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Opened 78 minutes ago
#20337 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Linux-6.17.0-23-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Selected a chain of my model and started the simulation, then got the error.
Log:
Startup Messages
---
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.
> camera ortho
> lighting simple shadows false depthCue false
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> isolde start
> set selectionWidth 4
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
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
> open
> /home/mickey/Desktop/20260515_MaPkA_1mMAMPPNP-2mMF6P_pH7.4/cryosparc_P950_J41_010_volume_map.mrc
Opened cryosparc_P950_J41_010_volume_map.mrc as #1, grid size 384,384,384,
pixel 0.866, shown at level 0.0497, step 2, values float32
> volume #1 step 1
> volume #1 level 0.0815
> open
> /home/mickey/Desktop/20260515_MaPkA_1mMAMPPNP-2mMF6P_pH7.4/cryosparc_P950_J41_010_volume_map.mrc
Opened cryosparc_P950_J41_010_volume_map.mrc as #2, grid size 384,384,384,
pixel 0.866, shown at level 0.0497, step 2, values float32
> close #2
> open
> /home/mickey/Desktop/20260515_MaPkA_1mMAMPPNP-2mMF6P_pH7.4/20251007_MaPfkA_aFBP_isolde_v1_filament.pdb
Chain information for 20251007_MaPfkA_aFBP_isolde_v1_filament.pdb #2
---
Chain | Description
A B C D E F G H I J K L | No description available
> close #2
> open
> /home/mickey/Desktop/20260515_MaPkA_1mMAMPPNP-2mMF6P_pH7.4/20260515_MaPfkA_AMPPNP-F6P
'/home/mickey/Desktop/20260515_MaPkA_1mMAMPPNP-2mMF6P_pH7.4/20260515_MaPfkA_AMPPNP-F6P'
has no suffix
> open
> /home/mickey/Desktop/20260515_MaPkA_1mMAMPPNP-2mMF6P_pH7.4/20260515_MaPfkA_AMPPNP-F6P
'/home/mickey/Desktop/20260515_MaPkA_1mMAMPPNP-2mMF6P_pH7.4/20260515_MaPfkA_AMPPNP-F6P'
has no suffix
> open
> /home/mickey/Desktop/20260515_MaPkA_1mMAMPPNP-2mMF6P_pH7.4/20250515_MaPfkA_AMPPNP-F6P_v1.pdb
Chain information for 20250515_MaPfkA_AMPPNP-F6P_v1.pdb #2
---
Chain | Description
A B C D E F G H I J K L | No description available
> hide atoms
> show ribbons
> view orient
> select #2
63024 atoms, 63540 bonds, 4152 residues, 1 model selected
> move y -1 models sel
[Repeated 44 time(s)]
> move z 1 models sel
[Repeated 43 time(s)]
> move z -1 models sel
[Repeated 95 time(s)]
> move x -1 models sel
[Repeated 48 time(s)]
> fitmap sel inMap #1
Fit molecule 20250515_MaPfkA_AMPPNP-F6P_v1.pdb (#2) to map
cryosparc_P950_J41_010_volume_map.mrc (#1) using 63024 atoms
average map value = 0.07251, steps = 84
shifted from previous position = 5.37
rotated from previous position = 0.0101 degrees
atoms outside contour = 38971, contour level = 0.081505
Position of 20250515_MaPfkA_AMPPNP-F6P_v1.pdb (#2) relative to
cryosparc_P950_J41_010_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
1.00000000 0.00004105 -0.00001647 -47.50278150
-0.00004105 0.99999998 -0.00017138 -47.44899245
0.00001647 0.00017138 0.99999999 -47.53006511
Axis 0.96826853 -0.09306054 -0.23193922
Axis point 0.00000000 318664.08554356 -293485.50479240
Rotation angle (degrees) 0.01014115
Shift along axis -30.55573343
> delete :FBP
> show :FBP atoms
> select clear
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time
Chain information for 20250515_MaPfkA_AMPPNP-F6P_v1.pdb #2.2
---
Chain | Description
A B C D E F G H I J K L | No description available
> clipper associate #1 toModel #2
Opened cryosparc_P950_J41_010_volume_map.mrc as #2.1.1.1, grid size
384,384,384, pixel 0.866, shown at step 1, values float32
> select /A
5218 atoms, 5261 bonds, 345 residues, 1 model selected
> volume #2.1.1.1 level 0.106
> volume #2.1.1.1 level 0.0777
> isolde sim start /A
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 166, in run_provider
toolbar_command(session, name)
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 23, in toolbar_command
run(session, f'isolde sim start {_current_residue_sel_string(session)}')
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim
isolde.start_sim()
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim
sm.start_sim()
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 409, in start_sim
sh.start_sim()
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1453, in start_sim
self._prepare_sim()
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1398, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/simulation.py", line 106, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 15354, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 15354, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> isolde sim start /A
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 166, in run_provider
toolbar_command(session, name)
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 23, in toolbar_command
run(session, f'isolde sim start {_current_residue_sel_string(session)}')
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim
isolde.start_sim()
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/isolde.py", line 896, in start_sim
sm.start_sim()
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 409, in start_sim
sh.start_sim()
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1453, in start_sim
self._prepare_sim()
File "/home/mickey/.local/share/ChimeraX/1.11/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1398, in
_prepare_sim
s = self._simulation = app.Simulation(self.topology, self._system,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/simulation.py", line 106, in __init__
self.context = mm.Context(self.system, self.integrator, platform,
platformProperties)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 15354, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
openmm.OpenMMException: Error initializing context: clCreateContext (-5)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/openmm/openmm.py",
line 15354, in __init__
_openmm.Context_swiginit(self, _openmm.new_Context(*args))
^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 535.288.01
OpenGL renderer: Quadro P2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3650 Tower
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 11th Gen Intel(R) Core(TM) i7-11700K @ 3.60GHz
Cache Size: 16384 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 7.5Gi 14Gi 158Mi 9.1Gi 23Gi
Swap: 8.0Gi 0B 8.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation RocketLake-S GT1 [UHD Graphics 750] [8086:4c8a] (rev 04)
DeviceName: OnBoard - Video
Subsystem: Dell RocketLake-S GT1 [UHD Graphics 750] [1028:0a58]
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2026.1.4
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
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: 0.26.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
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: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ISOLDE: 1.11.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
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: 1.0.1
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: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
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: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
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
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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