OpenFold 3 on Linux requires CUDA 12 nvcc compiler installed

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-26.5.2-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.13.dev202607152159 (2026-07-15 21:59:48 UTC)
Description
OpenFold prediction does not work with CUDA 13 nvcc compiler.  I tried this on Trooper.ai and got this error.  On minsky the cuda compiler nvcc is at cuda 12 even though the nvidia drivers is at 13.0 and that works.  Apparently the cuda toolkit including nvcc is installed separately from the driver.  I wonder what happens if OpenFold is installed on a machine without the cuda toolkit, does it fail because no nvcc is found?

Log:
UCSF ChimeraX version: 1.13.dev202607152159 (2026-07-15)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8ef5 format mmcif fromDatabase pdb

8ef5 title:  
Fentanyl-bound mu-opioid receptor-Gi complex [more info...]  
  
Chain information for 8ef5 #1  
---  
Chain | Description | UniProt  
A F | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340  
C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_BOVIN 1-68  
E | scFv16 |   
M R | Mu-type opioid receptor | OPRM_HUMAN 2-368  
  
Non-standard residues in 8ef5 #1  
---  
7V7 — N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide  
CLR — cholesterol  
  

> ui tool show Boltz

> boltz predict protein /R name 8ef5_R useServer true serverHost
> connect01.trooper.ai serverPort 35070

Running Boltz prediction of protein with 367 residues on gpu  
Using cached multiple sequence alignment
/Users/goddard/Downloads/ChimeraX/BoltzMSA/boltz_62  
Sending job request to server (1699595 bytes)  
Server connect01.trooper.ai:35070 queued job mca2pvaa  
Confidence score 0.80, pTM 0.80, ipTM 0.00, pLDDT 0.80  
Boltz prediction completed in 243 seconds (start boltz 0 sec, sequence search
0 sec, load weights 0 sec, structure inference 0 sec)  
Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.  

> open
> /Users/goddard/Desktop/boltz/boltz_8ef5_R_2/boltz_results_8ef5_R/predictions/8ef5_R/8ef5_R_model_0.cif
> logInfo false

Matchmaker 8ef5, chain M (#1) with 8ef5_R_model_0.cif, chain R (#2), sequence
alignment score = 1815.3  
RMSD between 196 pruned atom pairs is 1.074 angstroms; (across all 288 pairs:
3.080)  
  

> hide cartoons

> hide atoms

> show cartoons

> open 24km

Summary of feedback from opening 24km fetched from pdb  
---  
note | Fetching compressed mmCIF 24km from https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/4k/pdb_000024km/structures/pdb_000024km.cif.gz  
  
24km title:  
Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with
Nimesulide [more info...]  
  
Chain information for 24km #3  
---  
Chain | Description | UniProt  
A | Bromodomain-containing protein 4 | BRD4_HUMAN 44-168  
  
Non-standard residues in 24km #3  
---  
NIM — 4-nitro-2-phenoxymethanesulfonanilide (nimesulide)  
  

> hide #2 models

> hide #!1 models

> view

> ui tool show OpenFold

> openfold predict protein #3/A ligandCcd NIM name 24km useServer true
> serverHost connect01.trooper.ai serverPort 35071

Running OpenFold prediction of protein with 128 residues, 1 ligands NIM on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Sending job request to server (787 bytes)  
Server connect01.trooper.ai:35071 queued job oiequzjo  
Running openfold prediction failed with exit code 1:  
command:  
/Users/goddard/openfold3_py311/bin/run_openfold predict --query_json=24km.json
--runner_yaml=msa_path.yaml --num_diffusion_samples=1 --device=gpu  
stdout:  
  
==================================================  
PREDICTION SUMMARY (COMPLETE)  
==================================================  
Total Queries Processed: 1  
\- Successful Queries: 0  
\- Failed Queries: 1  
  
