Crash using File→Open on Windows and/or in return statement

[chimerax-bug-report@…]

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 0x800706ba

Thread 0x0000071c (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
Windows fatal exception: code 0x80010012

Thread 0x0000071c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 135 in show_open_file_dialog
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\open_command\dialog.py", line 107 in 
  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
Windows fatal exception: code 0x800706ba

Thread 0x0000071c (most recent call first):
  File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\numpy\core\_methods.py", line 57 in _any
Windows fatal exception: access violation

===== 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  

> open "C:\\\Users\\\Thorben Schulze\\\Documents\\\Visual Studio
> 2017\\\UNI\\\Masterthesis\\\Data\\\density_analysis\\\ChimeraFiles\\\PAPAINLIKE\\\PDB\\\7qcj.pdb"

7qcj.pdb title:  
Structure of sars-cov-2 papain-like protease bound to N-(2,4-
dihydroxybenzylidene)-thiosemicarbazone [more info...]  
  
Chain information for 7qcj.pdb #1  
---  
Chain | Description | UniProt  
A | papain-like protease NSP3 | R1A_SARS2  
  
Non-standard residues in 7qcj.pdb #1  
---  
A4O — N-(2,4-dihydroxybenzylidene)-thiosemicarbazone
(1-[(E)-[2,4-bis(oxidanyl)phenyl]methylideneamino]thiourea)  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
PO4 — phosphate ion  
ZN — zinc ion  
  


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

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

> open "C:\\\Users\\\Thorben Schulze\\\Documents\\\Visual Studio
> 2017\\\UNI\\\Masterthesis\\\Data\\\density_analysis\\\ChimeraFiles\\\TestsMA\\\9953_0\\\Resolve9953_0Session.cxs"

Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 3.75, step 1, values
float32  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_subdogblobbed.ccp4 as #5,
grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.08, step 1,
values float32  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN20_APON7.ccp4 as
#8.1, grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.04,
step 1, values float32  
Opened PLpr_9953_0_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN20_APON7_enhanced.ccp4 as #8.2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 3.17, step 1, values
float32  
Opened PLpr_9953_1_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN20_APON7.ccp4 as
#8.3, grid size 226,182,178, pixel 0.435,0.435,0.448, shown at level 0.0698,
step 1, values float32  
Opened PLpr_9953_1_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN20_APON7_enhanced.ccp4 as #8.4, grid size
226,182,178, pixel 0.435,0.435,0.448, shown at level 5.68, step 1, values
float32  
Opened PLpr_9953_0Delta-03.ccp4 as #9.1, grid size 214,169,171, pixel
0.463,0.463,0.465, shown at level 0.0861, step 1, values float32  
Opened PLpr_9953_0Delta-03_enhanced.ccp4 as #9.2, grid size 214,169,171, pixel
0.463,0.463,0.465, shown at level 0.00016, step 1, values float32  
Opened PLpr_9953_0Delta-05_enhanced.ccp4 as #9.4, grid size 214,169,171, pixel
0.463,0.463,0.465, shown at level 0.000259, step 1, values float32  
Opened PLpr_9953_0NoPlausibilityBadHit_enhanced.ccp4 as #9.6, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 0.000213, step 1, values
float32  
Opened PLpr_9953_050percentOverlap_enhanced.ccp4 as #9.8, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 0.000263, step 1, values
float32  
Opened PLpr_9998_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #10, grid size
242,192,194, pixel 0.415,0.415,0.413, shown at level 3.85, step 1, values
float32  
Opened PLpr_9998_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 copy as #12, grid
size 242,192,194, pixel 0.415,0.415,0.413, shown at level 0.0237, step 1,
values float32  
Log from Mon May 9 17:02:35 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/PAPAINLIKE/HitSessionsPLpr/9953_0_1WithLigandPDB.cxs"

Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 3.75, step 1, values
float32  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_subdogblobbed.ccp4 as #5,
grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.08, step 1,
values float32  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN20_APON7.ccp4 as
#8.1, grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.0861,
step 1, values float32  
Opened PLpr_9953_0_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN20_APON7_enhanced.ccp4 as #8.2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 0.000213, step 1, values
float32  
Opened PLpr_9953_1_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN20_APON7.ccp4 as
#8.3, grid size 226,182,178, pixel 0.435,0.435,0.448, shown at level 0.0698,
step 1, values float32  
Opened PLpr_9953_1_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN20_APON7_enhanced.ccp4 as #8.4, grid size
226,182,178, pixel 0.435,0.435,0.448, shown at level 5.68, step 1, values
float32  
Log from Wed May 4 21:35:51 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:\\\Users\\\Thorben Schulze\\\Documents\\\Visual Studio
> 2017\\\UNI\\\Masterthesis\\\Data\\\density_analysis\\\ChimeraFiles\\\PAPAINLIKE\\\9953_0withLigandPDB.cxs"

Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 3.75, step 1, values
float32  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_subdogblobbed.ccp4 as #5,
grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.08, step 1,
values float32  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN15_APON7.ccp4 as
#7.1, grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.0863,
step 1, values float32  
Opened PLpr_9953_0_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN15_APON7_enhanced.ccp4 as #7.2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 0.201, step 1, values
float32  
Log from Mon Apr 25 18:36:07 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/9953_0withLigandPDB.cxs"

Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 3.75, step 1, values
float32  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_subdogblobbed.ccp4 as #5,
grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.08, step 1,
values float32  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN15_APON7.ccp4 as
#6.1, grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.0863,
step 1, values float32  
Opened PLpr_9953_0_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN15_APON7_enhanced.ccp4 as #6.2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 1.38e-05, step 1, values
float32  
Log from Mon Apr 25 15:28:43 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:\\\Users\\\Thorben Schulze\\\Documents\\\Visual Studio
> 2017\\\UNI\\\Masterthesis\\\Data\\\density_analysis\\\ChimeraFiles\\\Papainlike\\\9953_0withLigandPDB.cxs"

Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 3.75, step 1, values
float32  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_subdogblobbed.ccp4 as #5,
grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.08, step 1,
values float32  
Log from Sat Apr 16 14:04:26 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:\\\Users\\\Thorben Schulze\\\Documents\\\Visual Studio
> 2017\\\UNI\\\Masterthesis\\\Data\\\density_analysis\\\ChimeraFiles\\\Papainlike\\\9953_1withLigandPDB.cxs"

Opened PLpr_9953_1_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #1, grid size
226,182,178, pixel 0.435,0.435,0.448, shown at level 2.18, step 1, values
float32  
Opened PLpr9953_1_10blobs.ccp4 as #2, grid size 226,182,178, pixel
0.435,0.435,0.448, shown at level 0.1, step 1, values float32  
Log from Thu Apr 14 19:36:27 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:\\\Users\\\Thorben Schulze\\\Documents\\\Visual Studio
> 2017\\\UNI\\\Masterthesis\\\Data\\\density_analysis\\\ChimeraFiles\\\Papainlike\\\pdbsitesmarked.cxs"

Opened PLpr_9973_0_001_003_2mFo-DFc.ccp4 as #2, grid size 215,170,174, pixel
0.463,0.463,0.466, shown at level 3.81, step 1, values float32  
Log from Tue Apr 12 20:31:20 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/pdbsitesmarked.cxs"

Opened PLpr_9973_0_001_003_2mFo-DFc.ccp4 as #2, grid size 215,170,174, pixel
0.463,0.463,0.466, shown at level 3.81, step 1, values float32  
Log from Tue Apr 12 15:16:18 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\Thorben Schulze\\\Documents\\\Visual Studio
> 2017\\\UNI\\\Masterthesis\\\Data\\\density_analysis\\\density_analysis_PLpro\\\hits\\\PLpr_9973_0\\\PLpr_9973_0_001_003.pdb"

Chain information for PLpr_9973_0_001_003.pdb #1  
---  
Chain | Description  
A | No description available  
  

> rainbow

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/density_analysis_PLpro/hits/PLpr_9973_0/PLpr_9973_0_001_003_2mFo-
> DFc.ccp4"

