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Opened 3 hours ago
#20831 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-6.17.0-1030-oem-x86_64-with-glibc2.39
ChimeraX Version: 1.12rc202605142114 (2026-05-14 21:14:16 UTC)
Description
I'm trying to run Boltz2 in Chimera and the installation went fine. However, I'm getting the error in the attached file. I have triton 3.3.0 installed as shown below.
(base) swlovell@crystal15:~$ python -c "import triton; print(triton.__version__)"
3.3.0
Log:
Startup Messages
---
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.
UCSF ChimeraX version: 1.12rc202605142114 (2026-05-14)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
dbus reply error: [ "org.freedesktop.DBus.Error.UnknownMethod" ] "No such
interface “org.freedesktop.portal.Settings” on object at path
/org/freedesktop/portal/desktop"
[Repeated 1 time(s)]
> open
> /home/swlovell/structures/Gonzalez_Lina/TANGO2/PDBs/TANGO2_Protein_no_OCS.pdb
> format pdb
Chain information for TANGO2_Protein_no_OCS.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> ui tool show Boltz
> boltz predict protein
> CIIFFKFDPRPVSKNAYRLILAANRDEFYSRPSKLADFWGNNNEILSGLDMEEGKEGGTWLGISTRGKLAALTNYLQPQLDWQARGRGELVTHFLTTDVDSLSYLKKVSMEGHLYNGFNLIAADLSTAKGDVICYYGNRGEPDPIVLTPGTYGLSNALLETPWRKLCFGKQLFLEAVERSQALPKDVLIASLLDVLNNEEAQLPDPAIEDQGGEYVQPMLSKYAAVCVRCPGYGTRTNTIILVDADGHVTFTERSMMDKDLSHWETRTYEFTLQS
> ligandSmiles
> C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
> resultsDirectory
> /home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/
> affinity
> C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
> steering true
Boltz prediction directory
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/
already exists. Files will be overwritten.
Running Boltz prediction of protein with 275 residues, 1 ligands
C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
on gpu
Using cached multiple sequence alignment
/home/swlovell/Downloads/ChimeraX/BoltzMSA/TANGO2_lithocholic
Running boltz prediction failed with exit code 0:
command:
/home/swlovell/boltz22/bin/boltz predict
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/.yaml
--use_potentials --accelerator gpu
stdout:
Boltz version 2.2.0
Checking input data.
Processing 1 inputs with 1 threads.
Failed to process
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/.yaml.
Skipping. Error: Unable to parse filetype , please provide a .fasta or .yaml
file..
stderr:
0%| | 0/1 [00:00<?, ?it/s]Traceback (most recent call last):
File "/home/swlovell/boltz22/lib/python3.11/site-packages/boltz/main.py", line
553, in process_input
raise RuntimeError(msg) # noqa: TRY301
^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: Unable to parse filetype , please provide a .fasta or .yaml
file.
100%|██████████| 1/1 [00:00<00:00, 6765.01it/s]
Using bfloat16 Automatic Mixed Precision (AMP)
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76:
Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the
`pytorch_lightning` package, due to potential conflicts with other packages in
the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the
default logger, unless the `tensorboard` or `tensorboardX` packages are found.
Please `pip install lightning[extra]` or one of them to enable TensorBoard
support by default
> boltz predict protein
> CIIFFKFDPRPVSKNAYRLILAANRDEFYSRPSKLADFWGNNNEILSGLDMEEGKEGGTWLGISTRGKLAALTNYLQPQLDWQARGRGELVTHFLTTDVDSLSYLKKVSMEGHLYNGFNLIAADLSTAKGDVICYYGNRGEPDPIVLTPGTYGLSNALLETPWRKLCFGKQLFLEAVERSQALPKDVLIASLLDVLNNEEAQLPDPAIEDQGGEYVQPMLSKYAAVCVRCPGYGTRTNTIILVDADGHVTFTERSMMDKDLSHWETRTYEFTLQS
> ligandSmiles
> C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
> name TANGO2_lithocholic_acid resultsDirectory
> /home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/
> affinity
> C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
> steering true
Boltz prediction directory
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/
already exists. Files will be overwritten.
