id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17639 'BoltzPredictionGUI' object has no attribute '_save_option_defaults' howell@… Tom Goddard "{{{ 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 138.5/138.5 kB 7.3 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 815.2/815.2 kB 18.7 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 27.9/27.9 MB 17.8 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 110.7/110.7 kB 10.5 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.2/43.2 kB 4.0 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 266.3/266.3 kB 20.8 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting mashumaro==3.14 (from boltz==0.4.1) Downloading mashumaro-3.14-py3-none-any.whl (92 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 92.2/92.2 kB 9.0 MB/s eta 0:00:00 Collecting modelcif==1.2 (from boltz==0.4.1) Downloading modelcif-1.2.tar.gz (66 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.8/66.8 kB 4.9 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting wandb==0.18.7 (from boltz==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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 10.9 MB/s eta 0:00:00 Collecting pyyaml==6.0.2 (from boltz==0.4.1) Downloading PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 172.0/172.0 kB 15.3 MB/s eta 0:00:00 Collecting biopython==1.84 (from boltz==0.4.1) Downloading biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB 11.6 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 30.3/30.3 MB 17.6 MB/s eta 0:00:00 Collecting sympy (from einx==0.3.0->boltz==0.4.1) Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.3/6.3 MB 14.2 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 79.5/79.5 kB 6.7 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.0/117.0 kB 8.5 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: packaging in /Applications/ChimeraX-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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 9.3 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 194.4/194.4 kB 15.3 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 961.5/961.5 kB 18.4 MB/s eta 0:00:00 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 /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) (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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 207.6/207.6 kB 12.4 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 417.8/417.8 kB 19.7 MB/s eta 0:00:00 Requirement already satisfied: psutil>=5.0.0 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) (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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 341.7/341.7 kB 14.9 MB/s eta 0:00:00 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 /Users/lynnehowell/boltz/lib/python3.11/site-packages (from wandb==0.18.7->boltz==0.4.1) (65.5.0) Requirement already satisfied: python-dateutil>=2.8.2 in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==0.4.1) (2.9.0.post0) Requirement already satisfied: pytz>=2020.1 in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==0.4.1) (2025.2) Requirement already satisfied: tzdata>=2022.7 in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==0.4.1) (2025.2) Requirement already satisfied: Pillow in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from rdkit>=2024.3.2->boltz==0.4.1) (10.4.0) Requirement already satisfied: filelock in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==0.4.1) (3.18.0) Requirement already satisfied: networkx in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==0.4.1) (3.3) Requirement already satisfied: jinja2 in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==0.4.1) (3.1.6) Requirement already satisfied: six>=1.4.0 in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz==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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 457.8/457.8 kB 21.3 MB/s eta 0:00:00 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 7.1 MB/s eta 0:00:00 Requirement already satisfied: msgpack in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 23.1 MB/s eta 0:00:00 Requirement already satisfied: MarkupSafe>=2.0 in /Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- 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 }}} " defect closed normal Structure Prediction fixed all ChimeraX