Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-113-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x00007f3145973700 (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 0x00007f336ed6a740 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/app/forcefield.py", line 628 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/app/forcefield.py", line 628 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/app/forcefield.py", line 1213 in createSystem
  File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1255 in _create_openmm_system
  File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 1097 in __init__
  File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/openmm/openmm_interface.py", line 321 in __init__
  File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/isolde.py", line 876 in start_sim
  File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/cmd/cmd.py", line 122 in isolde_sim
  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 "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/toolbar.py", line 21 in toolbar_command
  File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/isolde/__init__.py", line 183 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in 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.map._map, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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.linalg._flinalg, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, 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.__nnls, 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.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 120)
===== 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 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/alphafold/Downloads/OneDrive_1_24-07-2024/0017-01_refmacat.mtz

Reflection data must be associated with an atomic structure, provided via the
structure_model argument.  

> open /home/alphafold/Downloads/OneDrive_1_24-07-2024/0017-01_refmacat.mtz

Summary of feedback from opening
/home/alphafold/Downloads/OneDrive_1_24-07-2024/0017-01_refmacat.mtz  
---  
warnings | WARNING: multiple experimental reflection datasets found:  
(dataset) HKL_base,  
(dataset) F, SIGF  
Automatically choosing "(dataset) F, SIGF".  
No free flags detected in this dataset! Automatically generated a new random
set with 2064 free from 177649 observed reflections. You should save your data
to a new MTZ file and use this for any future rebuilding/refinement.  
notes |  
  
  
| Chain information for 0017-01_refmacat.pdb #1  
  
---  
  
  
Chain  
| Description  
  
  
  
  
  
  
A  
| No description available  
  
  
  
  
B I  
| No description available  
  
  
  
  
C  
| No description available  
  
  
  
  
D  
| No description available  
  
  
  
  
E J  
| No description available  
  
  
  
  
F L  
| No description available  
  
  
  
  
G  
| No description available  
  
  
  
  
H K  
| No description available  
  
  
  
  
  
Discarding unrecognised/unsupported data array /xw941/SAD/FOM W  
Launching live xmap mgr took 2.708101272583008 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.62, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level -0.188,0.188, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_8 as #1.1.1.4, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.219, step 1, values float32  
Opened (STATIC) (dataset) FC, PHIC as #1.1.1.5, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.559, step 1, values float32  
Opened (STATIC) (dataset) FC_ALL, PHIC_ALL as #1.1.1.6, grid size 46,44,42,
pixel 0.579,0.578,0.581, shown at level -0.481,0.481, step 1, values float32  
Opened (STATIC) (dataset) FWT, PHWT as #1.1.1.7, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.433, step 1, values float32  
Opened (STATIC) (dataset) DELFWT, PHDELWT as #1.1.1.8, grid size 46,44,42,
pixel 0.579,0.578,0.581, shown at level -0.201,0.201, step 1, values float32  
Opened (STATIC) (dataset) FAN, PHAN as #1.1.1.9, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level -0.0361,0.0361, step 1, values float32  
Opened (STATIC) (dataset) DELFAN, PHDELAN as #1.1.1.10, grid size 46,44,42,
pixel 0.579,0.578,0.581, shown at level -0.0361,0.0361, step 1, values float32  
Opened (STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS as #1.1.1.11, grid size
46,44,42, pixel 0.579,0.578,0.581, shown at level -0.501,0.501, step 1, values
float32  
Chain information for 0017-01_refmacat.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B 1.2/I | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E 1.2/J | No description available  
1.2/F 1.2/L | No description available  
1.2/G | No description available  
1.2/H 1.2/K | No description available  
  
Opened crystallographic dataset from
/home/alphafold/Downloads/OneDrive_1_24-07-2024/0017-01_refmacat.mtz  
Found experimental reflection data:  
(dataset) F, SIGF  
Rwork: 0.2682; Rfree: 0.2689  
Generated maps:  
Reflection Data  
(LIVE) 2mFo-DFc  
(LIVE) mFo-DFc  
(LIVE) 2mFo-DFc_smooth_8  
(STATIC) (dataset) FC, PHIC  
(STATIC) (dataset) FC_ALL, PHIC_ALL  
(STATIC) (dataset) FWT, PHWT  
(STATIC) (dataset) DELFWT, PHDELWT  
(STATIC) (dataset) FAN, PHAN  
(STATIC) (dataset) DELFAN, PHDELAN  
(STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS  
Any unwanted maps may be safely closed via the Model panel.  

