mrc z flip as #11.1.1.1, grid
size 400,400,400, pixel 1.63, shown at step 1, values float32  

> isolde sim start
> #11.2/A:19-20,22-29,32-33,36,73-77,79-85,87,115-131,137-147,156-161,163,165,167-170,186,189-190,193,199,203,206-207,209-211,213-239,280/B,D:800-819,823-825,827,857-862,870,882-888/C:20,22,25-29,32-33,36,65,72-77,79-85,89,93,126-134,136-162,165,167-170,174-175,177-182,184-185,187-197,199-200,203-204,206-239,280/E:25-29,32-33,36,52,62,64-67,75-77,79-85,92-94,113,115-120,123,129,131-155,159-160,162-163,167-171,177-239,280-283,395/F:800-816,818-819,823-825,827,857-862,870,882-888/G:25-29,32-33,36,52,62,65-67,75-77,79-85,93-94,112-120,123,128-147,159,162-163,167-171,178-179,181-239,280,393,395/H:800-812,814-816,818-819,823-825,827,857-862,870,882-888/I:93,114-120,123,126,130,133-134,137-154,158,167-170,178,181-191,193-201,203-239,280/J:800-810/K:93,115-120,123,126-127,129-130,133,137-145,167-170,175,182-184,187-188,191,193-201,203,205-207,209-239,277,280-287,289,393-398

Sim termination reason: None  
ISOLDE: stopped sim  

> hide #!11.1 models

> hide #!11 models

> show #!11 models

> select add #11.2

41148 atoms, 41772 bonds, 5328 residues, 14 models selected  

> select add #11.2

41148 atoms, 41772 bonds, 5328 residues, 14 models selected  

> select add #11

41148 atoms, 41772 bonds, 5328 residues, 21 models selected  

> select add #11

41148 atoms, 41772 bonds, 5328 residues, 21 models selected  

> select add #11

41148 atoms, 41772 bonds, 5328 residues, 21 models selected  

> hide #11.3 models

> select subtract #11.3

41148 atoms, 41772 bonds, 5328 residues, 19 models selected  

> select subtract #11.1

41148 atoms, 41772 bonds, 5328 residues, 14 models selected  

> select add #11

41148 atoms, 41772 bonds, 5328 residues, 21 models selected  

> select subtract #11.1

41148 atoms, 41772 bonds, 5328 residues, 16 models selected  

> select subtract #11.3

41148 atoms, 41772 bonds, 5328 residues, 15 models selected  

> hide sel atoms

> save "/home/azinas/projects/Lon-LarA/Max-predicted_rebuild on J67.pdb"
> models #11 relModel #3

> show #!11.1 models

> hide #!11.1 models

> hide #!3 models

> show #!3 models

> show #!1 models

> show #11.3 models

> hide #11.3 models

> show #!11.1 models

> close #11

> vop flip #1

Opened cryosparc_P7_J120_007_volume_map_sharp.mrc z flip as #2, grid size
400,400,400, pixel 1.63, shown at step 1, values float32  

> open "/home/azinas/projects/Lon-LarA/Max-predicted_rebuild on J67.pdb"
> format pdb

Chain information for Max-predicted_rebuild on J67.pdb #11  
---  
Chain | Description  
A C E G I K | No description available  
B D F H J L | No description available  
  

> close

> open "/home/azinas/projects/Lon-LarA/Max-predicted_rebuild on J67.pdb"
> format pdb

Chain information for Max-predicted_rebuild on J67.pdb #1  
---  
Chain | Description  
A C E G I K | No description available  
B D F H J L | No description available  
  

> show cartoons

> hide atoms

> open /home/azinas/Downloads/cryosparc_P7_J120_007_volume_map_sharp.mrc

Opened cryosparc_P7_J120_007_volume_map_sharp.mrc as #2, grid size
400,400,400, pixel 1.63, shown at level 0.0644, step 2, values float32  

> volume #2 level 0.1315

> close #2

> open /home/azinas/Downloads/cryosparc_P7_J67_map_sharp.mrc

Opened cryosparc_P7_J67_map_sharp.mrc as #2, grid size 400,400,400, pixel
0.85, shown at level 0.00205, step 2, values float32  


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

Log:
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/azinas/projects/230404_dwbClpC-P_MecA-FtsZ/J104_rechain-
> coot-16.pdb

