MemoryError opening mmCIF files

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

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 C:/Users/lilyh/Downloads/cryosparc_P122_J1642_class_01_00044_volume.mrc

Opened cryosparc_P122_J1642_class_01_00044_volume.mrc as #1, grid size
100,100,100, pixel 2.78, shown at level 0.033, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1642_class_00_00044_volume.mrc

Opened cryosparc_P122_J1642_class_00_00044_volume.mrc as #2, grid size
100,100,100, pixel 2.78, shown at level 0.0321, step 1, values float32  

> volume level 0.246

> volume level 0.1

> volume level 0.07

> tile

2 models tiled  

> ~tile

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1573_001_volume_map_sharp.mrc

Opened cryosparc_P122_J1573_001_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.09, shown at level 0.018, step 1, values float32  

> volume #3 level 0.12

> ~tile

> volume #1 level 0.07

> volume #1 level 0.06559

> volume #1 level 0.07

> volume #1 level 0.07441

> volume #1 level 0.07882

> volume #1 level 0.08102

> volume #1 level 0.08323

> volume #1 level 0.08764

> volume #1 level 0.09205

> volume #1 level 0.09425

> volume #1 level 0.09646

> volume #1 level 0.1031

> volume #1 level 0.1053

> volume #1 level 0.1097

> volume #1 level 0.1119

> volume #1 level 0.1163

> volume #1 level 0.1229

> volume #1 level 0.1339

> volume #1 level 0.1361

> volume #1 level 0.1405

> volume #1 level 0.1472

> volume #1 level 0.1494

> volume #1 level 0.1516

> volume #1 level 0.2089

> volume #1 level 0.2376

> volume #1 level 0.2398

> volume #1 level 0.2442

> volume #1 level 0.2464

> volume #1 level 0.2486

> volume #1 level 0.2574

> volume #1 level 0.264

> volume #1 level 0.2618

> volume #1 level 0.2552

> volume #1 level 0.2508

> volume #1 level 0.2486

> volume #1 level 0.2309

> volume #1 level 0.1824

> volume #1 level 0.1428

> volume #1 level 0.1339

> volume #1 level 0.1119

> volume #1 level 0.09646

> volume #1 level 0.1009

> volume #1 level 0.1185

> volume #1 level 0.1295

> volume #1 level 0.1251

> volume #1 level 0.1075

> volume #1 level 0.08984

> volume #1 level 0.08764

> volume #1 level 0.07661

> volume #1 level 0.07441

> volume #1 level 0.07

> volume #1 level 0.0678

> volume #1 level 0.06559

> volume #1 level 0.0678

> volume #1 level 0.07

> volume #1 level 0.07882

> volume #1 level 0.08323

> volume #1 level 0.08764

> volume #1 level 0.09646

> volume #1 level 0.09866

> volume #1 level 0.1009

> volume #1 level 0.1075

> volume #1 level 0.1163

> volume #1 level 0.1185

> volume #1 level 0.1207

> volume #1 level 0.1229

> volume #1 level 0.1295

> volume #1 level 0.1383

> volume #1 level 0.1472

> volume #1 level 0.1494

> volume #1 level 0.1516

> volume #1 level 0.1626

> volume #1 level 0.1758

> volume #1 level 0.1957

> volume #1 level 0.2023

> volume #1 level 0.2155

> volume #1 level 0.2177

> close #1

> volume #3 level 0.172

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1573_001_volume_map.mrc

Opened cryosparc_P122_J1573_001_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.09, shown at level 0.000775, step 1, values float32  

> ~tile

> volume #1 level 0.09009

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1335_002_volume_map.mrc

Opened cryosparc_P122_J1335_002_volume_map.mrc as #4, grid size 256,256,256,
pixel 1.09, shown at level 0.0119, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1388_002_volume_map_sharp.mrc

Opened cryosparc_P122_J1388_002_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 1.09, shown at level 0.0298, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1623_001_volume_map.mrc

Opened cryosparc_P122_J1623_001_volume_map.mrc as #6, grid size 256,256,256,
pixel 1.09, shown at level 0.0041, step 1, values float32  

> ~tile

> volume level 0.07

[Repeated 1 time(s)]

