Error downloading Boltz parameters

[lvwei.aca@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.11.dev202509201954 (2025-09-20 19:54:21 UTC)
Description
Trying to install boltz in chimeraX Sep22 daily version, the following error appears. 
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\urllib\request.py", line 1351, in do_open

raise URLError(err)

urllib.error.URLError: <urlopen error [WinError 10013] An attempt was made to access a socket in a way forbidden by its access permissions>

Downloading Boltz model parameters and CCD database to ~/.boltz or creating CCD atom counts file failed.

Log:
UCSF ChimeraX version: 1.11.dev202509201954 (2025-09-20)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Boltz

> boltz install C:\Users\wlv/boltz22

Successfully created Boltz Python virtual environment C:\Users\wlv/boltz22.  
Now installing machine learning package torch.  
C:\Users\wlv/boltz22\Scripts\python.exe -m pip install torch --index-url
https://download.pytorch.org/whl/cu126  
Looking in indexes: https://download.pytorch.org/whl/cu126  
  
Collecting torch  
  
Using cached
https://download.pytorch.org/whl/cu126/torch-2.8.0%2Bcu126-cp311-cp311-win_amd64.whl.metadata
(29 kB)  
  
Requirement already satisfied: filelock in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from torch) (3.19.1)  
  
Requirement already satisfied: typing-extensions>=4.10.0 in c:\program
files\chimerax 1.11.dev202509201954\bin\lib\site-packages (from torch)
(4.15.0)  
  
Collecting sympy>=1.13.3 (from torch)  
  
Using cached https://download.pytorch.org/whl/sympy-1.13.3-py3-none-
any.whl.metadata (12 kB)  
  
Requirement already satisfied: networkx in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from torch) (3.3)  
  
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from torch) (3.1.6)  
  
Collecting fsspec (from torch)  
  
Using cached https://download.pytorch.org/whl/fsspec-2024.6.1-py3-none-
any.whl.metadata (11 kB)  
  
Collecting mpmath<1.4,>=1.1.0 (from sympy>=1.13.3->torch)  
  
Using cached https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl
(536 kB)  
  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from jinja2->torch) (3.0.2)  
  
Using cached
https://download.pytorch.org/whl/cu126/torch-2.8.0%2Bcu126-cp311-cp311-win_amd64.whl
(2915.5 MB)  
  
Using cached https://download.pytorch.org/whl/sympy-1.13.3-py3-none-any.whl
(6.2 MB)  
  
Using cached https://download.pytorch.org/whl/fsspec-2024.6.1-py3-none-any.whl
(177 kB)  
  
Installing collected packages: mpmath, sympy, fsspec, torch  
  
Successfully installed fsspec-2024.6.1 mpmath-1.3.0 sympy-1.13.3
torch-2.8.0+cu126  
  
  
  
[notice] A new release of pip is available: 24.0 -> 25.2  
  
[notice] To update, run: C:\Users\wlv\boltz22\Scripts\python.exe -m pip
install --upgrade pip  
  
Successfully installed torch.  
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...  
C:\Users\wlv/boltz22\Scripts\python.exe -m pip install
git+https://github.com/RBVI/boltz@chimerax_boltz22  
Collecting git+https://github.com/RBVI/boltz@chimerax_boltz22  
  
Cloning https://github.com/RBVI/boltz (to revision chimerax_boltz22) to
c:\users\wlv\appdata\local\temp\pip-req-build-ucnto4ww  
  
Running command git clone --filter=blob:none --quiet
https://github.com/RBVI/boltz 'C:\Users\wlv\AppData\Local\Temp\pip-req-build-
ucnto4ww'  
  
Running command git checkout -b chimerax_boltz22 --track
origin/chimerax_boltz22  
  
branch 'chimerax_boltz22' set up to track 'origin/chimerax_boltz22'.  
  