Opened PLpr_9973_0_001_003_2mFo-DFc.ccp4 as #2, grid size 215,170,174, pixel
0.463,0.463,0.466, shown at level 3.81, step 1, values float32  

> volume #2 color magenta

> select : 208,47,48,51,203,166,174,49,167,42

169 atoms, 153 bonds, 20 residues, 1 model selected  

> color sel white

> select : 23,31,27,69,75,65,62,70,20,18,3

208 atoms, 190 bonds, 22 residues, 1 model selected  

> color sel grey

> cd "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike"

Current working directory is: C:\Users\Thorben Schulze\Documents\Visual Studio
2017\UNI\Masterthesis\Data\density_analysis\ChimeraFiles\Papainlike  

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/pdbsitesmarked.cxs"

——— End of log from Tue Apr 12 15:16:18 2022 ———

opened ChimeraX session  

> color sel purple

> cd "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike"

Current working directory is: C:\Users\Thorben Schulze\Documents\Visual Studio
2017\UNI\Masterthesis\Data\density_analysis\ChimeraFiles\Papainlike  

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/pdbsitesmarked.cxs"

——— End of log from Tue Apr 12 20:31:20 2022 ———

opened ChimeraX session  

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/PDB/7qcj.pdb"

7qcj.pdb title:  
Structure of sars-cov-2 papain-like protease bound to N-(2,4-
dihydroxybenzylidene)-thiosemicarbazone [more info...]  
  
Chain information for 7qcj.pdb #3  
---  
Chain | Description | UniProt  
A | papain-like protease NSP3 | R1A_SARS2  
  
Non-standard residues in 7qcj.pdb #3  
---  
A4O — N-(2,4-dihydroxybenzylidene)-thiosemicarbazone
(1-[(E)-[2,4-bis(oxidanyl)phenyl]methylideneamino]thiourea)  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
PO4 — phosphate ion  
ZN — zinc ion  
  

> select #1

5194 atoms, 5025 bonds, 543 residues, 1 model selected  

> ~select #1

Nothing selected  

> select #3

5275 atoms, 5079 bonds, 4 pseudobonds, 571 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,9.3739,0,1,0,4.0069,0,0,1,49.452

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.75414,0.61246,-0.237,91.846,-0.65604,-0.68629,0.31402,97.602,0.029675,0.39229,0.91936,34.851

> ui mousemode right "move picked models"

> view matrix models
> #3,-0.75414,0.61246,-0.237,53.687,-0.65604,-0.68629,0.31402,79.438,0.029675,0.39229,0.91936,29.302

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.19968,0.97861,-0.049592,14.786,-0.96603,-0.20508,-0.15723,73.426,-0.16404,0.016512,0.98632,52.909

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.19968,0.97861,-0.049592,19.604,-0.96603,-0.20508,-0.15723,67.291,-0.16404,0.016512,0.98632,54.106

> view matrix models
> #3,-0.19968,0.97861,-0.049592,20.396,-0.96603,-0.20508,-0.15723,67.081,-0.16404,0.016512,0.98632,51.728

> hide #1 models

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/density_analysis_PLpro/hits/PLpr_9953_1/PLpr_9953_1_001_003.pdb"

Chain information for PLpr_9953_1_001_003.pdb #4  
---  
Chain | Description  
A | No description available  
  

> ~select #3

Nothing selected  

> close #1

> select #4

5250 atoms, 5025 bonds, 599 residues, 1 model selected  

> ~select #4

Nothing selected  

> select #3

5275 atoms, 5079 bonds, 4 pseudobonds, 571 residues, 2 models selected  

> view matrix models
> #3,-0.19968,0.97861,-0.049592,21.346,-0.96603,-0.20508,-0.15723,67.038,-0.16404,0.016512,0.98632,54.039

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.53889,0.83745,-0.09099,44.609,-0.83748,-0.54425,-0.049165,71.316,-0.090695,0.049708,0.99464,48.902

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.53889,0.83745,-0.09099,42.852,-0.83748,-0.54425,-0.049165,71.151,-0.090695,0.049708,0.99464,48.296