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1155_001_volume_map.mrc

Opened cryosparc_P122_J1155_001_volume_map.mrc as #7, grid size 256,256,256,
pixel 1.09, shown at level 0.0124, step 1, values float32  

> ~tile

> volume #7 level 0.04166

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1388_002_volume_map.mrc

Opened cryosparc_P122_J1388_002_volume_map.mrc as #8, grid size 256,256,256,
pixel 1.09, shown at level 0.0118, step 1, values float32  

> volume #8 level 0.05422

> ~tile

> close #5

> tile

5 models tiled  

> ~tile

> hide #!1 models

> hide #!4 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> open C:/Users/lilyh/Downloads/cryosparc_P122_J868_002_volume_map.mrc

Opened cryosparc_P122_J868_002_volume_map.mrc as #5, grid size 256,256,256,
pixel 1.09, shown at level 0.00446, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J904_001_volume_map.mrc

Opened cryosparc_P122_J904_001_volume_map.mrc as #9, grid size 256,256,256,
pixel 1.09, shown at level 0.0162, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J902_003_volume_map.mrc

Opened cryosparc_P122_J902_003_volume_map.mrc as #10, grid size 256,256,256,
pixel 1.09, shown at level 0.0189, step 1, values float32  

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J900_002_volume_map (2).mrc"

Opened cryosparc_P122_J900_002_volume_map (2).mrc as #11, grid size
256,256,256, pixel 1.09, shown at level 0.0107, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J901_004_volume_map.mrc

Opened cryosparc_P122_J901_004_volume_map.mrc as #12, grid size 256,256,256,
pixel 1.09, shown at level 0.0204, step 1, values float32  

> open C:/Users/lilyh/Downloads/cryosparc_P122_J903_002_volume_map.mrc

Opened cryosparc_P122_J903_002_volume_map.mrc as #13, grid size 256,256,256,
pixel 1.09, shown at level 0.00538, step 1, values float32  

> volume level 0.07

> tile

6 models tiled  

> volume level 0.01

> volume level 0.02

> volume level 0.03

> hide #!13 models

> close #9-11,13

> close #5

> volume #12 level 0.02814

> show #!8 models

> show #!7 models

> show #!6 models

> show #!4 models

> show #!3 models

> show #!1 models

> show #!2 models

> ~tile

> volume level 0.2

> volume level 0.1

> hide #!1 models

> hide #!3 models

> hide #!6 models

> hide #!4 models

> hide #!7 models

> hide #!8 models

> hide #!12 models

> show #!3 models

> hide #!2 models

> show #!2 models

> close #2

> show #!1 models

> hide #!3 models

> volume #1 level 0.08502

> show #!3 models

> volume #3 level 0.1601

> volume #3 level 0.1923

> volume #3 level 0.1944

> volume #4 level 0.05338

> volume #6 level 0.04262

> volume #6 level 0.04848

> volume #7 level 0.05945

> volume #8 level 0.0564

> hide #!8 models

> hide #!7 models

> hide #!6 models

> hide #!4 models

> hide #4.1 models

> hide #!3 models

> show #!7 models

> show #!6 models

> hide #!7 models

> hide #!6 models

> show #4.1 models

> hide #4.1 models

> show #!7 models

> hide #!7 models

> show #!8 models

> volume #8 level 0.05398

> volume #8 level 0.06972

> volume #12 level 0.03295

> volume #12 level 0.02643

[Repeated 1 time(s)]

> open C:/Users/lilyh/Downloads/cryosparc_P122_J717_002_volume_map_sharp.mrc

Opened cryosparc_P122_J717_002_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.09, shown at level 0.0244, step 1, values float32  