Switched to a new branch 'chimerax_boltz22'  
  
Resolved https://github.com/RBVI/boltz to commit
f1638c67006f656dc78fa7062f852077e7016018  
  
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'  
  
Requirement already satisfied: torch>=2.2 in c:\users\wlv\boltz22\lib\site-
packages (from boltz==2.2.0) (2.8.0+cu126)  
  
Requirement already satisfied: numpy<2.0,>=1.26 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from boltz==2.2.0) (1.26.4)  
  
Collecting hydra-core==1.3.2 (from boltz==2.2.0)  
  
Using cached hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)  
  
Collecting pytorch-lightning==2.5.0 (from boltz==2.2.0)  
  
Using cached pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB)  
  
Collecting rdkit>=2024.3.2 (from boltz==2.2.0)  
  
Using cached rdkit-2025.3.6-cp311-cp311-win_amd64.whl.metadata (4.2 kB)  
  
Collecting dm-tree==0.1.8 (from boltz==2.2.0)  
  
Using cached dm_tree-0.1.8-cp311-cp311-win_amd64.whl.metadata (2.0 kB)  
  
Collecting requests==2.32.3 (from boltz==2.2.0)  
  
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)  
  
Collecting pandas>=2.2.2 (from boltz==2.2.0)  
  
Using cached pandas-2.3.2-cp311-cp311-win_amd64.whl.metadata (19 kB)  
  
Collecting types-requests (from boltz==2.2.0)  
  
Using cached types_requests-2.32.4.20250913-py3-none-any.whl.metadata (2.0 kB)  
  
Collecting einops==0.8.0 (from boltz==2.2.0)  
  
Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)  
  
Collecting einx==0.3.0 (from boltz==2.2.0)  
  
Using cached einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)  
  
Collecting fairscale==0.4.13 (from boltz==2.2.0)  
  
Using cached fairscale-0.4.13-py3-none-any.whl  
  
Collecting mashumaro==3.14 (from boltz==2.2.0)  
  
Using cached mashumaro-3.14-py3-none-any.whl.metadata (114 kB)  
  
Collecting modelcif==1.2 (from boltz==2.2.0)  
  
Using cached modelcif-1.2-py3-none-any.whl  
  
Collecting wandb==0.18.7 (from boltz==2.2.0)  
  
Using cached wandb-0.18.7-py3-none-win_amd64.whl.metadata (9.7 kB)  
  
Collecting click==8.1.7 (from boltz==2.2.0)  
  
Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)  
  
Collecting pyyaml==6.0.2 (from boltz==2.2.0)  
  
Using cached PyYAML-6.0.2-cp311-cp311-win_amd64.whl.metadata (2.1 kB)  
  
Collecting biopython==1.84 (from boltz==2.2.0)  
  
Using cached biopython-1.84-cp311-cp311-win_amd64.whl.metadata (13 kB)  
  
Collecting scipy==1.13.1 (from boltz==2.2.0)  
  
Using cached scipy-1.13.1-cp311-cp311-win_amd64.whl.metadata (60 kB)  
  
Collecting numba==0.61.0 (from boltz==2.2.0)  
  
Using cached numba-0.61.0-cp311-cp311-win_amd64.whl.metadata (2.8 kB)  
  
Collecting gemmi==0.6.5 (from boltz==2.2.0)  
  
Using cached gemmi-0.6.5-cp311-cp311-win_amd64.whl.metadata (2.3 kB)  
  
Collecting scikit-learn==1.6.1 (from boltz==2.2.0)  
  
Using cached scikit_learn-1.6.1-cp311-cp311-win_amd64.whl.metadata (15 kB)  
  
Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.2.0)  
  
Using cached 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)  
  
Using cached cuequivariance_torch-0.6.1-py3-none-any.whl.metadata (15 kB)  
  
Requirement already satisfied: setuptools>=46.4.0 in
c:\users\wlv\boltz22\lib\site-packages (from
chembl_structure_pipeline==1.2.2->boltz==2.2.0) (65.5.0)  
  
Requirement already satisfied: colorama in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from click==8.1.7->boltz==2.2.0)
(0.4.6)  
  
Requirement already satisfied: sympy in c:\users\wlv\boltz22\lib\site-packages
(from einx==0.3.0->boltz==2.2.0) (1.13.3)  
  
Collecting frozendict (from einx==0.3.0->boltz==2.2.0)  
  
Using cached frozendict-2.4.6-py311-none-any.whl.metadata (23 kB)  
  
Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==2.2.0)  
  
Using cached 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)  
  
Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl  
  
Requirement already satisfied: packaging in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from hydra-
core==1.3.2->boltz==2.2.0) (25.0)  
  
Requirement already satisfied: typing-extensions>=4.1.0 in c:\program
files\chimerax 1.11.dev202509201954\bin\lib\site-packages (from
mashumaro==3.14->boltz==2.2.0) (4.15.0)  
  
Requirement already satisfied: ihm>=1.7 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\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)  
  
Using cached llvmlite-0.44.0-cp311-cp311-win_amd64.whl.metadata (5.0 kB)  
  
Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)  
  
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)  
  
Requirement already satisfied: fsspec>=2022.5.0 in
c:\users\wlv\boltz22\lib\site-packages (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0) (2024.6.1)  
  
Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)  
  
Using cached 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)  
  
Using cached lightning_utilities-0.15.2-py3-none-any.whl.metadata (5.7 kB)  
  
Requirement already satisfied: charset-normalizer<4,>=2 in c:\program
files\chimerax 1.11.dev202509201954\bin\lib\site-packages (from
requests==2.32.3->boltz==2.2.0) (3.4.3)  
  
Requirement already satisfied: idna<4,>=2.5 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from
requests==2.32.3->boltz==2.2.0) (3.10)  
  
Requirement already satisfied: urllib3<3,>=1.21.1 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from
requests==2.32.3->boltz==2.2.0) (2.5.0)  
  
Requirement already satisfied: certifi>=2017.4.17 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from
requests==2.32.3->boltz==2.2.0) (2025.8.3)  
  
Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.2.0)  
  
Using cached joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB)  
  
Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.2.0)  
  
Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)  
  
Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==2.2.0)  
  
Using cached 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)  
  
Using cached gitpython-3.1.45-py3-none-any.whl.metadata (13 kB)  
  
Requirement already satisfied: platformdirs in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from wandb==0.18.7->boltz==2.2.0)
(4.4.0)  
  
Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from
wandb==0.18.7->boltz==2.2.0)  
  
Using cached protobuf-5.29.5-cp310-abi3-win_amd64.whl.metadata (592 bytes)  
  
Requirement already satisfied: psutil>=5.0.0 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\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)  
  
Using cached sentry_sdk-2.38.0-py2.py3-none-any.whl.metadata (10 kB)  
  
Collecting setproctitle (from wandb==0.18.7->boltz==2.2.0)  
  
Using cached setproctitle-1.3.7-cp311-cp311-win_amd64.whl.metadata (11 kB)  
  
Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.2.0)  
  
Using cached cuequivariance-0.6.1-py3-none-any.whl.metadata (15 kB)  
  
Requirement already satisfied: python-dateutil>=2.8.2 in c:\program
files\chimerax 1.11.dev202509201954\bin\lib\site-packages (from
pandas>=2.2.2->boltz==2.2.0) (2.9.0.post0)  
  
Requirement already satisfied: pytz>=2020.1 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.2.0)
(2025.2)  
  
Requirement already satisfied: tzdata>=2022.7 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.2.0)
(2025.2)  
  
Requirement already satisfied: Pillow in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from
rdkit>=2024.3.2->boltz==2.2.0) (11.3.0)  
  
Requirement already satisfied: filelock in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from torch>=2.2->boltz==2.2.0)
(3.19.1)  
  
Requirement already satisfied: networkx in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from torch>=2.2->boltz==2.2.0)
(3.3)  
  
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from torch>=2.2->boltz==2.2.0)
(3.1.6)  
  
Requirement already satisfied: six>=1.4.0 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from docker-
pycreds>=0.4.0->wandb==0.18.7->boltz==2.2.0) (1.17.0)  
  
Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Using cached aiohttp-3.12.15-cp311-cp311-win_amd64.whl.metadata (7.9 kB)  
  
Collecting gitdb<5,>=4.0.1 (from
gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0)  
  
Using cached gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)  
  
Requirement already satisfied: msgpack in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from
ihm>=1.7->modelcif==1.2->boltz==2.2.0) (1.1.1)  
  
Requirement already satisfied: mpmath<1.4,>=1.1.0 in
c:\users\wlv\boltz22\lib\site-packages (from sympy->einx==0.3.0->boltz==2.2.0)
(1.3.0)  
  
Collecting opt-einsum (from
cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.2.0)  
  
Using cached opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)  
  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages (from
jinja2->torch>=2.2->boltz==2.2.0) (3.0.2)  
  
Collecting aiohappyeyeballs>=2.5.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)  
  
Collecting aiosignal>=1.4.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)  
  
Collecting attrs>=17.3.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB)  
  
Collecting frozenlist>=1.1.1 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Using cached frozenlist-1.7.0-cp311-cp311-win_amd64.whl.metadata (19 kB)  
  
Collecting multidict<7.0,>=4.5 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Using cached multidict-6.6.4-cp311-cp311-win_amd64.whl.metadata (5.4 kB)  
  
