Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-26-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x000073eb88824b80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 526 in _cursor_position
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 483 in mouse_pause_tracking
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 151 in _redraw_timer_callback
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 57)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/em313/Documents/ATP-Vi-HF380/ATPVimodel001-coot-0.pdb

Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/ATPVimodel001-coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 TRP A 171
ALA A 187 1 17  
Start residue of secondary structure not found: HELIX 2 2 MET A 188 MET A 190
1 3  
Start residue of secondary structure not found: HELIX 3 3 LYS A 195 PHE A 197
1 3  
Start residue of secondary structure not found: HELIX 4 4 GLU A 199 GLY A 234
1 36  
Start residue of secondary structure not found: HELIX 5 5 GLY A 236 LEU A 241
1 6  
25 messages similar to the above omitted  
PDB SEQRES record for chain A is incomplete. Ignoring input sequence records
as basis for sequence.  
  
Chain information for ATPVimodel001-coot-0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open /home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/1059-1146_ver2.pdb /home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/1388-1694.pdb /home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/1388-1694_ver2.pdb

Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/J50-2-30A-resolution/1059-1146_ver2.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 6 6 LEU A
1148 ASP A 1155 1 8  
Start residue of secondary structure not found: HELIX 7 7 ALA A 1156 GLN A
1158 1 3  
Start residue of secondary structure not found: HELIX 8 8 ARG A 1167 LEU A
1191 1 25  
Start residue of secondary structure not found: HELIX 9 9 PRO A 1199 GLY A
1219 1 21  
Start residue of secondary structure not found: HELIX 10 10 LEU A 1224 ILE A
1237 1 14  
212 messages similar to the above omitted  
  
Summary of feedback from opening /home/em313/Documents/ATP-Vi-
HF380/J50-2-30A-resolution/1388-1694.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 THR A
1060 ASN A 1073 1 14  
Start residue of secondary structure not found: HELIX 2 2 PRO A 1078 GLN A
1097 1 20  
Start residue of secondary structure not found: HELIX 3 3 THR A 1098 ILE A
1100 1 3  
Start residue of secondary structure not found: HELIX 4 4 ALA A 1127 ILE A
1139 1 13  
Start residue of secondary structure not found: HELIX 5 5 SER A 1140 PHE A
1143 1 4  
202 messages similar to the above omitted  
  
Chain information for 1059-1146_ver2.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for 1388-1694.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for 1388-1694_ver2.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open /home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/J50_007_volume_map_sharp.mrc

Opened J50_007_volume_map_sharp.mrc as #5, grid size 600,600,600, pixel 0.873,
shown at level 0.0778, step 4, values float32  

> open /home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/J50_007_volume_map_sharp_1mol.mrc

Opened J50_007_volume_map_sharp_1mol.mrc as #6, grid size 600,600,600, pixel
0.873, shown at level 0.0679, step 4, values float32  

> hide #!5 models

> volume gaussian #6 sDev 1.3

Opened J50_007_volume_map_sharp_1mol.mrc gaussian as #7, grid size
600,600,600, pixel 0.873, shown at step 1, values float32  

> select add #7

2 models selected  

> transparency #7.1 50

> dlear

Unknown command: dlear  

> select clear

> ui mousemode right "map eraser"

> select add #8

1 model selected  

> volume erase #7 center 351.25,82.435,258.31 radius 93.801

> volume erase #7 center 209.48,87.082,288.98 radius 93.801

> volume erase #7 center 170.06,87.167,285.83 radius 93.801

> volume erase #7 center 249.54,439.29,333.45 radius 70.147

> hide #8 models

> save "/home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/J50_007_volume_map_sharp_1mol ver2.mrc" models #7

> hide #!7 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> show #!6 models

> hide #!6 models

> show #!5 models

> hide #!5 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A

Alignment identifier is 1/A  

> select
> #1/A:1060-1073,1078-1100,1127-1143,1148-1158,1167-1191,1199-1219,1224-1237,1249-1251,1264-1266,1274-1284,1287-1290,1295-1317,1330-1348,1356-1358,1361-1372,1374-1376,1380-1393,1396-1399,1419-1427,1435-1438,1559-1574,1581-1584,1588-1617,1623-1626,1632-1652,1656-1661,1665-1691,1695-1699,1702-1710,1715-1717,1719-1724,1766-1794,1800-1809,1812-1830,1838-1864,1869-1892,1904-1907,1921-1923,1951-1965,1980-1990,2006-2019,2028-2030,2033-2051,2089-2094,2105-2116,2121-2138,2149-2165,2177-2202,2204-2206,2209-2211,2213-2222,2233-2246,2253-2266,2282-2297,2308-2310,2313-2317,2331-2341,2346-2348,2361-2371,2405-2410,2638-2640,2651-2665,2680-2690,2707-2717,2758-2769,2805-2810,2821-2838,2840-2863,2876-2892,2898-2914,2920-2937,2943-2946,2965-2982,2992-3006,3022-3032,3048-3063,3075-3077,3081-3093,3103-3118,3126-3140,3154-3160,3162-3167,3178-3188,3203-3212,3223-3249,3257-3368,3373-3482,3485-3502,3512-3515,3641-3649,3656-3666,3680-3688,3690-3692,3704-3714,3723-3725,3728-3734,3775-3778,3790-3804,3889-3905,3913-3925,3928-3930,3936-3958,3961-3976,3985-3993,3998-4000,4006-4008,4014-4026,4028-4030,4033-4039,4041-4048,4060-4067,4075-4089,4091-4106,4118-4125,4142-4152,4165-4181,4190-4192,4194-4206,4227-4232,4414-4435,4456-4476,4489-4491,4494-4524,4532-4541,4561-4577,4597-4611,4713-4718

