copick: 'CopickRunFSSpec' object has no attribute 'tomograms'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-4.18.0-553.33.1.el8_10.x86_64-x86_64-with-glibc2.28
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Current thread 0x000014b314b59b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, 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, numcodecs.compat_ext, numcodecs.blosc, numcodecs.zstd, numcodecs.lz4, numcodecs._shuffle, numcodecs.jenkins, numcodecs.vlen, numcodecs.fletcher32, msgpack._cmsgpack, psutil._psutil_linux, psutil._psutil_posix, lz4._version, lz4.frame._frame, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, cython.cimports.libc.math, pyarrow.lib, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pyarrow._compute, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, Cython.Utils, Cython.StringIOTree, Cython.Plex.Actions, Cython.Plex.Transitions, Cython.Plex.Machines, Cython.Plex.DFA, Cython.Plex.Scanners, Cython.Compiler.Scanning, Cython.Compiler.Code, Cython.Tempita._tempita, Cython.Compiler.Visitor, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._group_columns, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.optimize._direct, lxml._elementpath, lxml.etree, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, multidict._multidict, yarl._quoting_c, propcache._helpers_c, aiohttp._http_writer, aiohttp._http_parser, aiohttp._websocket.mask, aiohttp._websocket.reader_c, frozenlist._frozenlist (total: 183)
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> copick start
> /hpc/projects/group.czii/rahel.woldeyes/20250729_proc/25jun02a_run003_config.json

Note: detected 128 virtual cores but NumExpr set to maximum of 64, check
"NUMEXPR_MAX_THREADS" environment variable.  
Note: NumExpr detected 128 cores but "NUMEXPR_MAX_THREADS" not set, so
enforcing safe limit of 16.  
NumExpr defaulting to 16 threads.  
Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  
🔧 ChimeraX Worker Manager initialized with max_concurrent_workers=4 (reduced
from 16 to prevent blocking)  
🔧 ChimeraX Worker Manager initialized with max_concurrent_workers=4 (reduced
from 16 to prevent blocking)  

> ui mousemode shift wheel 'move copick planes'

> cks

💥 Worker: Exception in worker for 'Position_110_5': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_125_6': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_160_8': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_47_5': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_97_5': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
Opened Position_100 - 10.0 as #3, grid size 630,630,246, pixel 10, shown at
step 4, values float32  
Opened Position_100 - 10.0 as #1.1.1, grid size 630,630,246, pixel 10, shown
at level 2.82e-06, step 4, values float32  

> artiax clip off

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> copick start
> /hpc/projects/group.czii/rahel.woldeyes/20250729_proc/25jun02a_run003_config.json

💥 Worker: Exception in worker for 'Position_110_5': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_125_6': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_160_8': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_47_5': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_97_5': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
Opened Position_1 - 10.0 as #3, grid size 630,630,246, pixel 10, shown at step
4, values float32  
Opened Position_1 - 10.0 as #1.1.1, grid size 630,630,246, pixel 10, shown at
level 1.14e-06, step 4, values float32  

> artiax clip off

> artiax tomo #1.1.1 sliceDirection 0,0,1

> artiax view xy

> copick start
> /hpc/projects/group.czii/rahel.woldeyes/20250729_proc/25jun02a_run003_config.json

💥 Worker: Exception in worker for 'Position_110_5': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_125_6': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_160_8': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_47_5': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  
💥 Worker: Exception in worker for 'Position_97_5': 'CopickRunFSSpec' object
has no attribute 'tomograms'  
Traceback (most recent call last):  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/unified_workers.py", line 90, in
load_thumbnail  
pixmap, error = self.generate_thumbnail_pixmap()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/home/rahel.woldeyes/.local/share/ChimeraX/1.9/lib/python3.11/site-
packages/copick_shared_ui/workers/base.py", line 170, in
generate_thumbnail_pixmap  
for tomo in run.tomograms:  
^^^^^^^^^^^^^  
AttributeError: 'CopickRunFSSpec' object has no attribute 'tomograms'  


===== 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: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open InitialModel/job001/run_it000_class00*.mrc

Opened run_it000_class001.mrc as #1.1, grid size 56,56,56, pixel 14.8, shown
at level 0.000829, step 1, values float32  
Opened run_it000_class002.mrc as #1.2, grid size 56,56,56, pixel 14.8, shown
at level 0.0002, step 1, values float32  




OpenGL version: 4.5 (Core Profile) Mesa 23.1.4
OpenGL renderer: llvmpipe (LLVM 17.0.6, 256 bits)
OpenGL vendor: Mesa

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

XDG_SESSION_TYPE=
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: AS -2124GQ-NART
OS: Rocky Linux 8.10 Green Obsidian
Architecture: 64bit ELF
Virtual Machine: none
CPU: 128 AMD EPYC 7742 64-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          2.0Ti        54Gi       786Gi        32Gi       1.1Ti       1.9Ti
	Swap:          31Gi       2.6Gi        29Gi

Graphics:
	63:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 51)	
	DeviceName: ASPEED Video AST2500	
	Subsystem: Super Micro Computer Inc Device [15d9:1c11]

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    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
    pexpect: 4.8.0
    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
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    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
    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
    zipp: 3.15.0