Collecting propcache>=0.2.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Using cached propcache-0.3.2-cp311-cp311-win_amd64.whl.metadata (12 kB)  
  
Collecting yarl<2.0,>=1.17.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Using cached yarl-1.20.1-cp311-cp311-win_amd64.whl.metadata (76 kB)  
  
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)  
  
Using cached smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)  
  
Using cached biopython-1.84-cp311-cp311-win_amd64.whl (2.8 MB)  
  
Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl (17 kB)  
  
Using cached click-8.1.7-py3-none-any.whl (97 kB)  
  
Using cached dm_tree-0.1.8-cp311-cp311-win_amd64.whl (101 kB)  
  
Using cached einops-0.8.0-py3-none-any.whl (43 kB)  
  
Using cached einx-0.3.0-py3-none-any.whl (102 kB)  
  
Using cached gemmi-0.6.5-cp311-cp311-win_amd64.whl (2.3 MB)  
  
Using cached hydra_core-1.3.2-py3-none-any.whl (154 kB)  
  
Using cached mashumaro-3.14-py3-none-any.whl (92 kB)  
  
Using cached numba-0.61.0-cp311-cp311-win_amd64.whl (2.8 MB)  
  
Using cached pytorch_lightning-2.5.0-py3-none-any.whl (819 kB)  
  
Using cached PyYAML-6.0.2-cp311-cp311-win_amd64.whl (161 kB)  
  
Using cached requests-2.32.3-py3-none-any.whl (64 kB)  
  
Using cached scikit_learn-1.6.1-cp311-cp311-win_amd64.whl (11.1 MB)  
  
Using cached scipy-1.13.1-cp311-cp311-win_amd64.whl (46.2 MB)  
  
Using cached wandb-0.18.7-py3-none-win_amd64.whl (15.5 MB)  
  
Using cached cuequivariance_torch-0.6.1-py3-none-any.whl (214 kB)  
  
Using cached pandas-2.3.2-cp311-cp311-win_amd64.whl (11.3 MB)  
  
Using cached rdkit-2025.3.6-cp311-cp311-win_amd64.whl (23.5 MB)  
  
Using cached types_requests-2.32.4.20250913-py3-none-any.whl (20 kB)  
  
Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)  
  
Using cached gitpython-3.1.45-py3-none-any.whl (208 kB)  
  
Using cached joblib-1.5.2-py3-none-any.whl (308 kB)  
  
Using cached lightning_utilities-0.15.2-py3-none-any.whl (29 kB)  
  
Using cached llvmlite-0.44.0-cp311-cp311-win_amd64.whl (30.3 MB)  
  
Using cached omegaconf-2.3.0-py3-none-any.whl (79 kB)  
  
Using cached protobuf-5.29.5-cp310-abi3-win_amd64.whl (434 kB)  
  
Using cached sentry_sdk-2.38.0-py2.py3-none-any.whl (370 kB)  
  
Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)  
  
Using cached torchmetrics-1.8.2-py3-none-any.whl (983 kB)  
  
Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)  
  
Using cached cuequivariance-0.6.1-py3-none-any.whl (266 kB)  
  
Using cached frozendict-2.4.6-py311-none-any.whl (16 kB)  
  
Using cached setproctitle-1.3.7-cp311-cp311-win_amd64.whl (13 kB)  
  
Using cached aiohttp-3.12.15-cp311-cp311-win_amd64.whl (453 kB)  
  
Using cached gitdb-4.0.12-py3-none-any.whl (62 kB)  
  
Using cached opt_einsum-3.4.0-py3-none-any.whl (71 kB)  
  
Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)  
  
Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)  
  
Using cached attrs-25.3.0-py3-none-any.whl (63 kB)  
  
Using cached frozenlist-1.7.0-cp311-cp311-win_amd64.whl (44 kB)  
  
Using cached multidict-6.6.4-cp311-cp311-win_amd64.whl (46 kB)  
  
Using cached propcache-0.3.2-cp311-cp311-win_amd64.whl (41 kB)  
  
Using cached smmap-5.0.2-py3-none-any.whl (24 kB)  
  
Using cached yarl-1.20.1-cp311-cp311-win_amd64.whl (86 kB)  
  
Building wheels for collected packages: boltz  
  
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=270978
sha256=53228cb0cd185807a2398f1c22cd19ee611d24372dbdc0c8b10dc4baacee4d0d  
  