13990 atoms, 14112 bonds, 1704 residues, 1 model selected  

> select #1 /A:1695

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1 /A:1695

5 atoms, 4 bonds, 1 residue, 1 model selected  

> color sel red

> select #1 /A:1695-1700

57 atoms, 59 bonds, 6 residues, 1 model selected  

> color sel red

> show #!7 models

> hide #!7 models

> show #!7 models

> transparency sel 50

> color #7 #ffbe6fff models

> volume #7 level 0.00546

> hide #!4 models

> hide #2 models

> transparency sel 30

> hide #!1 models

> transparency #7 40

> show #2 models

> volume #7 level 0.007892

> volume #7 level 0.01519

> volume #7 level 0.03384

> show #!1 models

> color #1 #f66151ff

> color #1 #8ff0a4ff

> color #1 #1c71d8ff

> color #1 #613583ff

> select
> #1/A:1252-1254,1261-1263,1578-1580,1731-1734,1741-1745,1751-1753,1911-1914,1925-1929,1932-1934,1969-1973,1995-1999,2022-2026,2056-2058,2064-2066,2072-2075,2095-2099,2271-2275,2301-2306,2318-2321,2326-2329,2350-2356,2376-2378,2384-2386,2391-2397,2412-2415,2670-2673,2694-2700,2718-2722,2728-2732,2738-2744,2771-2774,2779-2783,2786-2792,2813-2815,3011-3016,3035-3039,3069-3074,3141-3147,3168-3173,3672-3675,3695-3698,3718-3721,3738-3741,3744-3749,3752-3755,3762-3766,3782-3785,4132-4136,4157-4161,4184-4188,4214-4220,4234-4238,4620-4626,4636-4640,4666-4672,4686-4691,4699-4705

2282 atoms, 2292 bonds, 277 residues, 1 model selected  

> select clear

> select #1/A:1778

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:1776-1778

26 atoms, 25 bonds, 3 residues, 1 model selected  

> select #1/A:1767

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #1/A:1767

10 atoms, 10 bonds, 1 residue, 1 model selected  

> hide #!7 models

> show #!7 models

> open /home/em313/Documents/ATP-Vi-
> HF380/J50-2-30A-resolution/1388-1694_ver2.pdb

Chain information for 1388-1694_ver2.pdb #9  
---  
Chain | Description  
A | No description available  
  

> hide #!7 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!7 models

> select add #9

1676 atoms, 1716 bonds, 1 pseudobond, 206 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,1,0,0,1.7469,0,1,0,-1.4313,0,0,1,-2.3122,#9,1,0,0,1.7469,0,1,0,-1.4313,0,0,1,-2.3122

> undo

> hide #!7 models

> hide #2 models

> hide #!1 models

> select add #1

26240 atoms, 26781 bonds, 6 pseudobonds, 3269 residues, 4 models selected  

> select subtract #1

1666 atoms, 1706 bonds, 1 pseudobond, 205 residues, 2 models selected  

> show #!7 models

> show #!1 models

> ui mousemode right "translate selected models"

> view matrix models #9,1,0,0,-6.1253,0,1,0,14.12,0,0,1,2.4779

> view matrix models #9,1,0,0,-6.5062,0,1,0,13.881,0,0,1,3.7725

> ui tool show "Fit in Map"

> fitmap #3 inMap #7

Fit molecule 1388-1694.pdb (#3) to map J50_007_volume_map_sharp_1mol ver2.mrc
(#7) using 1666 atoms  
average map value = 0.09281, steps = 84  
shifted from previous position = 0.0117  
rotated from previous position = 0.00679 degrees  
atoms outside contour = 442, contour level = 0.033838  
  
Position of 1388-1694.pdb (#3) relative to J50_007_volume_map_sharp_1mol
ver2.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00003930 -0.00011140 0.04315210  
0.00003930 1.00000000 -0.00000874 -0.00062872  
0.00011140 0.00000874 0.99999999 -0.02063871  
Axis 0.07377471 -0.94045229 0.33182343  
Axis point 176.13980892 0.00000000 389.40187265  
Rotation angle (degrees) 0.00678663  
Shift along axis -0.00307359  
  

