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Opened 2 days ago
#19177 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
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Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Per defaut Isolde is not "using" my Nvidia GPU although ChimeraX uses it for 3D rendering. When I use the command "isolde set gpuDeviceIndex 1" I get the following error as soon as I start a simulation with Isolde:
isolde set gpuDeviceIndex 1
isolde sim start /A-T
Traceback (most recent call last): File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\toolbar\tool.py", line 230, in callback bundle_info.run_provider(session, name, session.toolbar, display_name=display_name) File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\toolshed\info.py", line 397, in run_provider return api._api_caller.run_provider(api, session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 1419, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\__init__.py", line 166, in run_provider toolbar_command(session, name) File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\toolbar.py", line 23, in toolbar_command run(session, f'isolde sim start {_current_residue_sel_string(session)}') File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\commands\run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\chimerax\core\commands\cli.py", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim isolde.start_sim() File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\isolde.py", line 896, in start_sim sm.start_sim() File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim sh.start_sim() File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim self._prepare_sim() File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in _prepare_sim s = self._simulation = app.Simulation(self.topology, self._system, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\openmm\app\simulation.py", line 106, in __init__ self.context = mm.Context(self.system, self.integrator, platform, platformProperties) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\openmm\openmm.py", line 5082, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) ^^^^^^^^^^^^^^^^^^^^^^^^^^ openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex. When multiple platforms are available, a platform index is needed to specify a device. File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-packages\openmm\openmm.py", line 5082, in __init__ _openmm.Context_swiginit(self, _openmm.new_Context(*args)) ^^^^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback.
Log:
> functionkey F1 save session.cxs
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> C:\Users\simon\Nextcloud\Dokumente\Promotion\Auswertungen\Insulin_Fibrils\reconstruction-20230721-SiSo-
> Ins_Glarg_Dil_2_Acqui_Grid2_2\atomic_model_building\pmL1\models\5layers.pdb
> format pdb
Chain information for 5layers.pdb #1
---
Chain | Description
A C E G I K M O Q S | No description available
B D F H J L N P R T | No description available
> lighting full
> isolde set
> set selectionWidth 4
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
> help islode
No help found for 'islode'
> help isolde
> isolde set gpuDeviceIndex 1
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for 5layers.pdb
---
Chain | Description
1.2/A 1.2/C 1.2/E 1.2/G 1.2/I 1.2/K 1.2/M 1.2/O 1.2/Q 1.2/S | No description available
1.2/B 1.2/D 1.2/F 1.2/H 1.2/J 1.2/L 1.2/N 1.2/P 1.2/R 1.2/T | No description available
> open
> C:/Users/simon/Nextcloud/Dokumente/Promotion/Auswertungen/Insulin_Fibrils/reconstruction-20230721-SiSo-
> Ins_Glarg_Dil_2_Acqui_Grid2_2/atomic_model_building/pmL1/models/maps/job458_postprocess_masked-
> rhsymp-5layers_boxed.mrc
Opened job458_postprocess_masked-rhsymp-5layers_boxed.mrc as #2, grid size
320,320,320, pixel 1.02, shown at level 5.45e-06, step 2, values float32
> volume #2 step 1
> volume #2 level 5.451e-06
> volume #2 level 0.02462
> clipper associate #2 toModel #1
Opened job458_postprocess_masked-rhsymp-5layers_boxed.mrc as #1.1.1.1, grid
size 320,320,320, pixel 1.02, shown at step 1, values float32
> set bgColor gray
> set bgColor #80808000
> isolde sim start /A-T
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\\__init__.py", line 166, in run_provider
toolbar_command(session, name)
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\toolbar.py", line 23, in toolbar_command
run(session, f'isolde sim start {_current_residue_sel_string(session)}')
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim
isolde.start_sim()
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim
sm.start_sim()
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim
sh.start_sim()
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim
self._prepare_sim()
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\app\simulation.py", line 106, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> isolde set gpuDeviceIndex 1
> isolde sim start /A-T
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\toolbar\tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\\__init__.py", line 166, in run_provider
toolbar_command(session, name)
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\toolbar.py", line 23, in toolbar_command
run(session, f'isolde sim start {_current_residue_sel_string(session)}')
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim
isolde.start_sim()
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim
sm.start_sim()
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim
sh.start_sim()
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim
self._prepare_sim()
File "C:\Users\simon\AppData\Local\UCSF\ChimeraX\1.10\Python311\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1377, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\app\simulation.py", line 106, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
openmm.OpenMMException: Specified DeviceIndex but not OpenCLPlatformIndex.
When multiple platforms are available, a platform index is needed to specify a
device.
File "C:\Program Files\ChimeraX 1.10.1\bin\Lib\site-
packages\openmm\openmm.py", line 5082, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 581.42
OpenGL renderer: NVIDIA GeForce RTX 3050 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: de_DE.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: XPS 15 9520
OS: Microsoft Windows 11 Home (Build 26100)
Memory: 16,834,945,024
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700H
OSLanguage: de-DE
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
WMI: 1.5.1
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