'BoltzPredictionGUI' object has no attribute '_save_option_defaults'

[howell@…]

The following bug report has been submitted:
Platform:        macOS-15.4.1-arm64-arm-64bit
ChimeraX Version: 1.10rc202505100155 (2025-05-10 01:55:54 UTC)
Description
TRying to install Blotz-1 on my macbook pro

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10rc202505100155 (2025-05-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Boltz

> boltz install /Users/lynnehowell/boltz

Successfully created Boltz Python virtual environment
/Users/lynnehowell/boltz.  
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/lynnehowell/boltz/bin/python -m pip install boltz==0.4.1  
Collecting boltz==0.4.1  
  
Downloading boltz-0.4.1-py3-none-any.whl (138 kB)  
  
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Collecting torch>=2.2 (from boltz==0.4.1)  
  
Downloading torch-2.7.0-cp311-none-macosx_11_0_arm64.whl (68.6 MB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 68.6/68.6 MB 17.0 MB/s eta 0:00:00  
  
Collecting numpy==1.26.3 (from boltz==0.4.1)  
  
Downloading numpy-1.26.3-cp311-cp311-macosx_11_0_arm64.whl (14.0 MB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 14.0/14.0 MB 21.3 MB/s eta 0:00:00  
  
Collecting hydra-core==1.3.2 (from boltz==0.4.1)  
  
Downloading hydra_core-1.3.2-py3-none-any.whl (154 kB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.5/154.5 kB 15.8 MB/s eta 0:00:00  
  
Collecting pytorch-lightning==2.4.0 (from boltz==0.4.1)  
  
Downloading pytorch_lightning-2.4.0-py3-none-any.whl (815 kB)  
  
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Collecting rdkit>=2024.3.2 (from boltz==0.4.1)  
  
Downloading rdkit-2025.3.1-cp311-cp311-macosx_11_0_arm64.whl (27.9 MB)  
  
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Collecting dm-tree==0.1.8 (from boltz==0.4.1)  
  
Downloading dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB)  
  
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Requirement already satisfied: requests==2.32.3 in
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from boltz==0.4.1) (2.32.3)  
  
Collecting pandas>=2.2.2 (from boltz==0.4.1)  
  
Downloading pandas-2.2.3-cp311-cp311-macosx_11_0_arm64.whl (11.3 MB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.3/11.3 MB 18.6 MB/s eta 0:00:00  
  
Collecting types-requests (from boltz==0.4.1)  
  
Downloading types_requests-2.32.0.20250328-py3-none-any.whl (20 kB)  
  
Collecting einops==0.8.0 (from boltz==0.4.1)  
  
Downloading einops-0.8.0-py3-none-any.whl (43 kB)  
  
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Collecting einx==0.3.0 (from boltz==0.4.1)  
  
Downloading einx-0.3.0-py3-none-any.whl (102 kB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.0/103.0 kB 12.7 MB/s eta 0:00:00  
  
Collecting fairscale==0.4.13 (from boltz==0.4.1)  
  
Downloading fairscale-0.4.13.tar.gz (266 kB)  
  
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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==0.4.1)  
  
Downloading mashumaro-3.14-py3-none-any.whl (92 kB)  
  
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Collecting modelcif==1.2 (from boltz==0.4.1)  
  
Downloading modelcif-1.2.tar.gz (66 kB)  
  
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Preparing metadata (setup.py): started  
  
Preparing metadata (setup.py): finished with status 'done'  
  
Collecting wandb==0.18.7 (from boltz==0.4.1)  
  
Downloading wandb-0.18.7-py3-none-macosx_11_0_arm64.whl (15.2 MB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.2/15.2 MB 15.6 MB/s eta 0:00:00  
  
Collecting click==8.1.7 (from boltz==0.4.1)  
  
Downloading click-8.1.7-py3-none-any.whl (97 kB)  
  
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Collecting pyyaml==6.0.2 (from boltz==0.4.1)  
  
Downloading PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB)  
  
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Collecting biopython==1.84 (from boltz==0.4.1)  
  
Downloading biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB)  
  
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Collecting scipy==1.13.1 (from boltz==0.4.1)  
  
Downloading scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl (30.3 MB)  
  
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Collecting sympy (from einx==0.3.0->boltz==0.4.1)  
  
Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB)  
  
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Collecting frozendict (from einx==0.3.0->boltz==0.4.1)  
  
Downloading frozendict-2.4.6-py311-none-any.whl (16 kB)  
  
Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==0.4.1)  
  