Running Boltz prediction of protein with 275 residues, 1 ligands
C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
on gpu
Using cached multiple sequence alignment
/home/swlovell/Downloads/ChimeraX/BoltzMSA/TANGO2_lithocholic
Running boltz prediction failed with exit code 1:
command:
/home/swlovell/boltz22/bin/boltz predict
/home/swlovell/structures/Gonzalez_Lina/TANGO2/Docking/boltz2/Lithocholic_acid/TANGO2_lithocholic_acid.yaml
--use_potentials --accelerator gpu
stdout:
Boltz version 2.2.0
Checking input data.
All inputs are already processed.
Processing 0 inputs with 0 threads.
Running structure prediction for 1 input.
Predicting: | | 0/? [00:00<?, ?it/s] Predicting: 0%| | 0/1 [00:00<?, ?it/s] Predicting DataLoader 0: 0%| | 0/1 [00:00<?, ?it/s] Predicting DataLoader 0: 0%| | 0/1 [00:01<?, ?it/s]
stderr:
0it [00:00, ?it/s] 0it [00:00, ?it/s]
Using bfloat16 Automatic Mixed Precision (AMP)
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76:
Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the
`pytorch_lightning` package, due to potential conflicts with other packages in
the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the
default logger, unless the `tensorboard` or `tensorboardX` packages are found.
Please `pip install lightning[extra]` or one of them to enable TensorBoard
support by default
Fri Aug 7 05:37:27 2026: Loading Boltz structure prediction weights
/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/utilities/migration/utils.py:56: The loaded
checkpoint was produced with Lightning v2.5.0.post0, which is newer than your
current Lightning version: v2.5.0
Fri Aug 7 05:37:38 2026: Finished loading Boltz structure prediction weights
Fri Aug 7 05:37:38 2026: Starting structure inference
You are using a CUDA device ('NVIDIA RTX PRO 4500 Blackwell') that has Tensor Cores. To properly utilize them, you should set `torch.set_float32_matmul_precision('medium' | 'high')` which will trade-off precision for performance. For more details, read https://pytorch.org/docs/stable/generated/torch.set_float32_matmul_precision.html#torch.set_float32_matmul_precision
LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
Fri Aug 7 05:37:39 2026: Begin structure inference TANGO2_lithocholic_acid (1
of 1)
Traceback (most recent call last):
File "/home/swlovell/boltz22/bin/boltz", line 8, in <module>
sys.exit(cli())
^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
1078, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/click/core.py", line
783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-packages/boltz/main.py", line
1355, in predict
trainer.predict(
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 859, in predict
return call._call_and_handle_interrupt(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/call.py", line 47, in
_call_and_handle_interrupt
return trainer_fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 898, in _predict_impl
results = self._run(model, ckpt_path=ckpt_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 982, in _run
results = self._run_stage()
^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 1021, in _run_stage
return self.predict_loop.run()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/loops/utilities.py", line 179, in _decorator
return loop_run(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/loops/prediction_loop.py", line 125, in run
self._predict_step(batch, batch_idx, dataloader_idx, dataloader_iter)
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/loops/prediction_loop.py", line 255, in
_predict_step
predictions = call._call_strategy_hook(trainer, "predict_step", *step_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/trainer/call.py", line 323, in _call_strategy_hook
output = fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/pytorch_lightning/strategies/strategy.py", line 438, in predict_step
return self.lightning_module.predict_step(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/models/boltz2.py", line 1059, in predict_step
out = self(
^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/models/boltz2.py", line 464, in forward
z = z + template_module(
^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/modules/trunkv2.py", line 498, in forward
v = v + self.pairformer(v, pair_mask, use_kernels=use_kernels)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/layers/pairformer.py", line 329, in forward
z = layer(
^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/layers/pairformer.py", line 243, in forward
z = z + dropout * self.tri_mul_out(
^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
return self._call_impl(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1762, in _call_impl
return forward_call(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/layers/triangular_mult.py", line 92, in forward
return kernel_triangular_mult(
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/_dynamo/eval_frame.py", line 838, in _fn