Stored in directory: C:\Users\wlv\AppData\Local\Temp\pip-ephem-wheel-cache-
lsouxb6f\wheels\a2\57\a2\680a7866e1b7f1dc290112e8f82241f58511d33c66a8818e3d  
  
Successfully built boltz  
  
Installing collected packages: dm-tree, antlr4-python3-runtime, types-
requests, tqdm, threadpoolctl, smmap, setproctitle, sentry-sdk, scipy,
requests, rdkit, pyyaml, protobuf, propcache, opt-einsum, multidict,
mashumaro, llvmlite, lightning-utilities, joblib, gemmi, frozenlist,
frozendict, einops, docker-pycreds, click, biopython, attrs, aiohappyeyeballs,
yarl, scikit-learn, pandas, omegaconf, numba, modelcif, gitdb, einx,
cuequivariance, chembl_structure_pipeline, aiosignal, torchmetrics, hydra-
core, gitpython, fairscale, cuequivariance_torch, aiohttp, wandb, pytorch-
lightning, boltz  
  
Attempting uninstall: scipy  
  
Found existing installation: scipy 1.14.0  
  
Not uninstalling scipy at c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages, outside environment
C:\Users\wlv\boltz22  
  
Can't uninstall 'scipy'. No files were found to uninstall.  
  
Attempting uninstall: requests  
  
Found existing installation: requests 2.32.4  
  
Not uninstalling requests at c:\program files\chimerax
1.11.dev202509201954\bin\lib\site-packages, outside environment
C:\Users\wlv\boltz22  
  
Can't uninstall 'requests'. No files were found to uninstall.  
  
Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aiosignal-1.4.0
antlr4-python3-runtime-4.9.3 attrs-25.3.0 biopython-1.84 boltz-2.2.0
chembl_structure_pipeline-1.2.2 click-8.1.7 cuequivariance-0.6.1
cuequivariance_torch-0.6.1 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0
einx-0.3.0 fairscale-0.4.13 frozendict-2.4.6 frozenlist-1.7.0 gemmi-0.6.5
gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 joblib-1.5.2 lightning-
utilities-0.15.2 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 multidict-6.6.4
numba-0.61.0 omegaconf-2.3.0 opt-einsum-3.4.0 pandas-2.3.2 propcache-0.3.2
protobuf-5.29.5 pytorch-lightning-2.5.0 pyyaml-6.0.2 rdkit-2025.3.6
requests-2.32.3 scikit-learn-1.6.1 scipy-1.13.1 sentry-sdk-2.38.0
setproctitle-1.3.7 smmap-5.0.2 threadpoolctl-3.6.0 torchmetrics-1.8.2
tqdm-4.67.1 types-requests-2.32.4.20250913 wandb-0.18.7 yarl-1.20.1  
  
  
  
[notice] A new release of pip is available: 24.0 -> 25.2  
  
[notice] To update, run: C:\Users\wlv\boltz22\Scripts\python.exe -m pip
install --upgrade pip  
  
Downloading Boltz model parameters (4 GB) and chemical component database (1.8
GB) to ~/.boltz  
C:\Users\wlv/boltz22\Scripts\python.exe C:\Program Files\ChimeraX
1.11.dev202509201954\bin\Lib\site-
packages\chimerax\boltz\download_weights_and_ccd.py  
Downloading the CCD data to C:\Users\wlv\\.boltz\mols.tar. This may take a bit
of time. You may change the cache directory with the --cache flag.  
  
Traceback (most recent call last):  
  
File "C:\Program Files\ChimeraX
1.11.dev202509201954\bin\Lib\urllib\request.py", line 1348, in do_open  
  
h.request(req.get_method(), req.selector, req.data, headers,  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\http\client.py",
line 1303, in request  
  
self._send_request(method, url, body, headers, encode_chunked)  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\http\client.py",
line 1349, in _send_request  
  
self.endheaders(body, encode_chunked=encode_chunked)  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\http\client.py",
line 1298, in endheaders  
  
self._send_output(message_body, encode_chunked=encode_chunked)  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\http\client.py",
line 1058, in _send_output  
  
self.send(msg)  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\http\client.py",
line 996, in send  
  
self.connect()  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\http\client.py",
line 1468, in connect  
  
super().connect()  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\http\client.py",
line 962, in connect  
  
self.sock = self._create_connection(  
  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\socket.py", line
851, in create_connection  
  
raise exceptions[0]  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\socket.py", line
836, in create_connection  
  
sock.connect(sa)  
  