> volume #2 level 0.1505

> ~tile

> volume #2 level 0.1126

> show #!12 models

> hide #!12 models

> show #!12 models

> volume #2 level 0.09584

> volume #2 level 0.2135

> volume #2 level 0.1295

> hide #!7 models

> hide #!6 models

> hide #!8 models

> hide #4.1 models

> hide #!4 models

> volume #2 level 0.2009

> show #!8 models

> volume #2 level 0.1126

> show #!7 models

> hide #!7 models

> volume #2 level 0.1442

> show #!7 models

> hide #!7 models

> show #!7 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #12.1 models

> hide #!12 models

> hide #!8 models

> show #!8 models

> show #!6 models

> show #12.1 models

> hide #12.1 models

> show #4.1 models

> show #!3 models

> hide #!3 models

> hide #3.1 models

> show #!3 models

> show #3.1 models

> show #!1 models

> ~tile

> show #!2 models

> volume #2 level 0.1337

> volume #2 level 0.1568

> open C:/Users/lilyh/Downloads/cryosparc_P122_J711_006_volume_map.mrc

Opened cryosparc_P122_J711_006_volume_map.mrc as #5, grid size 256,256,256,
pixel 1.09, shown at level 0.00809, step 1, values float32  

> volume #5 level 0.03988

> ~tile

> hide #!5 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!5 models

> volume #5 level 0.07534

> volume #5 level 0.08879

> open C:/Users/lilyh/Downloads/cryosparc_P122_J711_006_volume_map_sharp.mrc

Opened cryosparc_P122_J711_006_volume_map_sharp.mrc as #9, grid size
256,256,256, pixel 1.09, shown at level 0.00807, step 1, values float32  

> volume #9 level 0.04842

> ~tile

> volume #9 level 0.07776

> volume #9 level 0.07654

> show #!9 models

> hide #!8 models

> hide #!12 models

> hide #!7 models

> hide #!9 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #3.1 models

> hide #!4 models

> hide #4.1 models

> show #!2 models

> hide #!2 models

> show #12.1 models

> hide #12.1 models

> hide #!12 models

> show #!12 models

> show #12.1 models

> hide #12.1 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!8 models

> show #!7 models

> show #!6 models

> show #!5 models

> show #4.1 models

> hide #!4 models

> show #3.1 models

> show #!4 models

> show #!2 models

> color #1-9 gray

> volume #5 level 0.03133

> volume #5 level 0.03988

> volume #2 level 0.1021

> hide #!1 models

> hide #3.1 models

> hide #!4 models

> hide #4.1 models

> hide #!6 models

> hide #!7 models

> hide #!8 models

> show #!6 models

> show #!5 models

> hide #!6 models

> hide #!2 models

> show #!2 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> volume #5 level 0.07045

> volume #5 level 0.06801

> hide #!5 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!4 models

> hide #!4 models

> show #4.1 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!6 models

> volume #4 level 0.05093

> hide #!4 models

> hide #!6 models

> hide #4.1 models

> show #!6 models

> volume #6 level 0.06604

> hide #!6 models

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1645_mask.mrc

Opened cryosparc_P122_J1645_mask.mrc as #10, grid size 256,256,256, pixel
1.09, shown at level 5e-05, step 1, values float32  

> show #!1 models

> ~tile

> hide #!1 models

> hide #!10 models

> show #!10 models

> show #!9 models

> hide #!9 models

> show #!5 models

> hide #!10 models

> volume #5 level 0.04233

[Repeated 1 time(s)]

> show #!1 models

> hide #!1 models

> show #!6 models

> hide #!5 models

> show #!1 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> hide #!6 models

> show #!1 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #4.1 models

> open C:/Users/lilyh/Downloads/cryosparc_P122_J1645_mask.mrc

Opened cryosparc_P122_J1645_mask.mrc as #11, grid size 256,256,256, pixel
1.09, shown at level 5e-05, step 1, values float32  

> ~tile

> select #11

2 models selected  

> transparency #11.1 70

> select clear

> hide #4.1 models

> hide #!4 models

> hide #!11 models

> show #!1 models

> open "C:/Users/lilyh/Downloads/cryosparc_P122_J1645_mask (2).mrc"

Opened cryosparc_P122_J1645_mask (2).mrc as #13, grid size 256,256,256, pixel
1.09, shown at level 5e-05, step 1, values float32  

> ~tile

> hide #!1 models

> show #!1 models

> hide #!13 models

> show #!3 models

> show #3.1 models

> hide #!1 models

> volume #3 level 0.1279

> open
> C:/Users/lilyh/Desktop/output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb

Chain information for
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
#14  
---  
Chain | Description  
B | No description available  
C | No description available  
  
