Ticket #20860: ChimeraX log for Boltz downlaod.txt

boltz install C:\Users\conno/boltz22
Successfully created Boltz Python virtual environment C:\Users\conno/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...
C:\Users\conno/boltz22\Scripts\python.exe -m pip install https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Collecting https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip

Using cached https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip

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)

Using cached torch-2.7.1-cp311-cp311-win_amd64.whl.metadata (28 kB)

Requirement already satisfied: numpy<2.0,>=1.26 in c:\program files\chimerax 1.12\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-2026.3.5-cp311-cp311-win_amd64.whl.metadata (3.9 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)

WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='pypi.org', port=443): Read timed out. (read timeout=15)")': /simple/pandas/

Collecting pandas>=2.2.2 (from boltz==2.2.0)

Using cached pandas-3.0.5-cp311-cp311-win_amd64.whl.metadata (19 kB)

Collecting types-requests (from boltz==2.2.0)

Using cached types_requests-2.33.0.20260712-py3-none-any.whl.metadata (2.2 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-0.11.1-py3-none-any.whl.metadata (15 kB)

Requirement already satisfied: setuptools>=46.4.0 in c:\users\conno\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 1.12\bin\lib\site-packages (from click==8.1.7->boltz==2.2.0) (0.4.6)

Collecting sympy (from einx==0.3.0->boltz==2.2.0)

Using cached sympy-1.14.0-py3-none-any.whl.metadata (12 kB)

Collecting frozendict (from einx==0.3.0->boltz==2.2.0)

Using cached 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)

Using cached omegaconf-2.3.1-py3-none-any.whl.metadata (4.5 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 1.12\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 1.12\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 1.12\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)

Requirement already satisfied: tqdm>=4.57.0 in c:\program files\chimerax 1.12\bin\lib\site-packages (from pytorch-lightning==2.5.0->boltz==2.2.0) (4.68.2)

Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0)

Using cached fsspec-2026.7.0-py3-none-any.whl.metadata (10 kB)

Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)

Using cached torchmetrics-1.9.0-py3-none-any.whl.metadata (23 kB)

Collecting lightning-utilities>=0.10.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)

Using cached lightning_utilities-0.15.3-py3-none-any.whl.metadata (5.5 kB)

Requirement already satisfied: charset-normalizer<4,>=2 in c:\program files\chimerax 1.12\bin\lib\site-packages (from requests==2.32.3->boltz==2.2.0) (3.4.7)

Requirement already satisfied: idna<4,>=2.5 in c:\program files\chimerax 1.12\bin\lib\site-packages (from requests==2.32.3->boltz==2.2.0) (3.18)

Requirement already satisfied: urllib3<3,>=1.21.1 in c:\program files\chimerax 1.12\bin\lib\site-packages (from requests==2.32.3->boltz==2.2.0) (2.7.0)

Requirement already satisfied: certifi>=2017.4.17 in c:\program files\chimerax 1.12\bin\lib\site-packages (from requests==2.32.3->boltz==2.2.0) (2026.5.20)

Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.2.0)

Using cached joblib-1.5.3-py3-none-any.whl.metadata (5.5 kB)

Requirement already satisfied: threadpoolctl>=3.1.0 in c:\program files\chimerax 1.12\bin\lib\site-packages (from scikit-learn==1.6.1->boltz==2.2.0) (3.6.0)

Requirement already satisfied: filelock in c:\program files\chimerax 1.12\bin\lib\site-packages (from torch==2.7.1->boltz==2.2.0) (3.19.1)

Requirement already satisfied: networkx in c:\program files\chimerax 1.12\bin\lib\site-packages (from torch==2.7.1->boltz==2.2.0) (3.3)

Requirement already satisfied: jinja2 in c:\program files\chimerax 1.12\bin\lib\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)

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-3.1.59-py3-none-any.whl.metadata (13 kB)

Requirement already satisfied: platformdirs in c:\program files\chimerax 1.12\bin\lib\site-packages (from wandb==0.18.7->boltz==2.2.0) (4.10.0)

Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from wandb==0.18.7->boltz==2.2.0)

Using cached protobuf-5.29.6-cp310-abi3-win_amd64.whl.metadata (592 bytes)

Requirement already satisfied: psutil>=5.0.0 in c:\program files\chimerax 1.12\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-2.68.0-py3-none-any.whl.metadata (11 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-0.11.1-py3-none-any.whl.metadata (15 kB)

Requirement already satisfied: python-dateutil>=2.8.2 in c:\program files\chimerax 1.12\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.2.0) (2.9.0.post0)

Requirement already satisfied: tzdata in c:\program files\chimerax 1.12\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.2.0) (2026.2)

Requirement already satisfied: Pillow in c:\program files\chimerax 1.12\bin\lib\site-packages (from rdkit>=2024.3.2->boltz==2.2.0) (11.3.0)

Requirement already satisfied: six>=1.4.0 in c:\program files\chimerax 1.12\bin\lib\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 c:\program files\chimerax 1.12\bin\lib\site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (3.13.4)

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 1.12\bin\lib\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)

Using cached 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)

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 1.12\bin\lib\site-packages (from jinja2->torch==2.7.1->boltz==2.2.0) (3.0.3)

Requirement already satisfied: aiohappyeyeballs>=2.5.0 in c:\program files\chimerax 1.12\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (2.6.2)

Requirement already satisfied: aiosignal>=1.4.0 in c:\program files\chimerax 1.12\bin\lib\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 c:\program files\chimerax 1.12\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (26.1.0)

Requirement already satisfied: frozenlist>=1.1.1 in c:\program files\chimerax 1.12\bin\lib\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 c:\program files\chimerax 1.12\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (6.7.1)

Requirement already satisfied: propcache>=0.2.0 in c:\program files\chimerax 1.12\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (0.5.2)

Requirement already satisfied: yarl<2.0,>=1.17.0 in c:\program files\chimerax 1.12\bin\lib\site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (1.24.2)

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-5.0.3-py3-none-any.whl.metadata (4.6 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 torch-2.7.1-cp311-cp311-win_amd64.whl (216.1 MB)

Using cached wandb-0.18.7-py3-none-win_amd64.whl (15.5 MB)

Using cached cuequivariance_torch-0.11.1-py3-none-any.whl (184 kB)

Using cached pandas-3.0.5-cp311-cp311-win_amd64.whl (10.0 MB)

Using cached rdkit-2026.3.5-cp311-cp311-win_amd64.whl (24.7 MB)

Using cached types_requests-2.33.0.20260712-py3-none-any.whl (21 kB)

Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)

Using cached fsspec-2026.7.0-py3-none-any.whl (206 kB)

Using cached gitpython-3.1.59-py3-none-any.whl (220 kB)

Using cached joblib-1.5.3-py3-none-any.whl (309 kB)

Using cached lightning_utilities-0.15.3-py3-none-any.whl (31 kB)

Using cached llvmlite-0.44.0-cp311-cp311-win_amd64.whl (30.3 MB)

Using cached omegaconf-2.3.1-py3-none-any.whl (79 kB)

Using cached protobuf-5.29.6-cp310-abi3-win_amd64.whl (435 kB)

Using cached sentry_sdk-2.68.0-py3-none-any.whl (518 kB)

Using cached sympy-1.14.0-py3-none-any.whl (6.3 MB)

Using cached torchmetrics-1.9.0-py3-none-any.whl (983 kB)

Using cached cuequivariance-0.11.1-py3-none-any.whl (250 kB)

Using cached frozendict-2.4.7-py3-none-any.whl (16 kB)

Using cached setproctitle-1.3.7-cp311-cp311-win_amd64.whl (13 kB)

Using cached gitdb-4.0.12-py3-none-any.whl (62 kB)

Using cached mpmath-1.3.0-py3-none-any.whl (536 kB)