Downloading omegaconf-2.3.0-py3-none-any.whl (79 kB)  
  
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Collecting antlr4-python3-runtime==4.9.* (from hydra-
core==1.3.2->boltz==0.4.1)  
  
Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB)  
  
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Preparing metadata (setup.py): started  
  
Preparing metadata (setup.py): finished with status 'done'  
  
Requirement already satisfied: packaging in
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from hydra-core==1.3.2->boltz==0.4.1) (24.2)  
  
Requirement already satisfied: typing-extensions>=4.1.0 in
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from mashumaro==3.14->boltz==0.4.1) (4.13.2)  
  
Requirement already satisfied: ihm>=1.7 in
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from modelcif==1.2->boltz==0.4.1) (2.2)  
  
Collecting tqdm>=4.57.0 (from pytorch-lightning==2.4.0->boltz==0.4.1)  
  
Downloading tqdm-4.67.1-py3-none-any.whl (78 kB)  
  
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Collecting fsspec[http]>=2022.5.0 (from pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading fsspec-2025.3.2-py3-none-any.whl (194 kB)  
  
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Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz==0.4.1)  
  
Downloading torchmetrics-1.7.1-py3-none-any.whl (961 kB)  
  
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Collecting lightning-utilities>=0.10.0 (from pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading lightning_utilities-0.14.3-py3-none-any.whl (28 kB)  
  
Requirement already satisfied: charset-normalizer<4,>=2 in
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==0.4.1) (3.4.2)  
  
Requirement already satisfied: idna<4,>=2.5 in
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==0.4.1) (3.10)  
  
Requirement already satisfied: urllib3<3,>=1.21.1 in
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packages (from requests==2.32.3->boltz==0.4.1) (2.4.0)  
  
Requirement already satisfied: certifi>=2017.4.17 in
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==0.4.1) (2023.11.17)  
  
Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==0.4.1)  
  
Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)  
  
Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==0.4.1)  
  
Downloading GitPython-3.1.44-py3-none-any.whl (207 kB)  
  
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Requirement already satisfied: platformdirs in
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from wandb==0.18.7->boltz==0.4.1) (4.3.8)  
  
Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from
wandb==0.18.7->boltz==0.4.1)  
  
Downloading protobuf-5.29.4-cp38-abi3-macosx_10_9_universal2.whl (417 kB)  
  
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Requirement already satisfied: psutil>=5.0.0 in
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packages (from wandb==0.18.7->boltz==0.4.1) (7.0.0)  
  
Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==0.4.1)  
  
Downloading sentry_sdk-2.28.0-py2.py3-none-any.whl (341 kB)  
  
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Collecting setproctitle (from wandb==0.18.7->boltz==0.4.1)  
  
Downloading setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl (11 kB)  
  
Requirement already satisfied: setuptools in
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Requirement already satisfied: python-dateutil>=2.8.2 in
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packages (from pandas>=2.2.2->boltz==0.4.1) (2.9.0.post0)  
  
Requirement already satisfied: pytz>=2020.1 in
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packages (from pandas>=2.2.2->boltz==0.4.1) (2025.2)  
  
Requirement already satisfied: tzdata>=2022.7 in
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packages (from pandas>=2.2.2->boltz==0.4.1) (2025.2)  
  
Requirement already satisfied: Pillow in
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Requirement already satisfied: filelock in
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Requirement already satisfied: jinja2 in
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Requirement already satisfied: six>=1.4.0 in
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packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz==0.4.1) (1.16.0)  
  
Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading aiohttp-3.11.18-cp311-cp311-macosx_11_0_arm64.whl (457 kB)  
  
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Collecting gitdb<5,>=4.0.1 (from
gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==0.4.1)  
  
Downloading gitdb-4.0.12-py3-none-any.whl (62 kB)  
  
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Requirement already satisfied: msgpack in
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packages (from ihm>=1.7->modelcif==1.2->boltz==0.4.1) (1.1.0)  
  
Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==0.4.1)  
  
Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)  
  
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Requirement already satisfied: MarkupSafe>=2.0 in
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packages (from jinja2->torch>=2.2->boltz==0.4.1) (3.0.2)  
  
Collecting aiohappyeyeballs>=2.3.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)  
  
Collecting aiosignal>=1.1.2 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading aiosignal-1.3.2-py2.py3-none-any.whl (7.6 kB)  
  
Collecting attrs>=17.3.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading attrs-25.3.0-py3-none-any.whl (63 kB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.8/63.8 kB 6.2 MB/s eta 0:00:00  
  
