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Opened 6 days ago
Closed 5 days ago
#19699 closed defect (duplicate)
boltz predict: RuntimeError
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.12.dev202601052311 (2026-01-05 23:11:53 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.12.dev202601052311 (2026-01-05)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Boltz
> boltz install /Users/krendu/boltz22
Successfully created Boltz Python virtual environment /Users/krendu/boltz22.
Now installing Boltz and required packages from PyPi. This may take tens of of
minutes since Boltz uses many other packages totaling about 1 Gbyte of disk
space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb,
numba...
/Users/krendu/boltz22/bin/python -m pip install
https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Collecting https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Downloading https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
\- 2.3 MB 6.2 MB/s 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting torch==2.7.1 (from boltz==2.2.0)
Downloading torch-2.7.1-cp311-none-macosx_11_0_arm64.whl.metadata (29 kB)
Requirement already satisfied: numpy<2.0,>=1.26 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from boltz==2.2.0) (1.26.4)
Collecting hydra-core==1.3.2 (from boltz==2.2.0)
Downloading hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)
Collecting pytorch-lightning==2.5.0 (from boltz==2.2.0)
Downloading pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB)
Collecting rdkit>=2024.3.2 (from boltz==2.2.0)
Downloading rdkit-2025.9.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.2 kB)
Collecting dm-tree==0.1.8 (from boltz==2.2.0)
Downloading dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl.metadata (1.9 kB)
Collecting requests==2.32.3 (from boltz==2.2.0)
Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting pandas>=2.2.2 (from boltz==2.2.0)
Downloading pandas-2.3.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (91 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91.2/91.2 kB 5.7 MB/s eta 0:00:00
Collecting types-requests (from boltz==2.2.0)
Downloading types_requests-2.32.4.20250913-py3-none-any.whl.metadata (2.0 kB)
Collecting einops==0.8.0 (from boltz==2.2.0)
Downloading einops-0.8.0-py3-none-any.whl.metadata (12 kB)
Collecting einx==0.3.0 (from boltz==2.2.0)
Downloading einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)
Collecting fairscale==0.4.13 (from boltz==2.2.0)
Downloading fairscale-0.4.13.tar.gz (266 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 266.3/266.3 kB 11.0 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting mashumaro==3.14 (from boltz==2.2.0)
Downloading mashumaro-3.14-py3-none-any.whl.metadata (114 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 114.4/114.4 kB 12.9 MB/s eta 0:00:00
Collecting modelcif==1.2 (from boltz==2.2.0)
Downloading modelcif-1.2.tar.gz (66 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.8/66.8 kB 8.8 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting wandb==0.18.7 (from boltz==2.2.0)
Downloading wandb-0.18.7-py3-none-macosx_11_0_arm64.whl.metadata (9.7 kB)
Collecting click==8.1.7 (from boltz==2.2.0)
Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting pyyaml==6.0.2 (from boltz==2.2.0)
Downloading PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.1 kB)
Collecting biopython==1.84 (from boltz==2.2.0)
Downloading biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl.metadata (12 kB)
Collecting scipy==1.13.1 (from boltz==2.2.0)
Downloading scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (60 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 5.0 MB/s eta 0:00:00
Collecting numba==0.61.0 (from boltz==2.2.0)
Downloading numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.7 kB)
Collecting gemmi==0.6.5 (from boltz==2.2.0)
Downloading gemmi-0.6.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.3 kB)
Collecting scikit-learn==1.6.1 (from boltz==2.2.0)
Downloading scikit_learn-1.6.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (31
kB)
Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.2.0)
Downloading chembl_structure_pipeline-1.2.2-py3-none-any.whl.metadata (3.9 kB)
Collecting cuequivariance_torch>=0.5.0 (from boltz==2.2.0)
Downloading cuequivariance_torch-0.8.0-py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: setuptools>=46.4.0 in
/Users/krendu/boltz22/lib/python3.11/site-packages (from
chembl_structure_pipeline==1.2.2->boltz==2.2.0) (65.5.0)
Collecting sympy (from einx==0.3.0->boltz==2.2.0)
Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB)
Collecting frozendict (from einx==0.3.0->boltz==2.2.0)
Downloading frozendict-2.4.7-py3-none-any.whl.metadata (23 kB)
Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==2.2.0)
Downloading omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB)
Collecting antlr4-python3-runtime==4.9.* (from hydra-
core==1.3.2->boltz==2.2.0)
Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.0/117.0 kB 12.4 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: packaging in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from hydra-core==1.3.2->boltz==2.2.0) (25.0)