> ui mousemode right translate

> ~select #3

Nothing selected  

> select #4

5250 atoms, 5025 bonds, 599 residues, 1 model selected  

> hide #!3 models

> close #2

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/density_analysis_PLpro/hits/PLpr_9953_1/PLpr_9953_1_001_003_2mFo-
> DFc_no_fill_no_fill.ccp4"

Opened PLpr_9953_1_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #1, grid size
226,182,178, pixel 0.435,0.435,0.448, shown at level 3.88, step 1, values
float32  

> volume #1 level 2.182

> ~select #4

Nothing selected  

> select #3

5275 atoms, 5079 bonds, 4 pseudobonds, 571 residues, 2 models selected  

> select #1

2 models selected  

> hide #4 models

> show #!3 models

> fitmap #3 inMap #1

Fit molecule 7qcj.pdb (#3) to map PLpr_9953_1_001_003_2mFo-
DFc_no_fill_no_fill.ccp4 (#1) using 5275 atoms  
average map value = 2.185, steps = 116  
shifted from previous position = 0.922  
rotated from previous position = 6.63 degrees  
atoms outside contour = 3001, contour level = 2.1819  
  
Position of 7qcj.pdb (#3) relative to PLpr_9953_1_001_003_2mFo-
DFc_no_fill_no_fill.ccp4 (#1) coordinates:  
Matrix rotation and translation  
-0.49962183 0.86624364 -0.00002879 41.70660304  
-0.86624347 -0.49962171 0.00063838 72.32762726  
0.00053861 0.00034389 0.99999980 44.78616274  
Axis -0.00016998 -0.00032751 -0.99999993  
Axis point 41.73497147 24.11294988 0.00000000  
Rotation angle (degrees) 119.97498628  
Shift along axis -44.81693695  
  

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> rainbow #!3

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/hitout/PLpr9953_1_10blobs.ccp4"

Opened PLpr9953_1_10blobs.ccp4 as #2, grid size 226,182,178, pixel
0.435,0.435,0.448, shown at level 0.0642, step 1, values float32  

> volume #2 level 0.2916

> volume #2 level 0.1364

> volume #2 level 0.1003

> volume #2 color magenta

> transparency #2.1 50

> volume #2 level 0.09722

> volume #2 level 0.07418

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/9953_1withLigandPDB.cxs"

> open "C:/Users/Thorben
> Schulze/Downloads/PLpr9953_1_nocomputeallcomplexes.ccp4"

Opened PLpr9953_1_nocomputeallcomplexes.ccp4 as #5, grid size 226,182,178,
pixel 0.435,0.435,0.448, shown at level 0.0642, step 1, values float32  

> vop subtract #2 #5 minrms True

Opened volume difference as #6, grid size 226,182,178, pixel
0.435,0.435,0.448, shown at step 1, values float32  
Minimum RMS scale factor for "PLpr9953_1_nocomputeallcomplexes.ccp4 #5" above
level 0.064155 is 1  
  

> volume #6 level -0.04805

> close #6

> close #5

> volume #2 level 0.1003

> cd "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike"

Current working directory is: C:\Users\Thorben Schulze\Documents\Visual Studio
2017\UNI\Masterthesis\Data\density_analysis\ChimeraFiles\Papainlike  

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/9953_1withLigandPDB.cxs"

——— End of log from Thu Apr 14 19:36:27 2022 ———

opened ChimeraX session  

> ui tool show "Unit Cell"

> unitcell #3 cells 3,3,3 offset -1,-1,-1

> unitcell delete #3

> volume #2 level 0.2128

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/hitout/PLpr_9953_1_001_003_2mFo-
> DFc_no_fill_no_fill_subdogblobbed.ccp4"

Opened PLpr_9953_1_001_003_2mFo-DFc_no_fill_no_fill_subdogblobbed.ccp4 as #5,
grid size 226,182,178, pixel 0.435,0.435,0.448, shown at level 0.0642, step 1,
values float32  