Collecting frozenlist>=1.1.1 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading frozenlist-1.6.0-cp311-cp311-macosx_11_0_arm64.whl (122 kB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 122.2/122.2 kB 11.6 MB/s eta 0:00:00  
  
Collecting multidict<7.0,>=4.5 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading multidict-6.4.3-cp311-cp311-macosx_11_0_arm64.whl (37 kB)  
  
Collecting propcache>=0.2.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading propcache-0.3.1-cp311-cp311-macosx_11_0_arm64.whl (45 kB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 45.9/45.9 kB 5.9 MB/s eta 0:00:00  
  
Collecting yarl<2.0,>=1.17.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)  
  
Downloading yarl-1.20.0-cp311-cp311-macosx_11_0_arm64.whl (94 kB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.6/94.6 kB 10.9 MB/s eta 0:00:00  
  
Collecting smmap<6,>=3.0.1 (from
gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==0.4.1)  
  
Downloading smmap-5.0.2-py3-none-any.whl (24 kB)  
  
Building wheels for collected packages: fairscale, modelcif,
antlr4-python3-runtime  
  
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=332207
sha256=3e806581374fcbc2add35779674000ea6ff35f83197f184f8e5bead71bb6c4bc  
  
Stored in directory:
/Users/lynnehowell/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=4ce994729fca35d1082ed737dbe4dacb7285b9dad3cceeaeeb6db9bcf511694f  
  
Stored in directory:
/Users/lynnehowell/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=5cfff34a6811f6f4341c6d627469e184b0c7edc03e16219767cdad6f24c51cba  
  
Stored in directory:
/Users/lynnehowell/Library/Caches/pip/wheels/1a/97/32/461f837398029ad76911109f07047fde1d7b661a147c7c56d1  
  
Successfully built fairscale modelcif antlr4-python3-runtime  
  
Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types-
requests, tqdm, sympy, smmap, setproctitle, sentry-sdk, pyyaml, protobuf,
propcache, numpy, multidict, mashumaro, lightning-utilities, fsspec,
frozenlist, frozendict, einops, docker-pycreds, click, attrs,
aiohappyeyeballs, yarl, torch, scipy, rdkit, pandas, omegaconf, modelcif,
gitdb, einx, biopython, aiosignal, torchmetrics, hydra-core, gitpython,
fairscale, aiohttp, wandb, pytorch-lightning, boltz  
  
Attempting uninstall: numpy  
  
Found existing installation: numpy 1.26.4  
  
Not uninstalling numpy at
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/lynnehowell/boltz  
  
Can't uninstall 'numpy'. No files were found to uninstall.  
  
Attempting uninstall: scipy  
  
Found existing installation: scipy 1.14.0  
  
Not uninstalling scipy at
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/lynnehowell/boltz  
  
Can't uninstall 'scipy'. No files were found to uninstall.  
  
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.  
  
chimerax-bundlebuilder 1.5.1 requires numpy==1.26.4, but you have numpy 1.26.3
which is incompatible.  
  
chimerax-bundlebuilder 1.5.1 requires setuptools==78.1.0, but you have
setuptools 65.5.0 which is incompatible.  
  
Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.11.18 aiosignal-1.3.2
antlr4-python3-runtime-4.9.3 attrs-25.3.0 biopython-1.84 boltz-0.4.1
click-8.1.7 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-1.6.0 fsspec-2025.3.2
gitdb-4.0.12 gitpython-3.1.44 hydra-core-1.3.2 lightning-utilities-0.14.3
mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.4.3 numpy-1.26.3
omegaconf-2.3.0 pandas-2.2.3 propcache-0.3.1 protobuf-5.29.4 pytorch-
lightning-2.4.0 pyyaml-6.0.2 rdkit-2025.3.1 scipy-1.13.1 sentry-sdk-2.28.0
setproctitle-1.3.6 smmap-5.0.2 sympy-1.14.0 torch-2.7.0 torchmetrics-1.7.1
tqdm-4.67.1 types-requests-2.32.0.20250328 wandb-0.18.7 yarl-1.20.0  
  
  
  
[notice] A new release of pip is available: 23.1.2 -> 25.1.1  
  
[notice] To update, run: /Users/lynnehowell/boltz/bin/python -m pip install
--upgrade pip  
  
Successfully installed Boltz.  
Downloading Boltz model parameters (3.3 GB) and chemical component database
(330 MB) to ~/.boltz  
/Users/lynnehowell/boltz/bin/python
/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/download_weights_and_ccd.py  
Downloading the CCD dictionary to /Users/lynnehowell/.boltz/ccd.pkl. You may
change the cache directory with the --cache flag.  
  