> fitmap #9 inMap #7

Fit molecule 1388-1694_ver2.pdb (#9) to map J50_007_volume_map_sharp_1mol
ver2.mrc (#7) using 1666 atoms  
average map value = 0.07404, steps = 128  
shifted from previous position = 3.85  
rotated from previous position = 3.78 degrees  
atoms outside contour = 428, contour level = 0.033838  
  
Position of 1388-1694_ver2.pdb (#9) relative to J50_007_volume_map_sharp_1mol
ver2.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99789631 -0.02715052 0.05887103 -14.04262896  
0.02645745 0.99957153 0.01252057 0.58392422  
-0.05918574 -0.01093665 0.99818708 24.36356759  
Axis -0.17802601 0.89597896 0.40685187  
Axis point 316.27078430 0.00000000 210.71668926  
Rotation angle (degrees) 3.77746459  
Shift along axis 12.93549999  
  

> hide #!1 models

> show #!1 models

> hide #!7 models

> select #1 /A:1695-1700

57 atoms, 59 bonds, 6 residues, 1 model selected  

> color sel red

> show #!7 models

> hide #!7 models

> show #!7 models

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99072,-0.039316,0.1301,-23.195,0.038217,0.99921,0.010937,-13.207,-0.13043,-0.0058637,0.99144,39.353

> undo

> select add #1

24574 atoms, 25075 bonds, 5 pseudobonds, 3064 residues, 2 models selected  

> select subtract #1

Nothing selected  

> select add #9

1666 atoms, 1706 bonds, 1 pseudobond, 205 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.97512,0.2018,0.091692,-74.776,-0.19673,0.97853,-0.061444,85.78,-0.10212,0.041877,0.99389,23.672

> view matrix models
> #9,0.57712,0.72074,-0.38401,32.103,-0.81176,0.55773,-0.17319,386.5,0.089354,0.41167,0.90694,-96.425

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.57712,0.72074,-0.38401,31.05,-0.81176,0.55773,-0.17319,357.79,0.089354,0.41167,0.90694,-91.156

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.27355,0.51946,-0.80952,280.42,-0.80536,0.58386,0.10251,273.16,0.5259,0.62391,0.57807,-169.78

> view matrix models
> #9,0.49647,0.16842,-0.85156,321.2,-0.8206,0.41098,-0.39713,459.15,0.28309,0.89595,0.34225,-108.41

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.49647,0.16842,-0.85156,306.58,-0.8206,0.41098,-0.39713,459.22,0.28309,0.89595,0.34225,-93.018

> fitmap #9 inMap #7

Fit molecule 1388-1694_ver2.pdb (#9) to map J50_007_volume_map_sharp_1mol
ver2.mrc (#7) using 1666 atoms  
average map value = 0.09999, steps = 392  
shifted from previous position = 8.72  
rotated from previous position = 40.3 degrees  
atoms outside contour = 173, contour level = 0.033838  
  
Position of 1388-1694_ver2.pdb (#9) relative to J50_007_volume_map_sharp_1mol
ver2.mrc (#7) coordinates:  
Matrix rotation and translation  
0.79705959 -0.24589003 -0.55157420 251.42419103  
-0.26127343 0.68303763 -0.68205263 330.87279413  
0.54445588 0.68774827 0.48017717 -151.69718619  
Axis 0.78078614 -0.62473684 -0.00876853  
Axis point 0.00000000 430.02565154 276.96491101  
Rotation angle (degrees) 61.30563701  
Shift along axis -9.06974022  
  

> save "/home/em313/Documents/ATP-Vi-HF380/J50_007_volume_map_sharp_1mol
> ver3.pdb"

> delete #1 /A:1398-1694

> hide #!7 models

> ui tool show Matchmaker

> matchmaker #!4 to #9

Parameters  
---  
Chain pairing | bb  
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 1388-1694_ver2.pdb, chain A (#9) with 1388-1694_ver2.pdb, chain A
(#4), sequence alignment score = 1068.1  
RMSD between 205 pruned atom pairs is 0.000 angstroms; (across all 205 pairs:
0.000)  
  

> hide #!9 models

> show #!9 models

> save /home/em313/Documents/ATP-Vi-HF380/1388-1694.pdb models #9 selectedOnly
> true

> open /home/em313/Documents/ATP-Vi-HF380/1388-1694.pdb

Chain information for 1388-1694.pdb #10  
---  
Chain | Description  
A | No description available  
  

> hide #!9 models

> hide #!1 models

> delete #1 /A:1388-1441

> close #1


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 535.161.07
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 7 5700X 8-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           125Gi       3.0Gi       116Gi        23Mi       6.0Gi       121Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	0f:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1)	
	Subsystem: ZOTAC International (MCO) Ltd. TU102 [GeForce RTX 2080 Ti] [19da:2503]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.2
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9