Failed Queries: 24km  
==================================================  
  
  
stderr:  
2026-07-30 01:30:18,827 - INFO - No inference_ckpt_path or inference_ckpt_name
provided, selecting default checkpoint.  
2026-07-30 01:30:18,827 - INFO - Set diffusion samples to 1  
2026-07-30 01:30:18,857 - INFO - Setting RLIMIT_NOFILE to 32768 (was 1024)  
2026-07-30 01:30:18,857 - INFO - Setting RLIMIT_STACK to -1 (was 8388608)  
2026-07-30 01:30:18,865 - INFO - Loading weights from
/home/trooperai/.openfold3/of3-p2-155k.pt  
2026-07-30 01:30:22,557 - INFO - Finished loading weights  
2026-07-30 01:30:22,558 - INFO - Loading model state dictionary  
2026-07-30 01:31:22,439 - WARNING - No version_tensor is found for this
checkpoint.Assuming the user knows checkpoints are parameters are compatible,
continuing...  
2026-07-30 01:31:22,747 - INFO - Finished loading model state dictionary  
2026-07-30 01:31:22,751 - INFO - Beginning prediction inference  
2026-07-30 01:31:22,753 - INFO - Using bfloat16 Automatic Mixed Precision
(AMP)  
2026-07-30 01:31:22,759 - INFO - GPU available: True (cuda), used: True  
2026-07-30 01:31:22,759 - INFO - TPU available: False, using: 0 TPU cores  
2026-07-30 01:31:22,759 - INFO - 💡 Tip: For seamless cloud logging and
experiment tracking, try installing
[litlogger](https://pypi.org/project/litlogger/) to enable LitLogger, which
logs metrics and artifacts automatically to the Lightning Experiments
platform.  
2026-07-30 01:31:22,769 - INFO - 💡 Tip: For seamless cloud uploads and
versioning, try installing [litmodels](https://pypi.org/project/litmodels/) to
enable LitModelCheckpoint, which syncs automatically with the Lightning model
registry.  
2026-07-30 01:31:22,877 - INFO - Using output directory: colabfold_msas for
ColabFold MSAs.  
2026-07-30 01:31:22,877 - INFO - Submitting 1 sequences to the Colabfold MSA
server for main MSAs...  
  
0%| | 0/150 [elapsed: 00:00 remaining: ?]  
SUBMIT: 0%| | 0/150 [elapsed: 00:00 remaining: ?]  
PENDING: 0%| | 0/150 [elapsed: 00:00 remaining: ?]2026-07-30 01:31:23,622 - INFO - Sleeping for 9s. Reason: PENDING  
  
PENDING: 0%| | 0/150 [elapsed: 00:10 remaining: ?]2026-07-30 01:31:33,361 - INFO - Sleeping for 7s. Reason: PENDING  
  
PENDING: 0%| | 0/150 [elapsed: 00:19 remaining: ?]2026-07-30 01:31:42,099 - INFO - Sleeping for 9s. Reason: PENDING  
  
RUNNING: 0%| | 0/150 [elapsed: 00:28 remaining: ?]  
RUNNING: 6%|▌ | 9/150 [elapsed: 00:28 remaining: 07:33]2026-07-30 01:31:51,825 - INFO - Sleeping for 5s. Reason: RUNNING  
  
RUNNING: 6%|▌ | 9/150 [elapsed: 00:34 remaining: 07:33]  
RUNNING: 9%|▉ | 14/150 [elapsed: 00:34 remaining: 05:12]2026-07-30 01:31:57,539 - INFO - Sleeping for 10s. Reason: RUNNING  
  
RUNNING: 9%|▉ | 14/150 [elapsed: 00:45 remaining: 05:12]  
RUNNING: 16%|█▌ | 24/150 [elapsed: 00:45 remaining: 03:23]2026-07-30 01:32:08,250 - INFO - Sleeping for 10s. Reason: RUNNING  
  
