Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.12.10-76061203-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

Thread 0x0000762e93fff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000762f677e9b80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 464 in cxcmd
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 446 in defer
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 375 in thread_safe
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 455 in chimerax_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 353 in intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 93 in _intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 320 in interceptRequest
  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, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.graphics._graphics, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.mask._mask, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath (total: 65)
===== 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/poulpi/Desktop/mu/gp40vsMU.cxs format session

> surface cap true

Opened cryosparc_P25_J41_map_sharp_flip.mrc as #1, grid size 256,256,256,
pixel 0.885, shown at level 0.195, step 1, values float32  
Opened emdb 63137 as #5, grid size 440,440,440, pixel 1.06, shown at level 6,
step 1, values float32  
Opened MU_P79679.cif map 5 as #6, grid size 71,70,133, pixel 1.67, shown at
level 0.0913, step 1, values float32  

> surface cap false

opened ChimeraX session  

> molmap #3 10

Opened MU_P79679.cif map 10 as #7, grid size 45,44,76, pixel 3.33, shown at
level 0.07, step 1, values float32  

> select add #7

2 models selected  

> select add #5

4 models selected  

> vop subtract #5 #7 minrms True

Opened volume difference as #8, grid size 440,440,440, pixel 1.06, shown at
step 1, values float32  
Minimum RMS scale factor for "MU_P79679.cif map 10 #7" above level 0.069952 is
7.3347  
  

> select subtract #7

2 models selected  

> select subtract #5

Nothing selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> hide #!8 models

> show #!1 models

> hide #!1 models

> show #!5 models

> show #!8 models

> hide #!8 models

> hide #2 models

> show #2 models

> close #8

> select add #5

2 models selected  

> show #!7 models

> select add #7

4 models selected  

> select subtract #5

2 models selected  

> select add #5

4 models selected  

> vop subtract #5 #7 minrms True

Opened volume difference as #8, grid size 440,440,440, pixel 1.06, shown at
step 1, values float32  
Minimum RMS scale factor for "MU_P79679.cif map 10 #7" above level 0.069952 is
7.3347  
  

> ui tool show "Side View"

> hide #!8 models

> show #!8 models

> show #!1 models

> show #!5 models

> hide #!5 models

> select subtract #5

2 models selected  

> show #!7 models

> close #8

> volume mask #5 surfaces #7

Opened emdb 63137 masked as #8, grid size 87,87,186, pixel 1.06, shown at step
1, values float32  

> select subtract #7

Nothing selected  

> hide #2 models

> hide #!7 models

> view

> show #2 models

> hide #2 models

> hide #!3 models

> hide #5.1 models

> hide #!1 models

> color #8 #b2b2b266 models

> show #2 models

> ui tool show "Fit in Map"

> fitmap #3 inMap #8

Fit molecule MU_P79679.cif (#3) to map emdb 63137 masked (#8) using 23105
atoms  
average map value = 2.368, steps = 28  
shifted from previous position = 0.0144  
rotated from previous position = 0.00863 degrees  
atoms outside contour = 19477, contour level = 6  
  
Position of MU_P79679.cif (#3) relative to emdb 63137 masked (#8) coordinates:  
Matrix rotation and translation  
0.09389791 0.99558184 -0.00001263 109.77347753  
0.99558184 -0.09389790 0.00011946 131.03018049  
0.00011774 -0.00002379 -1.00000000 241.34790120  
Axis -0.73955607 -0.67309495 -0.00002903  
Axis point 0.00000000 15.56871684 120.67123916  
Rotation angle (degrees) 179.99445121  
Shift along axis -169.38640090  
  

> fitmap #3 inMap #8

Fit molecule MU_P79679.cif (#3) to map emdb 63137 masked (#8) using 23105
atoms  
average map value = 2.368, steps = 40  
shifted from previous position = 0.0133  
rotated from previous position = 0.00584 degrees  
atoms outside contour = 19471, contour level = 6  
  
Position of MU_P79679.cif (#3) relative to emdb 63137 masked (#8) coordinates:  
Matrix rotation and translation  
0.09391475 0.99558025 -0.00008336 109.76660831  
0.99558024 -0.09391473 0.00019079 131.02523949  
0.00018212 -0.00010091 -0.99999999 241.34860038  
Axis -0.73956375 -0.67308652 -0.00003019  
Axis point -0.00000000 15.57870471 120.67092517  
Rotation angle (degrees) 179.98870054  
Shift along axis -169.37801301  
  