> volume #5 level 0.2116

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/hitout/PLpr_9953_1_001_003_2mFo-
> DFc_no_fill_no_fill_subdogblobbed_allcomplexes.ccp4"

Opened PLpr_9953_1_001_003_2mFo-
DFc_no_fill_no_fill_subdogblobbed_allcomplexes.ccp4 as #6, grid size
226,182,178, pixel 0.435,0.435,0.448, shown at level 0.0533, step 1, values
float32  

> volume #6 level 0.1975

> volume #6 level 0.2388

> volume #6 level 0.2019

[Repeated 2 time(s)]

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/9953_1withLigandPDB.cxs"

> volume #6 level 0.06735

> transparency #6.1 50

> close #2

> close #5

> close #6

> close #1

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/density_analysis_PLpro/hits/PLpr_9953_0/PLpr_9953_0_001_003.pdb"
> "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/density_analysis_PLpro/hits/PLpr_9953_0/PLpr_9953_0_001_003_2mFo-
> DFc_no_fill_no_fill.ccp4"

Chain information for PLpr_9953_0_001_003.pdb #1  
---  
Chain | Description  
A | No description available  
  
Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 3.75, step 1, values
float32  

> hide #!3 models

> show #!3 models

> hide #1 models

> show #1 models

> hide #1 models

> hide #!3 models

> show #!3 models

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/9953_0withLigandPDB.cxs"

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/hitout/PLpr_9953_0_001_003_2mFo-
> DFc_no_fill_no_fill_subdogblobbed.ccp4"

Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_subdogblobbed.ccp4 as #5,
grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.0612, step 1,
values float32  

> volume #5 level 0.1634

> volume #5 level 0.1641

> volume #5 level 0.1767

> volume #5 level 0.1766

> volume #5 level 0.1767

> volume #5 level 0.1766

> volume #5 level 0.1767

> volume #5 level 0.1766

[Repeated 1 time(s)]

> volume #5 level 0.176

> volume #5 level 0.1701

> volume #5 level 0.0867

> volume #5 level 0.08

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/9953_0withLigandPDB.cxs"

——— End of log from Sat Apr 16 14:04:26 2022 ———

opened ChimeraX session  

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/hitout2504/PLpr_9953_0_001_003_2mFo-
> DFc_no_fill_no_fill_T-350_BN15_APON7.ccp4" "C:/Users/Thorben
> Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/hitout2504/PLpr_9953_0_001_003_2mFo-
> DFc_no_fill_no_fill_T-350_BN15_APON7_enhanced.ccp4"

Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN15_APON7.ccp4 as
#6.1, grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.0863,
step 1, values float32  
Opened PLpr_9953_0_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN15_APON7_enhanced.ccp4 as #6.2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 1.38e-05, step 1, values
float32  

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/9953_0withLigandPDB.cxs"

——— End of log from Mon Apr 25 15:28:43 2022 ———

opened ChimeraX session  

> close #6.1

> close #6.2

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/hitout2504/PLpr_9953_0_001_003_2mFo-
> DFc_no_fill_no_fill_T-350_BN15_APON7.ccp4" "C:/Users/Thorben
> Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/hitout2504/PLpr_9953_0_001_003_2mFo-
> DFc_no_fill_no_fill_T-350_BN15_APON7_enhanced.ccp4"

Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN15_APON7.ccp4 as
#7.1, grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.0863,
step 1, values float32  
Opened PLpr_9953_0_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN15_APON7_enhanced.ccp4 as #7.2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 1.38e-05, step 1, values
float32  

> volume #7.2 level 0.1132

> transparency #7.2.1 50

> ui tool show "Unit Cell"

> unitcell #3 cells 2,2,2 offset -1,-1,-1

> select ligand

5330 atoms, 4934 bonds, 445 residues, 51 models selected  

> unitcell delete #3

> unitcell #3 cells 2,2,2 offset -1,-1,-1

> hide #!8 models

> select ligand

5330 atoms, 4934 bonds, 445 residues, 51 models selected  

> show sel

> show #!8 models

> hide #!8 models

> unitcell #3 cells 2,2,2 offset -1,-1,-1

> show #!8 models

> unitcell delete #3

> unitcell #3 cells 2,2,2 offset -1,-1,-1

> select ligand

5330 atoms, 4934 bonds, 445 residues, 51 models selected  

> unitcell delete #3

> volume #7.2 level 0.2014

> ui tool show "Unit Cell"