RUNNING: 16%|█▌ | 24/150 [elapsed: 00:56 remaining: 03:23]  
RUNNING: 23%|██▎ | 34/150 [elapsed: 00:56 remaining: 02:39]2026-07-30 01:32:18,960 - INFO - Sleeping for 5s. Reason: RUNNING  
  
RUNNING: 23%|██▎ | 34/150 [elapsed: 01:01 remaining: 02:39]  
RUNNING: 26%|██▌ | 39/150 [elapsed: 01:01 remaining: 02:26]2026-07-30 01:32:24,703 - INFO - Sleeping for 5s. Reason: RUNNING  
  
RUNNING: 26%|██▌ | 39/150 [elapsed: 01:07 remaining: 02:26]  
RUNNING: 29%|██▉ | 44/150 [elapsed: 01:07 remaining: 02:15]2026-07-30 01:32:30,568 - INFO - Sleeping for 10s. Reason: RUNNING  
  
RUNNING: 29%|██▉ | 44/150 [elapsed: 01:18 remaining: 02:15]  
RUNNING: 36%|███▌ | 54/150 [elapsed: 01:18 remaining: 01:54]2026-07-30 01:32:41,298 - INFO - Sleeping for 7s. Reason: RUNNING  
  
COMPLETE: 36%|███▌ | 54/150 [elapsed: 01:26 remaining: 01:54]  
COMPLETE: 100%|██████████| 150/150 [elapsed: 01:26 remaining: 00:00]  
COMPLETE: 100%|██████████| 150/150 [elapsed: 01:32 remaining: 00:00]  
2026-07-30 01:32:56,113 - INFO - Preprocessing templates for 1 chains  
  
Preprocessing templates: 0%| | 0/1 [00:00<?, ?it/s]  
Preprocessing templates: 100%|██████████| 1/1 [00:13<00:00, 13.14s/it]  
Preprocessing templates: 100%|██████████| 1/1 [00:13<00:00, 13.14s/it]  
2026-07-30 01:33:09,738 - INFO - Finished preprocessing templates  
2026-07-30 01:33:10,392 - INFO - LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]  
2026-07-30 01:33:10,812 - INFO - Seeding DataModule DatasetMode.prediction
generator with 42  
/home/trooperai/openfold3/lib/python3.10/site-
packages/pytorch_lightning/utilities/_pytree.py:21: `isinstance(treespec,
LeafSpec)` is deprecated, use `isinstance(treespec, TreeSpec) and
treespec.is_leaf()` instead.  
/home/trooperai/openfold3/lib/python3.10/site-
packages/pytorch_lightning/trainer/connectors/data_connector.py:434: The
'predict_dataloader' does not have many workers which may be a bottleneck.
Consider increasing the value of the `num_workers` argument` to
`num_workers=5` in the `DataLoader` to improve performance.  
2026-07-30 01:33:10,885 - INFO - Creating features for 24km  
2026-07-30 01:33:15,269 - INFO - Finished creating features for 24km  
2026-07-30 01:33:15,331 - INFO - Seed set to 42  
2026-07-30 01:33:15,334 - INFO - Started inference for 24km (1) on rank 0 step
0  
/home/trooperai/openfold3/lib/python3.10/site-
packages/cutlass/library_defaults.py:40: FutureWarning: accessing
cuda.__version__ is deprecated, please switch to use cuda.bindings.__version__
instead  
from cuda import __version__  
<frozen importlib._bootstrap_external>:1184: FutureWarning: The cuda.cuda
module is deprecated and will be removed in a future release, please switch to
use the cuda.bindings.driver module instead.  
<frozen importlib._bootstrap_external>:1184: FutureWarning: The cuda.cudart
module is deprecated and will be removed in a future release, please switch to
use the cuda.bindings.runtime module instead.  
<frozen importlib._bootstrap_external>:1184: FutureWarning: The cuda.nvrtc
module is deprecated and will be removed in a future release, please switch to
use the cuda.bindings.nvrtc module instead.  
/home/trooperai/openfold3/lib/python3.10/site-
packages/cutlass/backend/operation.py:35: FutureWarning: accessing
cuda.__version__ is deprecated, please switch to use cuda.bindings.__version__
instead  
from cuda import __version__, cuda  
2026-07-30 01:33:16,573 - ERROR - Failed for query_id(s) 24km: Python CUDA
version of 12.9.4 must be greater than or equal to NVCC version of 13.0. See
logs/predict_err_rank0.log for details.  
/home/trooperai/openfold3/lib/python3.10/site-
packages/pytorch_lightning/loops/prediction_loop.py:257: predict returned None
if it was on purpose, ignore this warning...  
2026-07-30 01:33:17,289 - INFO - Finished prediction inference  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.14.6
Locale: C.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 Performance and 8 Efficiency)
      Memory: 64 GB
      System Firmware Version: 18000.121.3
      OS Loader Version: 18000.121.3