Requirement already satisfied: typing-extensions>=4.1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from mashumaro==3.14->boltz==2.2.0) (4.15.0)
Requirement already satisfied: ihm>=1.7 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from modelcif==1.2->boltz==2.2.0) (2.2)
Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==2.2.0)
Downloading llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.8
kB)
Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)
Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.7/57.7 kB 6.5 MB/s eta 0:00:00
Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Downloading fsspec-2025.12.0-py3-none-any.whl.metadata (10 kB)
Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)
Downloading torchmetrics-1.8.2-py3-none-any.whl.metadata (22 kB)
Collecting lightning-utilities>=0.10.0 (from pytorch-
lightning==2.5.0->boltz==2.2.0)
Downloading lightning_utilities-0.15.2-py3-none-any.whl.metadata (5.7 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (2.6.2)
Requirement already satisfied: certifi>=2017.4.17 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (2025.7.14)
Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.2.0)
Downloading joblib-1.5.3-py3-none-any.whl.metadata (5.5 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.2.0)
Downloading threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Requirement already satisfied: filelock in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch==2.7.1->boltz==2.2.0) (3.19.1)
Requirement already satisfied: networkx in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch==2.7.1->boltz==2.2.0) (3.3)
Requirement already satisfied: jinja2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch==2.7.1->boltz==2.2.0) (3.1.6)
Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==2.2.0)
Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==2.2.0)
Downloading gitpython-3.1.46-py3-none-any.whl.metadata (13 kB)
Requirement already satisfied: platformdirs in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from wandb==0.18.7->boltz==2.2.0) (4.5.1)
Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from
wandb==0.18.7->boltz==2.2.0)
Downloading protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl.metadata (592
bytes)
Requirement already satisfied: psutil>=5.0.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from wandb==0.18.7->boltz==2.2.0) (7.0.0)
Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==2.2.0)
Downloading sentry_sdk-2.48.0-py2.py3-none-any.whl.metadata (10 kB)
Collecting setproctitle (from wandb==0.18.7->boltz==2.2.0)
Downloading setproctitle-1.3.7-cp311-cp311-macosx_11_0_arm64.whl.metadata (10
kB)
Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.2.0)
Downloading cuequivariance-0.8.0-py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: python-dateutil>=2.8.2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==2.2.0) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==2.2.0) (2025.2)
Requirement already satisfied: tzdata>=2022.7 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==2.2.0) (2025.3)
Requirement already satisfied: Pillow in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from rdkit>=2024.3.2->boltz==2.2.0) (11.3.0)
Requirement already satisfied: six>=1.4.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz==2.2.0) (1.17.0)
Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0)
(3.13.1)
Collecting gitdb<5,>=4.0.1 (from
gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0)
Downloading gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)
Requirement already satisfied: msgpack in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ihm>=1.7->modelcif==1.2->boltz==2.2.0) (1.1.1)
Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==2.2.0)
Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
Collecting opt-einsum (from
cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.2.0)
Downloading opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)
Requirement already satisfied: MarkupSafe>=2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from jinja2->torch==2.7.1->boltz==2.2.0) (3.0.3)
Requirement already satisfied: aiohappyeyeballs>=2.5.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0) (2.6.1)
Requirement already satisfied: aiosignal>=1.4.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0) (1.4.0)
Requirement already satisfied: attrs>=17.3.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0) (25.4.0)
Requirement already satisfied: frozenlist>=1.1.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0) (1.8.0)
Requirement already satisfied: multidict<7.0,>=4.5 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0) (6.7.0)
Requirement already satisfied: propcache>=0.2.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0) (0.4.1)
Requirement already satisfied: yarl<2.0,>=1.17.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0) (1.22.0)
Collecting smmap<6,>=3.0.1 (from
gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0)
Downloading smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)