> unitcell #3 cells 2,2,2 offset -1,-1,-1

> unitcell delete #3

> volume #7.2 level 0.2014

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/Papainlike/9953_0withLigandPDB.cxs"

——— End of log from Mon Apr 25 18:36:07 2022 ———

opened ChimeraX session  

> close #7.1

> close #7.2

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/PAPAINLIKE/hitout0405/PLpr_9953_0_001_003_2mFo-
> DFc_no_fill_no_fill_T-350_BN20_APON7.ccp4" "C:/Users/Thorben
> Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/PAPAINLIKE/hitout0405/PLpr_9953_0_001_003_2mFo-
> DFc_no_fill_no_fill_T-350_BN20_APON7_enhanced.ccp4" "C:/Users/Thorben
> Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/PAPAINLIKE/hitout0405/PLpr_9953_1_001_003_2mFo-
> DFc_no_fill_no_fill_T-350_BN20_APON7.ccp4" "C:/Users/Thorben
> Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/PAPAINLIKE/hitout0405/PLpr_9953_1_001_003_2mFo-
> DFc_no_fill_no_fill_T-350_BN20_APON7_enhanced.ccp4"

Opened PLpr_9953_0_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN20_APON7.ccp4 as
#8.1, grid size 214,169,171, pixel 0.463,0.463,0.465, shown at level 0.0861,
step 1, values float32  
Opened PLpr_9953_0_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN20_APON7_enhanced.ccp4 as #8.2, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 0.000213, step 1, values
float32  
Opened PLpr_9953_1_001_003_2mFo-DFc_no_fill_no_fill_T-350_BN20_APON7.ccp4 as
#8.3, grid size 226,182,178, pixel 0.435,0.435,0.448, shown at level 0.0698,
step 1, values float32  
Opened PLpr_9953_1_001_003_2mFo-
DFc_no_fill_no_fill_T-350_BN20_APON7_enhanced.ccp4 as #8.4, grid size
226,182,178, pixel 0.435,0.435,0.448, shown at level 0.00036, step 1, values
float32  

> volume #8.3 color magenta

> volume #8.1 color magenta

> volume #8.1 color #5555ff

> volume #8.1 color #5500ff

> volume #8.2 color #5500ff

> volume #8.4 color magenta

> volume #8.4 level 7.146

> volume #8.4 level 5.68

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/PAPAINLIKE/HitSessionsPLpr/9953_0_1WithLigandPDB.cxs"

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/PAPAINLIKE/HitSessionsPLpr/9953_0_1WithLigandPDB.cxs"
> includeMaps true

——— End of log from Wed May 4 21:35:51 2022 ———

opened ChimeraX session  

> volume #8.1 level 0.06004

> volume #8.1 level 0.1632

> volume #8.1 level 0.04001

> volume #8.2 level 3.167

> ui tool show "Unit Cell"

> unitcell #3 cells 2,2,2 offset -1,-1,-1

> transparency #8.2.1 50

> transparency #8.2.1 0

> transparency #8.2.1 50

> transparency #8.2.1 0

> transparency #8.2.1 50

> color #3 #55ffff80

> unitcell delete #3

> unitcell #3 cells 2,2,2 offset -1,-1,-1

> select ligand

5330 atoms, 4934 bonds, 445 residues, 51 models selected  

> color sel red

> set bgColor white

> unitcell #3 cells 3,3,3 offset -1,-1,-1

> unitcell delete #3

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/TestsMA/9953_0/PLpr_9953_0Delta-03.ccp4"
> "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/TestsMA/9953_0/PLpr_9953_0Delta-03_enhanced.ccp4"
> "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/TestsMA/9953_0/PLpr_9953_0Delta-05.ccp4"
> "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/TestsMA/9953_0/PLpr_9953_0Delta-05_enhanced.ccp4"
> "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/TestsMA/9953_0/PLpr_9953_0NoPlausibilityBadHit.ccp4"
> "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/TestsMA/9953_0/PLpr_9953_0NoPlausibilityBadHit_enhanced.ccp4"
> "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/TestsMA/9953_0/PLpr_9953_050percentOverlap.ccp4"
> "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/TestsMA/9953_0/PLpr_9953_050percentOverlap_enhanced.ccp4"