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/boltz/model/layers/triangular_mult.py", line 23, in
kernel_triangular_mult
return triangle_multiplicative_update(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_torch/primitives/triangle.py", line 314, in
triangle_multiplicative_update
return f(
^^
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/__init__.py", line 97, in
triangle_multiplicative_update
_raise_triton_import_error("triangle_multiplicative_update")
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/__init__.py", line 91, in
_raise_triton_import_error
raise Exception(
Exception: Failed to import Triton-based component:
triangle_multiplicative_update:
Traceback (most recent call last):
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/attention_pair_bias.py", line 27, in
<module>
from torch.fx._symbolic_trace import is_fx_symbolic_tracing
ImportError: cannot import name 'is_fx_symbolic_tracing' from
'torch.fx._symbolic_trace' (/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/fx/_symbolic_trace.py)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/__init__.py", line 64, in <module>
from cuequivariance_ops_torch.attention_pair_bias import (
File "/home/swlovell/boltz22/lib/python3.11/site-
packages/cuequivariance_ops_torch/attention_pair_bias.py", line 29, in
<module>
from torch.fx._symbolic_trace import (
ImportError: cannot import name 'is_fx_tracing_symbolic_tracing' from
'torch.fx._symbolic_trace' (/home/swlovell/boltz22/lib/python3.11/site-
packages/torch/fx/_symbolic_trace.py)
Please make sure to install triton==3.3.0. Other versions may not work!
sys:1: DeprecationWarning: builtin type swigvarlink has no __module__
attribute
OpenGL version: 3.3.0 NVIDIA 580.173.02
OpenGL renderer: NVIDIA RTX PRO 4500 Blackwell/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=xfce
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: Dell Inc.
Model: Dell Pro Max Tower T2 FCT2250
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 Intel(R) Core(TM) Ultra 9 285K
Cache Size: 36864 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 7.2Gi 98Gi 373Mi 21Gi 118Gi
Swap: 8.0Gi 0B 8.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation Arrow Lake-U [Intel Graphics] [8086:7d67] (rev 06)
Subsystem: Dell Device [1028:0ce1]
Kernel driver in use: i915
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
biopython: 1.83
blockdiag: 3.0.0
blosc2: 4.2.0
bs4: 0.0.2
build: 1.3.0
certifi: 2026.4.22
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
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: 1.67.1
ChimeraX-AtomicLibrary: 14.4
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: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12rc202605142114
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: 1.2.1
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: 1.4.1
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.6.4
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
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: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.6
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 8.4.0
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.3.1
DiffFit: 0.7.0
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
fsspec: 2026.4.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.15
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
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: 0.2.2
mcp: 1.18.0
MolecularDynamicsViewer: 1.6
mpmath: 1.3.0
mrcfile: 1.5.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.21.2
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: 2.4.6
numpy: 1.26.4
nvidia-cublas-cu12: 12.1.3.1
nvidia-cuda-cupti-cu12: 12.1.105
nvidia-cuda-nvrtc-cu12: 12.1.105
nvidia-cuda-runtime-cu12: 12.1.105
nvidia-cudnn-cu12: 8.9.2.26
nvidia-cufft-cu12: 11.0.2.54
nvidia-curand-cu12: 10.3.2.106
nvidia-cusolver-cu12: 11.4.5.107
nvidia-cusparse-cu12: 12.1.0.106
nvidia-nccl-cu12: 2.19.3
nvidia-nvjitlink-cu12: 12.9.86
nvidia-nvtx-cu12: 12.1.105
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
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: 4.9.6
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
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: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.3
pynmrstar: 3.5.1
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: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.29
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 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: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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: 3.4.4
stack-data: 0.6.3
starlette: 1.0.0
superqt: 0.7.6
sympy: 1.14.0
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.15.1
torch: 2.2.1
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
triton: 2.2.0
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.47.0
wcwidth: 0.7.0
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.23.0
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