Downloading biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB)
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Downloading chembl_structure_pipeline-1.2.2-py3-none-any.whl (17 kB)
Downloading click-8.1.7-py3-none-any.whl (97 kB)
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Downloading dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB)
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Downloading einops-0.8.0-py3-none-any.whl (43 kB)
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Downloading einx-0.3.0-py3-none-any.whl (102 kB)
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Downloading gemmi-0.6.5-cp311-cp311-macosx_11_0_arm64.whl (3.0 MB)
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Downloading smmap-5.0.2-py3-none-any.whl (24 kB)
Building wheels for collected packages: boltz, fairscale, modelcif,
antlr4-python3-runtime
Building wheel for boltz (pyproject.toml): started
Building wheel for boltz (pyproject.toml): finished with status 'done'
Created wheel for boltz: filename=boltz-2.2.0-py3-none-any.whl size=268988
sha256=8d1bd97cefc0fe7735635607f6ef7be38801d20550dd592258f26c8b39b8997a
Stored in directory:
/private/var/folders/l1/6fvcl79557d_xx8q3m_q8_tr0000gp/T/pip-ephem-wheel-
cache-5z_adsb5/wheels/26/ba/5c/a8ae06e77eb74d03f129cbbe5d93bfea3b1259fabe4f838af4
Building wheel for fairscale (pyproject.toml): started
Building wheel for fairscale (pyproject.toml): finished with status 'done'
Created wheel for fairscale: filename=fairscale-0.4.13-py3-none-any.whl
size=332208
sha256=e33e730b3754694473befc6a2eb98739bd8e304bab34c8c0c694a47b7129f4ca
Stored in directory:
/Users/krendu/Library/Caches/pip/wheels/95/ef/96/5044bde220b2ea299bdc6ec05051e0ef187fad45b341d1c273
Building wheel for modelcif (setup.py): started
Building wheel for modelcif (setup.py): finished with status 'done'
Created wheel for modelcif: filename=modelcif-1.2-py3-none-any.whl size=41181
sha256=11c0f6508e33ef9ef3727a1cf6a8fe97ac1c867a2bd214673ddf53518fde5b10
Stored in directory:
/Users/krendu/Library/Caches/pip/wheels/d2/3a/8c/e28cb28a15568d1b1b6163c77c945a5961351340fd15b9b4df
Building wheel for antlr4-python3-runtime (setup.py): started
Building wheel for antlr4-python3-runtime (setup.py): finished with status
'done'
Created wheel for antlr4-python3-runtime:
filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144555
sha256=a736c31b073ba25d803f950ebbc8af1bb825874281b3ac8b20b116b701185dcc
Stored in directory:
/Users/krendu/Library/Caches/pip/wheels/1a/97/32/461f837398029ad76911109f07047fde1d7b661a147c7c56d1
Successfully built boltz fairscale modelcif antlr4-python3-runtime
Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types-
requests, tqdm, threadpoolctl, sympy, smmap, setproctitle, sentry-sdk, scipy,
requests, rdkit, pyyaml, protobuf, opt-einsum, mashumaro, llvmlite, lightning-
utilities, joblib, gemmi, fsspec, frozendict, einops, docker-pycreds, click,
biopython, torch, scikit-learn, pandas, omegaconf, numba, modelcif, gitdb,
einx, cuequivariance, chembl_structure_pipeline, torchmetrics, hydra-core,
gitpython, fairscale, cuequivariance_torch, wandb, pytorch-lightning, boltz
Attempting uninstall: scipy
Found existing installation: scipy 1.14.0
Not uninstalling scipy at
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/krendu/boltz22
Can't uninstall 'scipy'. No files were found to uninstall.
Attempting uninstall: requests
Found existing installation: requests 2.32.5
Not uninstalling requests at
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/krendu/boltz22
Can't uninstall 'requests'. No files were found to uninstall.
Attempting uninstall: click
Found existing installation: click 8.3.1
Not uninstalling click at
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/krendu/boltz22
Can't uninstall 'click'. No files were found to uninstall.
Successfully installed antlr4-python3-runtime-4.9.3 biopython-1.84 boltz-2.2.0
chembl_structure_pipeline-1.2.2 click-8.1.7 cuequivariance-0.8.0
cuequivariance_torch-0.8.0 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0
einx-0.3.0 fairscale-0.4.13 frozendict-2.4.7 fsspec-2025.12.0 gemmi-0.6.5
gitdb-4.0.12 gitpython-3.1.46 hydra-core-1.3.2 joblib-1.5.3 lightning-
utilities-0.15.2 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0
numba-0.61.0 omegaconf-2.3.0 opt-einsum-3.4.0 pandas-2.3.3 protobuf-5.29.5
pytorch-lightning-2.5.0 pyyaml-6.0.2 rdkit-2025.9.3 requests-2.32.3 scikit-
learn-1.6.1 scipy-1.13.1 sentry-sdk-2.48.0 setproctitle-1.3.7 smmap-5.0.2
sympy-1.14.0 threadpoolctl-3.6.0 torch-2.7.1 torchmetrics-1.8.2 tqdm-4.67.1
types-requests-2.32.4.20250913 wandb-0.18.7
[notice] A new release of pip is available: 24.0 -> 25.3
[notice] To update, run: /Users/krendu/boltz22/bin/python -m pip install
--upgrade pip
Downloading Boltz model parameters (4 GB) and chemical component database (1.8
GB) to ~/.boltz
/Users/krendu/boltz22/bin/python
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/download_weights_and_ccd.py
Downloading the CCD data to /Users/krendu/.boltz/mols.tar. This may take a bit
of time. You may change the cache directory with the --cache flag.
