id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18272 failure trying to run boltz-2 Elaine Meng Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.5-arm64-arm-64bit ChimeraX Version: 1.11.dev202507240055 (2025-07-24 00:55:16 UTC) Description First try on using boltz-2 with ligand prediction I got this error that says I need to pip install lightning[extra] after I did that (tried as a ChimeraX command, maybe that was wrong) it failed again with the same error Log: > open /Users/meng/Desktop/startup.cxc > alias reset view orient; view initial > alias start tool show $1 > alias whereprefs info path user unversioned config > alias captut open help:user/tutorials/binding-sites.html#cap-example > alias previewts toolshed url https://cxtoolshed- > preview.rbvi.ucsf.edu;toolshed reload available > alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload > available > alias btut open > https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding- > sites.html; ui dockable false ""Help Viewer"" > alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation- > coloring/conservation-coloring.html; ui dockable false ""Help Viewer"" > alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop- > modeling.html; ui dockable false ""Help Viewer"" > alias mtut open https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole- > channel.html; ui dockable false ""Help Viewer""; windowsize 600 800 executed startup.cxc UCSF ChimeraX version: 1.11.dev202507240055 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1plx coordsets true 1plx title: NMR structure of Methionine-Enkephalin in fast tumbling Bicelles/DMPG [more info...] Chain information for 1plx #1 --- Chain | Description | UniProt A | Met-enkephalin 1 | PENK_HUMAN 1-5 1plx has 80 coordinate sets > coordset slider Missing or invalid ""structures"" argument: empty atom specifier > coordset slider #1 > select /A:1@OH 1 atom, 1 residue, 1 model selected > select add /A:5@SD 2 atoms, 2 residues, 1 model selected > select clear > select /A:5@SD 1 atom, 1 residue, 1 model selected > select add /A:1@OH 2 atoms, 2 residues, 1 model selected > select add /A:1@N 3 atoms, 2 residues, 1 model selected > select subtract /A:1@N 2 atoms, 2 residues, 1 model selected > select clear > select add /A:1@N 1 atom, 1 residue, 1 model selected > select add /A:5@C 2 atoms, 2 residues, 1 model selected > hbonds sel restrict cross interModel false reveal true 0 hydrogen bonds found in 80 coordsets > close #1 > open 1g1p coordsets true 1g1p title: NMR Solution Structures of delta-Conotoxin EVIA from Conus ermineus that Selectively Acts on Vertebrate Neuronal Na+ Channels [more info...] Chain information for 1g1p #1 --- Chain | Description | UniProt A | CONOTOXIN EVIA | CXD6A_CONER 1-32 Non-standard residues in 1g1p #1 --- NH2 — amino group Computing secondary structure 1g1p has 18 coordinate sets > show > ui tool show Boltz > usage boltz boltz install [directory] [downloadModelWeightsAndCcd true or false] [branch a text string] — Install Boltz from PyPi in a virtual environment directory: name of a folder to save/write; a name of 'browse' will bring up a file browser boltz predict [sequences] [ligands a residues specifier] [excludeLigands a text string] [protein sequences] [dna sequences] [rna sequences] [ligandCcd ligands] [ligandSmiles ligands] [name a text string] [resultsDirectory name of a folder to save/write; a name of 'browse' will bring up a file browser] [device device] [kernels true or false] [precision precision] [float16 true or false] [affinity a text string] [steering true or false] [samples an integer] [recycles an integer] [seed an integer] [useMsaCache true or false] [open true or false] [installLocation name of a folder to save/write; a name of 'browse' will bring up a file browser] [wait true or false] — Predict a structure with Boltz sequences: sequences device: one of cpu, default, or gpu precision: one of 16, 32, bf16-mixed, or bf16-true > close > boltz install /Users/meng/boltz2 Successfully created Boltz Python virtual environment /Users/meng/boltz2. 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/meng/boltz2/bin/python -m pip install git+https://github.com/RBVI/boltz@chimerax_boltz2 Collecting git+https://github.com/RBVI/boltz@chimerax_boltz2 Cloning https://github.com/RBVI/boltz (to revision chimerax_boltz2) to /private/var/folders/5y/hlccmqph8xj29d001s70mt7r0000gr/T/pip-req-build- tmop_7l9 Running command git clone --filter=blob:none --quiet https://github.com/RBVI/boltz /private/var/folders/5y/hlccmqph8xj29d001s70mt7r0000gr/T/pip-req-build- tmop_7l9 Running command git checkout -b chimerax_boltz2 --track origin/chimerax_boltz2 Switched to a new branch 'chimerax_boltz2' branch 'chimerax_boltz2' set up to track 'origin/chimerax_boltz2'. Resolved https://github.com/RBVI/boltz to commit 6e47badce94c472cd66b543781a3fea9ee9186b9 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>=2.2 (from boltz==2.1.1) Using cached torch-2.7.1-cp311-none-macosx_11_0_arm64.whl (68.6 MB) Requirement already satisfied: numpy<2.0,>=1.26 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from boltz==2.1.1) (1.26.4) Collecting hydra-core==1.3.2 (from boltz==2.1.1) Using cached hydra_core-1.3.2-py3-none-any.whl (154 kB) Collecting pytorch-lightning==2.5.0 (from boltz==2.1.1) Downloading pytorch_lightning-2.5.0-py3-none-any.whl (819 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.4/819.4 kB 9.4 MB/s eta 0:00:00 Collecting rdkit>=2024.3.2 (from boltz==2.1.1) Using cached rdkit-2025.3.3-cp311-cp311-macosx_11_0_arm64.whl (27.7 MB) Collecting dm-tree==0.1.8 (from boltz==2.1.1) Using cached dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB) Requirement already satisfied: requests==2.32.3 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from boltz==2.1.1) (2.32.3) Collecting pandas>=2.2.2 (from boltz==2.1.1) Using cached pandas-2.3.1-cp311-cp311-macosx_11_0_arm64.whl (10.8 MB) Collecting types-requests (from boltz==2.1.1) Using cached types_requests-2.32.4.20250611-py3-none-any.whl (20 kB) Collecting einops==0.8.0 (from boltz==2.1.1) Using cached einops-0.8.0-py3-none-any.whl (43 kB) Collecting einx==0.3.0 (from boltz==2.1.1) Using cached einx-0.3.0-py3-none-any.whl (102 kB) Collecting fairscale==0.4.13 (from boltz==2.1.1) Using cached fairscale-0.4.13-py3-none-any.whl Collecting mashumaro==3.14 (from boltz==2.1.1) Using cached mashumaro-3.14-py3-none-any.whl (92 kB) Collecting modelcif==1.2 (from boltz==2.1.1) Using cached modelcif-1.2-py3-none-any.whl Collecting wandb==0.18.7 (from boltz==2.1.1) Using cached wandb-0.18.7-py3-none-macosx_11_0_arm64.whl (15.2 MB) Collecting click==8.1.7 (from boltz==2.1.1) Using cached click-8.1.7-py3-none-any.whl (97 kB) Collecting pyyaml==6.0.2 (from boltz==2.1.1) Using cached PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB) Collecting biopython==1.84 (from boltz==2.1.1) Using cached biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB) Collecting scipy==1.13.1 (from boltz==2.1.1) Using cached scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl (30.3 MB) Collecting numba==0.61.0 (from boltz==2.1.1) Using cached numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl (2.8 MB) Collecting gemmi==0.6.5 (from boltz==2.1.1) Downloading gemmi-0.6.5-cp311-cp311-macosx_11_0_arm64.whl (3.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.0/3.0 MB 33.0 MB/s eta 0:00:00 Collecting scikit-learn==1.6.1 (from boltz==2.1.1) Downloading scikit_learn-1.6.1-cp311-cp311-macosx_12_0_arm64.whl (11.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.1/11.1 MB 28.6 MB/s eta 0:00:00 Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.1.1) Downloading chembl_structure_pipeline-1.2.2-py3-none-any.whl (17 kB) Collecting cuequivariance_torch>=0.5.0 (from boltz==2.1.1) Downloading cuequivariance_torch-0.5.1-py3-none-any.whl (56 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.4/56.4 kB 5.8 MB/s eta 0:00:00 Requirement already satisfied: setuptools>=46.4.0 in /Users/meng/boltz2/lib/python3.11/site-packages (from chembl_structure_pipeline==1.2.2->boltz==2.1.1) (65.5.0) Collecting sympy (from einx==0.3.0->boltz==2.1.1) Using cached sympy-1.14.0-py3-none-any.whl (6.3 MB) Collecting frozendict (from einx==0.3.0->boltz==2.1.1) Using cached frozendict-2.4.6-py311-none-any.whl (16 kB) Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==2.1.1) Using cached omegaconf-2.3.0-py3-none-any.whl (79 kB) Collecting antlr4-python3-runtime==4.9.* (from hydra- core==1.3.2->boltz==2.1.1) Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl Requirement already satisfied: packaging in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from hydra-core==1.3.2->boltz==2.1.1) (24.2) Requirement already satisfied: typing-extensions>=4.1.0 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from mashumaro==3.14->boltz==2.1.1) (4.14.1) Requirement already satisfied: ihm>=1.7 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from modelcif==1.2->boltz==2.1.1) (2.2) Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==2.1.1) Using cached llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl (26.2 MB) Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.1.1) Using cached tqdm-4.67.1-py3-none-any.whl (78 kB) Collecting fsspec[http]>=2022.5.0 (from pytorch- lightning==2.5.0->boltz==2.1.1) Using cached fsspec-2025.7.0-py3-none-any.whl (199 kB) Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.1.1) Downloading torchmetrics-1.8.0-py3-none-any.whl (981 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 981.9/981.9 kB 25.7 MB/s eta 0:00:00 Collecting lightning-utilities>=0.10.0 (from pytorch- lightning==2.5.0->boltz==2.1.1) Using cached lightning_utilities-0.14.3-py3-none-any.whl (28 kB) Requirement already satisfied: charset-normalizer<4,>=2 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==2.1.1) (3.4.2) Requirement already satisfied: idna<4,>=2.5 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==2.1.1) (3.10) Requirement already satisfied: urllib3<3,>=1.21.1 