> select #1

27453 atoms, 26426 bonds, 10 pseudobonds, 4857 residues, 44 models selected  

> isolde start

> set selectionWidth 4

Removed all altlocs in #1.2 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 199 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.12, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.56, step 1, values float32  
Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> addh #1.2

Summary of feedback from adding hydrogens to 0017-01_refmacat.pdb #1.2  
---  
notes | Termini for 0017-01_refmacat.pdb (#1.2) chain A determined from SEQRES
records  
Termini for 0017-01_refmacat.pdb (#1.2) chain B determined from SEQRES records  
Termini for 0017-01_refmacat.pdb (#1.2) chain C determined from SEQRES records  
Termini for 0017-01_refmacat.pdb (#1.2) chain D determined from SEQRES records  
Termini for 0017-01_refmacat.pdb (#1.2) chain E determined from SEQRES records  
7 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A SER -1, /B MET 1, /C MET
1, /D SER 0, /E MET 1, /F MET 1, /G MET 1, /H MET 1, /I MET 1, /J MET 1, /K
MET 1, /L MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LEU 283, /B LEU 280, /C ASP
278, /D PHE 284, /E LEU 283, /F GLN 282, /G PHE 284, /H ASN 281, /I LEU 280,
/J LEU 283, /K ASN 281, /L GLN 282  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A LEU 283  
Missing OXT added to C-terminal residue /B LEU 280  
Missing OXT added to C-terminal residue /C ASP 278  
Missing OXT added to C-terminal residue /D PHE 284  
Missing OXT added to C-terminal residue /E LEU 283  
7 messages similar to the above omitted  
6545 hydrogen bonds  
28955 hydrogens added  
  
Loading residue template for DMS from internal database  
Loading residue template for ICT from internal database  

> select #1/A

4382 atoms, 4418 bonds, 286 residues, 1 model selected  

> isolde sim start /A

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/B

4310 atoms, 4346 bonds, 281 residues, 1 model selected  

> isolde sim start /B

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/C

4269 atoms, 4305 bonds, 279 residues, 1 model selected  

> isolde sim start /C

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/D

4392 atoms, 4429 bonds, 286 residues, 1 model selected  

> isolde sim start /D

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/E

4342 atoms, 4379 bonds, 283 residues, 1 model selected  

> isolde sim start /E

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 14 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/F

4342 atoms, 4378 bonds, 283 residues, 1 model selected  

> isolde sim start /F

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/G

4379 atoms, 4416 bonds, 285 residues, 1 model selected  

> isolde sim start /G

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 9 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/H

4305 atoms, 4342 bonds, 281 residues, 1 model selected  

> isolde sim start /H

ISOLDE: started sim  

> isolde sim pause

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select ~sel & ##selected

52119 atoms, 51055 bonds, 10 pseudobonds, 4576 residues, 2 models selected  

> select #1/G

4379 atoms, 4416 bonds, 285 residues, 1 model selected  

> isolde sim start /G

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1/I

4310 atoms, 4346 bonds, 281 residues, 1 model selected  

> isolde sim start /I

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 6 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/J

4343 atoms, 4380 bonds, 283 residues, 1 model selected  

> isolde sim start /J

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/K

4305 atoms, 4342 bonds, 281 residues, 1 model selected  

> isolde sim start /K

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/L

4325 atoms, 4362 bonds, 282 residues, 1 model selected  

> isolde sim start /L

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 4 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/L

4325 atoms, 4362 bonds, 282 residues, 1 model selected  

> select #1/M

11 atoms, 11 residues, 1 model selected  

> isolde sim start /M

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select #1/N

Nothing selected  

> select clear

> select #1/L

4325 atoms, 4362 bonds, 282 residues, 1 model selected  

> isolde sim start /L


===== 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 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.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 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 48 AMD Ryzen Threadripper 3960X 24-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          125Gi        63Gi        57Gi       356Mi       4.3Gi        59Gi
	Swap:          15Gi        15Gi       0.0Ki

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2231] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:147e]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    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: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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: 0.22.3
    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
    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
    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
    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: 1.5.13
    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: 1.0.3
    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-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: 1.12.3
    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: 2.2.2
    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: 1.33.2
    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: 0.2.0
    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: 4.47.0
    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: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    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: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    pprintpp: 0.4.0
    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: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    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: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9