Opened PLpr_9953_0Delta-03.ccp4 as #9.1, grid size 214,169,171, pixel
0.463,0.463,0.465, shown at level 0.0861, step 1, values float32  
Opened PLpr_9953_0Delta-03_enhanced.ccp4 as #9.2, grid size 214,169,171, pixel
0.463,0.463,0.465, shown at level 0.00016, step 1, values float32  
Opened PLpr_9953_0Delta-05.ccp4 as #9.3, grid size 214,169,171, pixel
0.463,0.463,0.465, shown at level 0.0861, step 1, values float32  
Opened PLpr_9953_0Delta-05_enhanced.ccp4 as #9.4, grid size 214,169,171, pixel
0.463,0.463,0.465, shown at level 0.000259, step 1, values float32  
Opened PLpr_9953_0NoPlausibilityBadHit.ccp4 as #9.5, grid size 214,169,171,
pixel 0.463,0.463,0.465, shown at level 0.0861, step 1, values float32  
Opened PLpr_9953_0NoPlausibilityBadHit_enhanced.ccp4 as #9.6, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 0.000213, step 1, values
float32  
Opened PLpr_9953_050percentOverlap.ccp4 as #9.7, grid size 214,169,171, pixel
0.463,0.463,0.465, shown at level 0.0861, step 1, values float32  
Opened PLpr_9953_050percentOverlap_enhanced.ccp4 as #9.8, grid size
214,169,171, pixel 0.463,0.463,0.465, shown at level 0.000263, step 1, values
float32  

> close #9.3

> close #9.5

> close #9.7

> set bgColor black

> open "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/density_analysis_PLpro/apo/PLpr_9998_0/PLpr_9998_0_001_003_2mFo-
> DFc_no_fill_no_fill.ccp4"

Opened PLpr_9998_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 as #10, grid size
242,192,194, pixel 0.415,0.415,0.413, shown at level 3.85, step 1, values
float32  

> ui tool show "Map Eraser"

> volume erase #10 center 40.873,4.6822,36.126 radius 8.5032 outside true

Opened PLpr_9998_0_001_003_2mFo-DFc_no_fill_no_fill.ccp4 copy as #12, grid
size 242,192,194, pixel 0.415,0.415,0.413, shown at step 1, values float32  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.49962,0.86624,-2.8789e-05,43.135,-0.86624,-0.49962,0.00063838,76.839,0.00053861,0.00034389,1,39.322,#4,1,0,0,1.4286,0,1,0,4.5114,0,0,1,-5.4644,#1,1,0,0,1.4286,0,1,0,4.5114,0,0,1,-5.4644

> undo

> ui mousemode right translate

> transparency #12.1 50

> volume #12 level 1.432

> volume #12 level 1.306

[Repeated 1 time(s)]

> ui tool show "Map Eraser"

> volume erase #12 center 47.913,16.698,40.304 radius 12.402

> volume #12 level 0.02373

> save "C:/Users/Thorben Schulze/Documents/Visual Studio
> 2017/UNI/Masterthesis/Data/density_analysis/ChimeraFiles/TestsMA/9953_0/Resolve9953_0Session.cxs"
> includeMaps true

——— End of log from Mon May 9 17:02:35 2022 ———

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 511.79
OpenGL renderer: NVIDIA GeForce RTX 3080 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: SchenkerTechnologiesGmbH
Model: XMG PRO (Late 2021)
OS: Microsoft Windows 10 Pro (Build 19044)
Memory: 34,128,322,560
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: de-DE
Locale: ('de_DE', '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-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-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

[pett]

1.3