Using cached opt_einsum-3.4.0-py3-none-any.whl (71 kB)

Using cached smmap-5.0.3-py3-none-any.whl (24 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=269018 sha256=2a5e4b5e9d4a1805abfb6f8eff2f8b21227d3b1bb10fad75bbc480dd23bac52d

Stored in directory: C:\Users\conno\AppData\Local\Temp\pip-ephem-wheel-cache-6aisl4l7\wheels\26\ba\5c\a8ae06e77eb74d03f129cbbe5d93bfea3b1259fabe4f838af4

Successfully built boltz

Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types-requests, 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 c:\program files\chimerax 1.12\bin\lib\site-packages, outside environment C:\Users\conno\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 c:\program files\chimerax 1.12\bin\lib\site-packages, outside environment C:\Users\conno\boltz22

Can't uninstall 'requests'. No files were found to uninstall.

Attempting uninstall: click

Found existing installation: click 8.4.1

Not uninstalling click at c:\program files\chimerax 1.12\bin\lib\site-packages, outside environment C:\Users\conno\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-0.11.1 cuequivariance_torch-0.11.1 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0 einx-0.3.0 fairscale-0.4.13 frozendict-2.4.7 fsspec-2026.7.0 gemmi-0.6.5 gitdb-4.0.12 gitpython-3.1.59 hydra-core-1.3.2 joblib-1.5.3 lightning-utilities-0.15.3 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 numba-0.61.0 omegaconf-2.3.1 opt-einsum-3.4.0 pandas-3.0.5 protobuf-5.29.6 pytorch-lightning-2.5.0 pyyaml-6.0.2 rdkit-2026.3.5 requests-2.32.3 scikit-learn-1.6.1 scipy-1.13.1 sentry-sdk-2.68.0 setproctitle-1.3.7 smmap-5.0.3 sympy-1.14.0 torch-2.7.1 torchmetrics-1.9.0 types-requests-2.33.0.20260712 wandb-0.18.7



[notice] A new release of pip is available: 24.0 -> 26.2.1

[notice] To update, run: C:\Users\conno\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\conno/boltz22\Scripts\python.exe C:\Program Files\ChimeraX 1.12\bin\Lib\site-packages\chimerax\boltz\download_weights_and_ccd.py
Downloading the CCD data to C:\Users\conno\.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 C:\Users\conno\.boltz\mols. 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 1.12\bin\Lib\site-packages\chimerax\boltz\download_weights_and_ccd.py", line 37, in <module>

download_weights_and_ccd()

File "C:\Program Files\ChimeraX 1.12\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\conno\boltz22\Lib\site-packages\lightning_utilities\core\rank_zero.py", line 42, in wrapped_fn

return fn(*args, **kwargs)

^^^^^^^^^^^^^^^^^^^

File "C:\Users\conno\boltz22\Lib\site-packages\boltz\main.py", line 224, in download_boltz2

tar.extractall(cache) # noqa: S202

^^^^^^^^^^^^^^^^^^^^^

File "C:\Program Files\ChimeraX 1.12\bin\Lib\tarfile.py", line 2265, in extractall

self._extract_one(tarinfo, path, set_attrs=not tarinfo.isdir(),

File "C:\Program Files\ChimeraX 1.12\bin\Lib\tarfile.py", line 2332, in _extract_one

self._handle_fatal_error(e)

File "C:\Program Files\ChimeraX 1.12\bin\Lib\tarfile.py", line 2328, in _extract_one

self._extract_member(tarinfo, os.path.join(path, tarinfo.name),

File "C:\Program Files\ChimeraX 1.12\bin\Lib\tarfile.py", line 2411, in _extract_member

self.makefile(tarinfo, targetpath)

File "C:\Program Files\ChimeraX 1.12\bin\Lib\tarfile.py", line 2457, in makefile

with bltn_open(targetpath, "wb") as target:

^^^^^^^^^^^^^^^^^^^^^^^^^^^

FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\conno\\.boltz\\mols\\AUX.pkl'

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