Summary of feedback from opening /home/azinas/projects/230404_dwbClpC-P_MecA-
FtsZ/J104_rechain-coot-16.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 263 263 THR p
233 ASP p 236 1 4  
Start residue of secondary structure not found: HELIX 264 264 ILE a 20 LYS a
26 1 7  
Start residue of secondary structure not found: HELIX 265 265 ASP a 38 GLN a
54 1 17  
Start residue of secondary structure not found: HELIX 266 266 VAL a 71 GLN a
82 1 11  
Start residue of secondary structure not found: HELIX 267 267 GLY a 100 ALA a
105 1 6  
36 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 304 304 LEU f 24 ASP f 27
1 4  
Start residue of secondary structure not found: HELIX 305 305 ASP f 38 GLN f
54 1 17  
Start residue of secondary structure not found: HELIX 306 306 VAL f 71 TYR f
78 1 8  
Start residue of secondary structure not found: HELIX 307 307 ASP f 79 HIS f
83 1 4  
Start residue of secondary structure not found: HELIX 308 308 GLY f 100 ALA f
105 1 6  
Start residue of secondary structure not found: HELIX 309 309 ALA f 133 THR f
158 1 26  
72 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 89 8989 ILE a 29 LEU a 32
0  
Start residue of secondary structure not found: SHEET 90 9090 ILE a 60 ILE a
64 0  
Start residue of secondary structure not found: SHEET 91 9191 VAL a 88 CYS a
92 0  
Start residue of secondary structure not found: SHEET 92 9292 ARG a 112 ALA a
114 0  
Start residue of secondary structure not found: SHEET 93 9393 GLU a 119 ILE a
122 0  
Start residue of secondary structure not found: SHEET 94 9494 LEU a 126 GLN a
132 0  
3 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 98 9898 ILE b 29 LEU b 32
0  
Start residue of secondary structure not found: SHEET 99 9999 ILE b 60 ILE b
64 0  
Start residue of secondary structure not found: SHEET 100 10010 VAL b 88 CYS b
92 0  
Start residue of secondary structure not found: SHEET 101 10110 ARG b 112 ALA
b 114 0  
Start residue of secondary structure not found: SHEET 102 10210 GLU b 119 ILE
b 122 0  
Start residue of secondary structure not found: SHEET 103 10310 GLY b 128 GLN
b 132 0  
3 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 107 10710 ILE c 29 LEU c
32 0  
Start residue of secondary structure not found: SHEET 108 10810 ILE c 60 ILE c
64 0  
Start residue of secondary structure not found: SHEET 109 10910 VAL c 88 CYS c
92 0  
Start residue of secondary structure not found: SHEET 110 11011 ARG c 112 ALA
c 114 0  
Start residue of secondary structure not found: SHEET 111 11111 GLU c 119 ILE
c 122 0  
Start residue of secondary structure not found: SHEET 112 11211 LEU c 126 GLN
c 132 0  
3 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 116 11611 ILE d 29 LEU d
32 0  
Start residue of secondary structure not found: SHEET 117 11711 ILE d 60 ILE d
64 0  
Start residue of secondary structure not found: SHEET 118 11811 VAL d 88 CYS d
92 0  
Start residue of secondary structure not found: SHEET 119 11911 ARG d 112 ALA
d 114 0  
Start residue of secondary structure not found: SHEET 120 12012 GLU d 119 ILE
d 122 0  
Start residue of secondary structure not found: SHEET 121 12112 GLY d 128 GLN
d 132 0  
3 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 125 12512 ILE e 29 LEU e
32 0  
Start residue of secondary structure not found: SHEET 126 12612 ILE e 60 ILE e
64 0  
Start residue of secondary structure not found: SHEET 127 12712 VAL e 88 CYS e
92 0  
Start residue of secondary structure not found: SHEET 128 12812 VAL e 120 ILE
e 122 0  
Start residue of secondary structure not found: SHEET 129 12912 LEU e 126 GLN
e 132 0  
Start residue of secondary structure not found: SHEET 130 13013 ASN e 173 LEU
e 175 0  
End residue of secondary structure not found: SHEET 131 13113 ILE f 29 LEU f
32 0  
Start residue of secondary structure not found: SHEET 132 13213 ILE f 60 ILE f
64 0  
Start residue of secondary structure not found: SHEET 133 13313 VAL f 88 CYS f
92 0  
Start residue of secondary structure not found: SHEET 134 13413 GLU f 119 ILE
f 122 0  
Start residue of secondary structure not found: SHEET 135 13513 LEU f 126 GLN
f 130 0  
Start residue of secondary structure not found: SHEET 136 13613 ASN f 173 THR
f 176 0  
52 messages similar to the above omitted  
PDB SEQRES record for chain a is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain b is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain c is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain d is incomplete. Ignoring input sequence records
as basis for sequence.  
PDB SEQRES record for chain e is incomplete. Ignoring input sequence records
as basis for sequence.  
1 messages similar to the above omitted  
  
Chain information for J104_rechain-coot-16.pdb #1  
---  
Chain | Description  
A B C D E F | No description available  
Aa | No description available  
Ap | No description available  
Aq | No description available  
Ba Bb Bd Bi | No description available  
Bc | No description available  
Be | No description available  
Bf | No description available  
Bg Bk | No description available  
Bh | No description available  
Bj | No description available  
Bl | No description available  
Bm | No description available  
Bn | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
  




OpenGL version: 4.6 (Core Profile) Mesa 22.3.5
OpenGL renderer: RENOIR (renoir, LLVM 15.0.6, DRM 3.49, 6.2.6-76060206-generic)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=pop
XDG_SESSION_DESKTOP=pop
XDG_CURRENT_DESKTOP=pop:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 20YM
OS: Pop!_OS 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 9 5900HX with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            30Gi       8.6Gi       3.0Gi       221Mi        19Gi        19Gi
	Swap:           31Gi       0.0Ki        31Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA106M [GeForce RTX 3060 Mobile / Max-Q] [10de:2520] (rev a1)	
	Subsystem: Lenovo GA106M [GeForce RTX 3060 Mobile / Max-Q] [17aa:3801]	
	Kernel driver in use: nvidia

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-Clipper: 0.21.0
    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-ISOLDE: 1.6.0
    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-XMAS: 1.1.2
    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
    et-xmlfile: 1.1.0
    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
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    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
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    openvr: 1.23.701
    packaging: 23.1
    pandas: 2.0.2
    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
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    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
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    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
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    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.28.2
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    seaborn: 0.12.2
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    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
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    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
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    sphinxcontrib-qthelp: 1.0.3
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    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
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    wcwidth: 0.2.6
    webcolors: 1.12
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    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0