Software:

    System Software Overview:

      System Version: macOS 26.5.2 (25F84)
      Kernel Version: Darwin 25.5.0
      Time since boot: 30 days, 22 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.7.1
    aiohttp: 3.11.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.14.2
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.2
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.8.1
    build: 1.5.0
    certifi: 2026.6.17
    cftime: 1.6.5
    charset-normalizer: 3.4.9
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.3.1
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2.2
    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: 1.70.2
    ChimeraX-AtomicLibrary: 14.4.2
    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: 1.13.dev202607152159
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.6
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.3
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.2
    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: 2.5.4
    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: 1.8.5
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    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: 1.2.1
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.4.3
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.17
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.24
    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-NMRSTAR: 1.0.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.16.2
    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-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.10.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.3
    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: 1.5.3
    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: 2.19.1
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.20
    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: 1.53.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.5
    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: 8.4.2
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.15.2
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 1.0.1
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h2: 4.3.0
    h5py: 3.16.0
    hpack: 4.2.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    hyperframe: 6.1.0
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2026.6.26
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.3.0
    ipython: 9.14.1
    ipython_pygments_lexers: 1.1.1
    jedi: 0.20.0
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.9.1
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.4.5
    Markdown: 3.8.2
    markdown-it-py: 4.2.0
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    maturin: 1.14.1
    mcp: 1.18.0
    mdurl: 0.1.2
    msgpack: 1.1.1
    multidict: 6.7.1
    ndindex: 1.10.1
    nest-asyncio2: 1.7.2
    netCDF4: 1.7.4
    networkx: 3.3
    numexpr: 2.14.1
    numpy: 2.4.6
    OpenMM: 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: 12.3.0
    pip: 26.1.2
    pkginfo: 1.12.1.2
    platformdirs: 4.10.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    ptyprocess: 0.7.0
    puccinialin: 0.1.13
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.2
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.20.0
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    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: 6.10.2
    PyQt6-WebEngine: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.1.1
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pyzmq: 27.1.0
    qtconsole: 5.7.2
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    rich: 15.0.0
    roman-numerals: 4.1.0
    rpds-py: 2026.6.3
    scipy: 1.18.0
    setuptools: 82.0.1
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    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: 3.4.5
    stack-data: 0.6.3
    starlette: 1.3.1
    superqt: 0.7.6
    tables: 3.11.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.7
    tqdm: 4.68.4
    traitlets: 5.15.1
    typing-inspection: 0.4.2
    typing_extensions: 4.16.0
    urllib3: 2.7.0
    uv: 0.11.26
    uvicorn: 0.51.0
    wcwidth: 0.8.2
    webcolors: 24.11.1
    wheel: 0.47.0
    wheel-filename: 1.4.2
    yarl: 1.24.2

[Tom Goddard]

Should probably catch this error of no nvcc or wrong nvcc version and give a clear error message about how the user installs the cuda toolkit to fix it.

Also should update ChimeraX OpenFold so it can work with Cuda 13 nvcc. Or maybe current OpenFold 3 does not need nvcc. Needs investigation.