Downloading the model weights to /Users/lynnehowell/.boltz/boltz1_conf.ckpt.
You may change the cache directory with the --cache flag.  
  
Boltz model parameters and CCD database are installed in ~/.boltz  
Successfully installed Boltz.  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/install.py", line 256, in _log_queued_lines  
self._finished()  
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/install.py", line 262, in _finished  
self._finished_callback(success)  
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/install.py", line 202, in
_finished_download_weights_and_ccd  
self._finished('download weights and ccd', success)  
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/install.py", line 219, in _finished  
self.finished_callback(success)  
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 762, in _boltz_install_finished  
self._save_option_defaults(install_dir_only = True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'BoltzPredictionGUI' object has no attribute
'_save_option_defaults'  
  
Error processing trigger "new frame":  
AttributeError: 'BoltzPredictionGUI' object has no attribute
'_save_option_defaults'  
  
File
"/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 762, in _boltz_install_finished  
self._save_option_defaults(install_dir_only = True)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,10
      Model Number: MRX83LL/A
      Chip: Apple M3 Max
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 36 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 11881.101.1

Software:

    System Software Overview:

      System Version: macOS 15.4.1 (24E263)
      Kernel Version: Darwin 24.4.0
      Time since boot: 13 days, 1 hour, 52 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      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:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.3.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.3.2
    build: 1.2.2.post1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.20.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.3
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.18
    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: 1.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.5.1
    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: 1.2.6
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10rc202505100155
    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: 2.5.1
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.6.2
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.10.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.19
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 1.5.1
    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: 2.17.1
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.45.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 0.2.2
    contourpy: 1.3.2
    coverage: 7.8.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.14
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.58.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    lxml: 5.3.1
    lz4: 4.4.4
    MarkupSafe: 3.0.2
    matplotlib: 3.10.0
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 2.2.2
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    plotly: 5.24.1
    pluggy: 1.5.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pyKVFinder: 0.7.2
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.1.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 26.4.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 78.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    tenacity: 9.0.0
    tifffile: 2025.3.13
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.13.2
    tzdata: 2025.2
    urllib3: 2.4.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[pett]

Reported by Lynne

[howell@…]

Not sure what the issue was.. I may have inadvertently pushed the wrong button.. after exited the program and restarting Boltz-1 works beautifully – thank you for making this part of ChimeraX.. its so very useful…
L

__________________________________________________________________________

P. Lynne Howell
Canada Research Chair (2006-2020)
Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children
Professor, Department of Biochemistry, University of Toronto

Office and Mailing address:
Room 20-9-715
Peter Gilgan Centre for Research and Learning (PGCRL)
686 Bay St. Toronto ON M5G 0A4

Phone: 416-813-5378 (Internal 305378)

Web page: https://lab.research.sickkids.ca/howell/


From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Monday, May 12, 2025 at 5:02 PM
To: Lynne Howell <howell@sickkids.ca>, goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #17639: 'BoltzPredictionGUI' object has no attribute '_save_option_defaults' (was: ChimeraX bug report submission)
#17639: 'BoltzPredictionGUI' object has no attribute '_save_option_defaults'
-------------------------------------------+-------------------------
          Reporter:  howell@…              |      Owner:  Tom Goddard
              Type:  defect                |     Status:  assigned
          Priority:  normal                |  Milestone:
         Component:  Structure Prediction  |    Version:
        Resolution:                        |   Keywords:
        Blocked By:                        |   Blocking:
Notify when closed:                        |   Platform:  all
           Project:  ChimeraX              |
-------------------------------------------+-------------------------
Changes (by pett):

 * component:  Unassigned => Structure Prediction
 * owner:  (none) => Tom Goddard
 * platform:   => all
 * project:   => ChimeraX
 * status:  new => assigned
 * summary:  ChimeraX bug report submission => 'BoltzPredictionGUI' object
     has no attribute '_save_option_defaults'

Comment:

 Reported by Lynne
--
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[Tom Goddard]

Fixed.

Thanks for reporting the problem. I changed some Boltz code last Friday and apparently forgot to test this installing Boltz. When you first install it ChimeraX tries to save the installation location (~/boltz) in preferences and I changed that function call on Friday and mistyped the name of the function and apparently forgot to test it. It will be fixed in tomorrow's release candidate and daily build.

That error will only happen when you first install boltz and the install was successful -- saving the location was the last thing it tried to do and was not even needed since it installs in the default location. So you are right that it should work fine from now on.