Extracting the CCD data to /Users/krendu/.boltz/mols. This may take a bit of
time. You may change the cache directory with the --cache flag.
Downloading the Boltz-2 weights to /Users/krendu/.boltz/boltz2_conf.ckpt. You
may change the cache directory with the --cache flag.
Downloading the Boltz-2 affinity weights to
/Users/krendu/.boltz/boltz2_aff.ckpt. You may change the cache directory with
the --cache flag.
Making CCD atom counts table for 45227 in /Users/krendu/.boltz/mols
Boltz model parameters and CCD database are installed in ~/.boltz
Successfully installed Boltz program and neural net weights.
Desktop color scheme is dark
Desktop color scheme is light
Unsupported scale factor (0.000000) detected on Display1
[Repeated 3 time(s)]Desktop color scheme is dark
Unsupported scale factor (0.000000) detected on Display0
[Repeated 3 time(s)]Desktop color scheme is light
> ui tool show Boltz
Populating font family aliases took 175 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
Running Boltz prediction of protein with 222 residues on gpu
Using multiple sequence alignment server https://api.colabfold.com
Confidence score 0.83, pTM 0.79, ipTM 0.00, pLDDT 0.83
Boltz prediction completed in 921 seconds (start boltz 7 sec, sequence search
0 sec, load weights 9 sec, structure inference 904 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/krendu/Desktop/boltz_1/boltz_results_boltz_1/predictions/boltz_1/boltz_1_model_0.cif
> logInfo false
> hide #1 models
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> resultsDirectory /Users/krendu/Desktop/Classes/Winter/Methods/Boltz
> useServer true serverHost 157.157.221.29 serverPort 31556
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/krendu/Downloads/ChimeraX/BoltzMSA/boltz_1
Sending job request to server (656475 bytes)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 595, in _predict
self._run_prediction(options = ' '.join(options))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 612, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 87, in boltz_predict
br.start()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 559, in start
self._run_boltz()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 669, in _run_boltz
self._run_on_server()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 706, in _run_on_server
job_id = predict_on_server(run_dir, self._server_host, self._server_port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server
raise RuntimeError(msg.decode('utf-8'))
RuntimeError
RuntimeError
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server
raise RuntimeError(msg.decode('utf-8'))
See log for complete Python traceback.
> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> resultsDirectory /Users/krendu/Desktop/Classes/Winter/Methods/Boltz
> useServer true serverHost 157.157.221.29 serverPort 31556
Boltz prediction directory /Users/krendu/Desktop/Classes/Winter/Methods/Boltz
already exists. Files will be overwritten.
Running Boltz prediction of protein with 222 residues on gpu
Using cached multiple sequence alignment
/Users/krendu/Downloads/ChimeraX/BoltzMSA/boltz_1
Sending job request to server (656475 bytes)
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 595, in _predict
self._run_prediction(options = ' '.join(options))
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 612, in _run_prediction
br = run(self.session, cmd)
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 87, in boltz_predict
br.start()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 559, in start
self._run_boltz()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 669, in _run_boltz
self._run_on_server()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 706, in _run_on_server
job_id = predict_on_server(run_dir, self._server_host, self._server_port)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server
raise RuntimeError(msg.decode('utf-8'))
RuntimeError
RuntimeError
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 298, in predict_on_server
raise RuntimeError(msg.decode('utf-8'))
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,1
Model Number: MW2W3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 55 days, 22 hours, 37 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
appnope: 0.1.4
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: 2025.7.14
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: 1.61.5
ChimeraX-AtomicLibrary: 14.2.3
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-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: 1.12.dev202601052311
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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8
ChimeraX-Label: 1.3
ChimeraX-LightingGUI: 1.0
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: 1.5.23
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: 1.7
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.2
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: 1.50
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
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: 4.25.1
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
OpenMM: 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: 3.3.1
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 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
pytz: 2025.2
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: 2.8.1
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: 3.1.2
stack-data: 0.6.3
starlette: 0.50.0
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
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.40.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
Change History (2)
comment:1 by , 6 days ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → boltz predict: RuntimeError |
comment:2 by , 5 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #19698