boltz predict: RuntimeError, ChimeraX not getting job id from RunPod Boltz server

[keana.davis@…]

The following bug report has been submitted:
Platform:        macOS-14.5-arm64-arm-64bit
ChimeraX Version: 1.12.dev202601052311 (2026-01-05 23:11:53 UTC)
Description
Retest on UCSF-wpa wifi
203.57.40.132:10290 >>> 30172
Unfortunately, encountered a RuntimeError. I will check in with Justin about anything I may be missing.

Log:
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/keanadavis/boltz22

Successfully created Boltz Python virtual environment
/Users/keanadavis/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/keanadavis/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  
  
Using cached https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip (2.3
MB)  
  
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-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)  
  
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-2025.9.3-cp311-cp311-macosx_11_0_arm64.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-macosx_11_0_arm64.whl.metadata (1.9 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-2.3.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (91 kB)  
  
Collecting types-requests (from boltz==2.2.0)  
  
Using cached types_requests-2.32.4.20260107-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-macosx_11_0_arm64.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-macosx_11_0_arm64.whl.metadata (2.1 kB)  
  
Collecting biopython==1.84 (from boltz==2.2.0)  
  
Using cached biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl.metadata (12 kB)  
  
Collecting scipy==1.13.1 (from boltz==2.2.0)  
  
Using cached scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (60 kB)  
  
Collecting numba==0.61.0 (from boltz==2.2.0)  
  
Using cached 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)  
  
Using cached 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)  
  
Using cached 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)  
  
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-0.8.0-py3-none-any.whl.metadata (15 kB)  
  
Requirement already satisfied: setuptools>=46.4.0 in
/Users/keanadavis/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)  
  
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-2.3.0-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
/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)  
  
Using cached 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)  
  
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)  
  
Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Downloading fsspec-2026.1.0-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-1.8.2-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
/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)  
  
Using cached 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)  
  
Using cached 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)  
  
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-3.1.46-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)  
  
Using cached 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)  
  
Using cached sentry_sdk-2.49.0-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-macosx_11_0_arm64.whl.metadata (10
kB)  
  
Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.2.0)  
  
Using cached cuequivariance-0.8.0-py3-none-any.whl.metadata (15 kB)  
  
Requirement already satisfied: python-dateutil>=2.8.2 in
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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
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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
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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
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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)  
  
Using cached 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)  
  
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
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packages (from jinja2->torch==2.7.1->boltz==2.2.0) (3.0.3)  
  
Requirement already satisfied: aiohappyeyeballs>=2.5.0 in
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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
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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
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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
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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
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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
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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
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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)  
  
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━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 201.8/201.8 kB 3.1 MB/s eta 0:00:00  
  
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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=268988
sha256=5bdbe24a54745231e1bccf9516936ca1ac8b9e2abbe8f0919882f66bdd99e619  
  
Stored in directory:
/private/var/folders/4z/xqjmk1yj1hq5d_t4b3zkfkp80000gp/T/pip-ephem-wheel-
cache-1y8b6_i6/wheels/26/ba/5c/a8ae06e77eb74d03f129cbbe5d93bfea3b1259fabe4f838af4  
  
Successfully built boltz  
  
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/keanadavis/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/keanadavis/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/keanadavis/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-2026.1.0 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-2.49.0 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-2.32.4.20260107 wandb-0.18.7  
  
  
  
[notice] A new release of pip is available: 24.0 -> 25.3  
  
[notice] To update, run: /Users/keanadavis/boltz22/bin/python -m pip install
--upgrade pip  
  
Downloading Boltz model parameters (4 GB) and chemical component database (1.8
GB) to ~/.boltz  
/Users/keanadavis/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  
Boltz model parameters and CCD database are installed in ~/.boltz  
Successfully installed Boltz program and neural net weights.  

QTextCursor::setPosition: Position '1' out of range  

[Repeated 15 time(s)]

No molecules specified for Boltz prediction  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name NTCA useServer true serverHost 203.57.40.206 serverPort 10237

Running Boltz prediction of protein with 222 residues on gpu  
Using cached multiple sequence alignment
/Users/keanadavis/Downloads/ChimeraX/BoltzMSA/boltz_1  
Sending job request to server (656463 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 290, in predict_on_server  
msg = send_to_server(zip_data, host, port)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 334, in send_to_server  
client_socket.send(zip_data)  
BrokenPipeError: [Errno 32] Broken pipe  
  
BrokenPipeError: [Errno 32] Broken pipe  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/server.py", line 334, in send_to_server  
client_socket.send(zip_data)  
  
See log for complete Python traceback.  
  

> boltz predict protein
> MLANENSLLTMFRELGSGKLPLQIEQFERGKTIFFPGDPAERVYLLVKGAVKLSRVYESGEEITVALLRENSVFGVLSLLTGQRSDRFYHAVAFTPVQLFSVPIEFMQKALIERPELANVMLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGIPSPDGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRESKLIAIHKKRITVFNPVALSQQFS
> name NTCA useServer true serverHost 203.57.40.132 serverPort 10290

Running Boltz prediction of protein with 222 residues on gpu  
Using cached multiple sequence alignment
/Users/keanadavis/Downloads/ChimeraX/BoltzMSA/boltz_1  
Sending job request to server (656463 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
> name NTCA useServer true serverHost 203.57.40.132 serverPort 10290

Running Boltz prediction of protein with 222 residues on gpu  
Using cached multiple sequence alignment
/Users/keanadavis/Downloads/ChimeraX/BoltzMSA/boltz_1  
Sending job request to server (656463 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 - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.9
Locale: 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 Air
      Model Identifier: Mac14,2
      Model Number: MLXW3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 23 days, 19 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 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
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File attachment: Screenshot 2026-01-09 at 10.49.26 AM.png

Screenshot 2026-01-09 at 10.49.26 AM.png​

[keana.davis@…]

Added by email2trac

[Tom Goddard]

Thanks Keana! Very useful and disturbing, since Justin was able to get the Boltz server working with the pre-installed Boltz. So your result makes me think it was just good luck. I suspect the fundamental problem that makes it always work for me on UCSF WPA wifi for the last month, but not work for you or the students is that all of your laptops have UCSF security software installed and mine does not. Somehow that software prevents ChimeraX from getting the response from the Boltz server that is giving the job identifier. That is the meaning of the "RuntimeError". (Last night I fixed the error handling in ChimeraX so it gives a better error message.)

My goal is to figure out how to get RunPod Boltz to work for the students to do team projects. I was hoping this morning that Justin's experience where it worked with his laptop meant it would work for everyone else, but it is very helpful to know it is not that simple. I need to think about what the next try will be. We'll get this to work.

[Tom Goddard]

This report where Keana gets a RuntimeError indicating ChimeraX did not receive a response from RunPod Boltz server is the one case where we have seen this with the US-IL-1 datacenter (using network drive Boltz). Keana, Justin and I have also had it run successfully with that data center and Justin and I have not seen it fail. So it seems this bug report is the one instance where we have seen it fail with the RunPod network drive so far.

The plan is to see if it works for the students so they can do their team projects.