> fitmap #2 inMap #8

Fit molecule 9lj8.cif (#2) to map emdb 63137 masked (#8) using 63696 atoms  
average map value = 1.96, steps = 108  
shifted from previous position = 5.28  
rotated from previous position = 4.56 degrees  
atoms outside contour = 60866, contour level = 6  
  
Position of 9lj8.cif (#2) relative to emdb 63137 masked (#8) coordinates:  
Matrix rotation and translation  
0.99903926 0.04382209 -0.00042741 -9.92264293  
-0.04382245 0.99903896 -0.00087092 10.57005931  
0.00038883 0.00088881 0.99999953 -31.64606053  
Axis 0.02007316 -0.00931077 -0.99975516  
Axis point 242.46365159 246.10179293 0.00000000  
Rotation angle (degrees) 2.51225088  
Shift along axis 31.34071808  
  

> select add #2

63696 atoms, 64980 bonds, 8364 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.4288,0.8976,0.10217,-94.768,0.88399,-0.44021,0.15741,100.95,0.18626,0.022818,-0.98223,281.65

> view matrix models
> #2,0.43324,0.88917,0.14721,-102.06,0.89918,-0.43757,-0.0032986,126.12,0.061482,0.1338,-0.9891,286.12

> view matrix models
> #2,0.43527,0.90004,0.02156,-82.134,0.89996,-0.43432,-0.037777,131.47,-0.024637,0.035846,-0.99905,330.87

> fitmap #2 inMap #8

Fit molecule 9lj8.cif (#2) to map emdb 63137 masked (#8) using 63696 atoms  
average map value = 2.114, steps = 72  
shifted from previous position = 2.3  
rotated from previous position = 2.92 degrees  
atoms outside contour = 60654, contour level = 6  
  
Position of 9lj8.cif (#2) relative to emdb 63137 masked (#8) coordinates:  
Matrix rotation and translation  
0.41039775 0.91190658 -0.00028790 -75.12425100  
0.91190641 -0.41039786 -0.00056347 116.33363638  
-0.00063198 -0.00003129 -0.99999980 336.09556656  
Axis 0.83976515 0.54294974 -0.00027441  
Axis point 0.00000000 82.42088770 168.04648377  
Rotation angle (degrees) 179.98184499  
Shift along axis -0.01563781  
  

> hide #2 models

> show #2 models

> select #2/G#2/H#2/I#2/J#2/K#2/L#2/M#2/N#2/O#2/P#2/Q#2/R

44664 atoms, 45552 bonds, 5916 residues, 1 model selected  

> hide sel cartoons

> show #!3 models

> ui tool show Matchmaker

> select #2/S#2/T#2/U#2/V#2/W#2/X#2/Y#2/Z#2/a#2/b#2/c#2/d

10620 atoms, 10812 bonds, 1392 residues, 1 model selected  

> matchmaker #!3 to #2 & sel

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 9lj8.cif, chain S (#2) with MU_P79679.cif, chain Aa (#3), sequence
alignment score = 539.3  
RMSD between 114 pruned atom pairs is 0.568 angstroms; (across all 115 pairs:
0.600)  
  

> select #2/S#2/T#2/U#2/V#2/W#2/X#2/Y#2/Z#2/a#2/b#2/c#2/d

10620 atoms, 10812 bonds, 1392 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/a #2/S #2/T #2/U #2/V #2/W #2/X #2/Y #2/Z #2/b #2/c #2/d

Alignment identifier is 1  

> ui tool show "Show Sequence Viewer"

> sequence chain #4/0

Alignment identifier is 4/0  

> fitmap #3 inMap #8

Fit molecule MU_P79679.cif (#3) to map emdb 63137 masked (#8) using 23105
atoms  
average map value = 2.292, steps = 136  
shifted from previous position = 2.75  
rotated from previous position = 0.598 degrees  
atoms outside contour = 19966, contour level = 6  
  
Position of MU_P79679.cif (#3) relative to emdb 63137 masked (#8) coordinates:  
Matrix rotation and translation  
0.90969339 0.41526364 -0.00374991 83.43606609  
-0.41525778 0.90970098 0.00226213 176.99782670  
0.00435068 -0.00050067 0.99999042 64.22076028  
Axis -0.00332641 -0.00975310 -0.99994690  
Axis point 447.11310751 -103.15980288 0.00000000  
Rotation angle (degrees) 24.53712424  
Shift along axis -66.22117023  
  

> volume #8 level 2.554

> fitmap sel inMap #8

Fit molecule 9lj8.cif (#2) to map emdb 63137 masked (#8) using 10620 atoms  
average map value = 2.746, steps = 60  
shifted from previous position = 0.803  
rotated from previous position = 0.0884 degrees  
atoms outside contour = 5991, contour level = 2.5536  
  