PermissionError: [WinError 10013] An attempt was made to access a socket in a
way forbidden by its access permissions  
  
  
  
During handling of the above exception, another exception occurred:  
  
  
  
Traceback (most recent call last):  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\site-
packages\chimerax\boltz\download_weights_and_ccd.py", line 37, in <module>  
  
download_weights_and_ccd()  
  
File "C:\Program Files\ChimeraX 1.11.dev202509201954\bin\Lib\site-
packages\chimerax\boltz\download_weights_and_ccd.py", line 11, in
download_weights_and_ccd  
  
download_boltz2(Path(data_path))  
  
File "C:\Users\wlv\boltz22\Lib\site-
packages\lightning_utilities\core\rank_zero.py", line 41, in wrapped_fn  
  
return fn(*args, **kwargs)  
  
^^^^^^^^^^^^^^^^^^^  
  
File "C:\Users\wlv\boltz22\Lib\site-packages\boltz\main.py", line 216, in
download_boltz2  
  
urllib.request.urlretrieve(MOL_URL, str(tar_mols)) # noqa: S310  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "C:\Program Files\ChimeraX
1.11.dev202509201954\bin\Lib\urllib\request.py", line 241, in urlretrieve  
  
with contextlib.closing(urlopen(url, data)) as fp:  
  
^^^^^^^^^^^^^^^^^^  
  
File "C:\Program Files\ChimeraX
1.11.dev202509201954\bin\Lib\urllib\request.py", line 216, in urlopen  
  
return opener.open(url, data, timeout)  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "C:\Program Files\ChimeraX
1.11.dev202509201954\bin\Lib\urllib\request.py", line 519, in open  
  
response = self._open(req, data)  
  
^^^^^^^^^^^^^^^^^^^^^  
  
File "C:\Program Files\ChimeraX
1.11.dev202509201954\bin\Lib\urllib\request.py", line 536, in _open  
  
result = self._call_chain(self.handle_open, protocol, protocol +  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "C:\Program Files\ChimeraX
1.11.dev202509201954\bin\Lib\urllib\request.py", line 496, in _call_chain  
  
result = func(*args)  
  
^^^^^^^^^^^  
  
File "C:\Program Files\ChimeraX
1.11.dev202509201954\bin\Lib\urllib\request.py", line 1391, in https_open  
  
return self.do_open(http.client.HTTPSConnection, req,  
  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
File "C:\Program Files\ChimeraX
1.11.dev202509201954\bin\Lib\urllib\request.py", line 1351, in do_open  
  
raise URLError(err)  
  
urllib.error.URLError: <urlopen error [WinError 10013] An attempt was made to
access a socket in a way forbidden by its access permissions>  
  
Downloading Boltz model parameters and CCD database to ~/.boltz or creating
CCD atom counts file failed.  




OpenGL version: 3.3.0 NVIDIA 573.22
OpenGL renderer: NVIDIA T500/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: LENOVO
Model: 20VX00FVUS
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 16,885,276,672
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.8.0
    build: 1.3.0
    certifi: 2025.8.3
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.17
    ChimeraX-AtomicLibrary: 14.2
    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
    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: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202509201954
    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: 1.7.1
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.1
    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-MDcrds: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    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: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.4
    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: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.2.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    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: 1.48.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.4.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.10.7
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.3
    debugpy: 1.8.17
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.60.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2025.4.15
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.1
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    msgpack: 1.1.1
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.12.1
    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
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.4.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    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: 3.2.5
    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: 8.4.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    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
    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
    stack-data: 0.6.3
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

[pett]

Reported by Wei Lv

[Tom Goddard]

This error means Boltz installation failed to get the chemical component dictionary used by Boltz.

urllib.error.URLError: <urlopen error 10013 An attempt was made to
access a socket in a way forbidden by its access permissions>

The error message looks like your computer blocked the fetching the parameters. It was trying to download

​https://huggingface.co/boltz-community/boltz-2/resolve/main/mols.tar

Possibly a firewall on your machine blocked this download. It was going to put these in directory

C:\Users\wlv\.boltz\mols.tar

as it says in the ChimeraX Log. In order to try again you should delete the directory

C:\Users\wlv\.boltz

then try to run a Boltz prediction from ChimeraX. It will automatically try to redownload the CCD and boltz network -- may take a while since those files are about 6 Gbytes.

I just tried deleting the ~/.boltz folder on Windows and running a prediction with the ChimeraX daily build and it worked.