Drag select of 585 residues  

> ui mousemode right "translate selected models"

> view matrix models #14,1,0,0,107.01,0,1,0,108.08,0,0,1,154.62

> view matrix models #14,1,0,0,132.5,0,1,0,155.37,0,0,1,140.82

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.12107,-0.96992,-0.21117,132.2,0.52635,-0.2431,0.81478,164.54,-0.84161,-0.012505,0.53995,136.79

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.12107,-0.96992,-0.21117,126.86,0.52635,-0.2431,0.81478,149.28,-0.84161,-0.012505,0.53995,125.38

> select clear

> fitmap #14 inMap #3

Fit molecule
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#14) to map cryosparc_P122_J1573_001_volume_map_sharp.mrc (#3) using 4737
atoms  
average map value = 0.1473, steps = 164  
shifted from previous position = 20.8  
rotated from previous position = 9.29 degrees  
atoms outside contour = 2333, contour level = 0.1279  
  
Position of
output_dir_COSMIC2JOBCOLABFOLD4BBB2580C9CA44C6B52A66BA6975777F_1c490_unrelaxed_rank_1_model_3-coot-0.pdb
(#14) relative to cryosparc_P122_J1573_001_volume_map_sharp.mrc (#3)
coordinates:  
Matrix rotation and translation  
-0.81442385 0.20948496 -0.54113754 140.13355312  
-0.52899742 -0.65131182 0.54401712 134.92255096  
-0.23848587 0.72932088 0.64126088 143.42910260  
Axis 0.22616666 -0.36939194 -0.90133137  
Axis point 97.62445085 17.45438470 0.00000000  
Rotation angle (degrees) 155.81639750  
Shift along axis -147.42291444  
  

> select clear

> select #14/B: 131, 149

13 atoms, 11 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #3

2 models selected  

> transparency #3.1 40

> set bgColor white

> view matrix models
> #3,0.070071,0.45765,-0.88637,214,-0.89655,0.41847,0.14519,188.99,0.43737,0.7845,0.43962,-97.023

> undo

> select clear

> select #14/B: 131, 149, 127, 128,

Expected an objects specifier or a keyword  

> select #14/B: 131, 149, 127, 128

25 atoms, 22 bonds, 4 residues, 1 model selected  

> select #14/B: 131, 149, 127, 128

25 atoms, 22 bonds, 4 residues, 1 model selected  

> color sel red

> show sel atoms

> select #14/B: 119

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel forest green

> select clear

> volume #3 level 0.1107

> hide #3.1 models

Drag select of 9 atoms, 278 residues, 6 bonds  

> show sel atoms

> select clear

> select #14/C: 1412, 1473

18 atoms, 16 bonds, 2 residues, 1 model selected  

> view matrix models
> #14,-0.087774,-0.92984,-0.35735,127.87,0.47418,-0.35448,0.80592,134.93,-0.87604,-0.098706,0.47202,140.54

> select #14/C: 1412, 1373

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #14/C: 1412, 1373

19 atoms, 18 bonds, 2 residues, 1 model selected  

> hide #!3 models

> show #3.1 models

> hide #!3 models

> show #!3 models

> hide #14 models

> transparency #3 0

> volume #3 level 0.1429

> volume #3 level 0.1279

> open 2f6h

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open  
models, status = collated_open(session, database_name, ident,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 464, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 97, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
File "src\mmcif.pyx", line 418, in chimerax.mmcif.mmcif.fetch_mmcif  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\manager.py", line 198, in open_data  
return provider_open(self.session, [path], _return_status=True,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 194, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 465, in collated_open  
return remember_data_format()  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 435, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX1.6.1\bin\lib\site-
packages\chimerax\mmcif\\__init__.py", line 43, in open  
return mmcif.open_mmcif(session, data, file_name, **kw)  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
MemoryError: not enough memory  
  
MemoryError: not enough memory  
  
File "src\mmcif.pyx", line 88, in chimerax.mmcif.mmcif.open_mmcif  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.14756 Core Profile Forward-Compatible Context 20.40.68.03 27.20.14068.3000
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Microsoft Corporation
Model: Surface Laptop 4
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 8,002,093,056
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 Microsoft Surface (R) Edition
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0