Position of 9lj8.cif (#2) relative to emdb 63137 masked (#8) coordinates:  
Matrix rotation and translation  
0.40933088 0.91238585 0.00055087 -75.12264428  
0.91238599 -0.40933094 -0.00000593 115.91115396  
0.00022008 0.00050504 -0.99999985 336.57444679  
Axis 0.83944764 0.54344053 0.00022901  
Axis point 0.00000000 82.24147035 168.30797633  
Rotation angle (degrees) 179.98256216  
Shift along axis 0.00637156  
  

> hide #!3 models

> select add #8

10620 atoms, 10812 bonds, 1392 residues, 3 models selected  

> color zone #8 near sel & #2 distance 6.36

> transparency sel 0

> transparency sel 50

> ui tool show "Basic Actions"

> ui tool show "Color Actions"

> color sel bychain

> color zone #8 near sel & #2 distance 6.36

> transparency sel 0

> transparency sel 50

> select subtract #8

10620 atoms, 10812 bonds, 1392 residues, 1 model selected  

> view matrix models
> #2,0.40773,-0.89723,-0.1695,378.28,0.91164,0.38949,0.13122,-94.144,-0.051714,-0.20802,0.97676,36.556

> view matrix models
> #2,0.36976,-0.92115,-0.1215,383.95,0.92806,0.35989,0.095834,-84.615,-0.04455,-0.1482,0.98795,18.89

> view matrix models
> #2,0.36976,-0.92115,-0.1215,384.47,0.92806,0.35989,0.095834,-83.836,-0.04455,-0.1482,0.98795,13.442

> fitmap sel inMap #8

Fit molecule 9lj8.cif (#2) to map emdb 63137 masked (#8) using 10620 atoms  
average map value = 2.022, steps = 96  
shifted from previous position = 2.9  
rotated from previous position = 6.03 degrees  
atoms outside contour = 6779, contour level = 2.5536  
  
Position of 9lj8.cif (#2) relative to emdb 63137 masked (#8) coordinates:  
Matrix rotation and translation  
0.34465592 -0.93802398 -0.03637728 378.01683922  
0.93838319 0.34321825 0.04047482 -72.75913420  
-0.02548101 -0.04808572 0.99851814 -18.03175364  
Axis -0.04714360 -0.00580043 0.99887128  
Axis point 240.81339392 232.97040880 0.00000000  
Rotation angle (degrees) 69.92827865  
Shift along axis -35.41044006  
  

> color zone #8 near sel & #2 distance 6.36

> transparency #8.1 0

> transparency #8.1 50

> graphics silhouettes false

> graphics silhouettes true

> hide #2 models

> lighting soft

> transparency #8.1 0

> close session

> open 9lj8 fromDatabase emdb format ccp4

Fetching url
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-9lj8/map/emd_9lj8.map.gz
failed:  
  

> open 63137 fromDatabase emdb format ccp4

Opened emdb 63137 as #1, grid size 440,440,440, pixel 1.06, shown at level 6,
step 2, values float32, fit PDB 9lj8  

> open 9lj8 fromDatabase pdb format mmcif

Summary of feedback from opening 9lj8 fetched from pdb  
---  
note | Fetching compressed mmCIF 9lj8 from
http://files.rcsb.org/download/9lj8.cif  
  
9lj8 title:  
Tail structure of bacteriophage μ in contracted state [more info...]  
  
Chain information for 9lj8 #2  
---  
Chain | Description | UniProt  
A B C D E F | Probable tail terminator protein | TRP_BPMU 1-182  
G H I J K L M N O P Q R | Tail sheath protein | TSP_BPMU 0-494  
S T U V W X Y Z a b c d | Tail tube protein | TUBE_BPMU 1-118  
  

> show cartoons

> hide atoms

> close session

> open /home/poulpi/Desktop/mu/MU_P79679/MU.cxs format session

> surface cap true


===== 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 565.77
OpenGL renderer: NVIDIA GeForce GTX 1060/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=pop
XDG_SESSION_DESKTOP=pop
XDG_CURRENT_DESKTOP=pop:GNOME
DISPLAY=:1
Manufacturer: GIGABYTE
Model: P64V7
OS: Pop!_OS 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
Cache Size: 6144 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       9.0Gi       3.6Gi       3.1Gi        18Gi        16Gi
	Swap:           19Gi        43Mi        19Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 630 [8086:591b] (rev 04)	
	DeviceName:  Onboard IGD	
	Subsystem: Gigabyte Technology Co., Ltd HD Graphics 630 [1458:3464]

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-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    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