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==2.1.1) (2.5.0) Requirement already satisfied: certifi>=2017.4.17 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==2.1.1) (2023.11.17) Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.1.1) Downloading joblib-1.5.1-py3-none-any.whl (307 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 307.7/307.7 kB 816.4 kB/s eta 0:00:00 Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.1.1) Downloading threadpoolctl-3.6.0-py3-none-any.whl (18 kB) Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==2.1.1) Using cached 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==2.1.1) Downloading gitpython-3.1.45-py3-none-any.whl (208 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 208.2/208.2 kB 17.2 MB/s eta 0:00:00 Requirement already satisfied: platformdirs in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from wandb==0.18.7->boltz==2.1.1) (4.3.8) Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from wandb==0.18.7->boltz==2.1.1) Using cached protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl (418 kB) Requirement already satisfied: psutil>=5.0.0 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from wandb==0.18.7->boltz==2.1.1) (7.0.0) Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==2.1.1) Downloading sentry_sdk-2.33.2-py2.py3-none-any.whl (356 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 356.7/356.7 kB 20.6 MB/s eta 0:00:00 Collecting setproctitle (from wandb==0.18.7->boltz==2.1.1) Using cached setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl (11 kB) Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.1.1) Downloading cuequivariance-0.5.1-py3-none-any.whl (126 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.2/126.2 kB 5.6 MB/s eta 0:00:00 Requirement already satisfied: python-dateutil>=2.8.2 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==2.1.1) (2.9.0.post0) Requirement already satisfied: pytz>=2020.1 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==2.1.1) (2025.2) Requirement already satisfied: tzdata>=2022.7 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==2.1.1) (2025.2) Requirement already satisfied: Pillow in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from rdkit>=2024.3.2->boltz==2.1.1) (10.4.0) Requirement already satisfied: filelock in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==2.1.1) (3.18.0) Requirement already satisfied: networkx in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==2.1.1) (3.3) Requirement already satisfied: jinja2 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==2.1.1) (3.1.6) Requirement already satisfied: six>=1.4.0 in ./ChimeraX_Daily.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==2.1.1) (1.16.0) Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.1.1) Using cached aiohttp-3.12.14-cp311-cp311-macosx_11_0_arm64.whl (470 kB) Collecting gitdb<5,>=4.0.1 (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.1.1) Using cached gitdb-4.0.12-py3-none-any.whl (62 kB) Requirement already satisfied: msgpack in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ihm>=1.7->modelcif==1.2->boltz==2.1.1) (1.1.0) Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==2.1.1) Using cached mpmath-1.3.0-py3-none-any.whl (536 kB) Collecting opt-einsum (from cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.1.1) Downloading opt_einsum-3.4.0-py3-none-any.whl (71 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 71.9/71.9 kB 7.7 MB/s eta 0:00:00 Requirement already satisfied: MarkupSafe>=2.0 in ./ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from jinja2->torch>=2.2->boltz==2.1.1) (3.0.2) Collecting aiohappyeyeballs>=2.5.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.1.1) Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB) Collecting aiosignal>=1.4.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.1.1) Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB) Collecting attrs>=17.3.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.1.1) Using cached attrs-25.3.0-py3-none-any.whl (63 kB) Collecting frozenlist>=1.1.1 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.1.1) Using cached frozenlist-1.7.0-cp311-cp311-macosx_11_0_arm64.whl (47 kB) Collecting multidict<7.0,>=4.5 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.1.1) Using cached multidict-6.6.3-cp311-cp311-macosx_11_0_arm64.whl (44 kB) Collecting propcache>=0.2.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.1.1) Using cached propcache-0.3.2-cp311-cp311-macosx_11_0_arm64.whl (43 kB) Collecting yarl<2.0,>=1.17.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.1.1) Using cached yarl-1.20.1-cp311-cp311-macosx_11_0_arm64.whl (89 kB) Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.1.1) Using cached smmap-5.0.2-py3-none-any.whl (24 kB) Building wheels for collected packages: boltz Building wheel for boltz (pyproject.toml): started Building wheel for boltz (pyproject.toml): finished with status 'done' Created wheel for boltz: filename=boltz-2.1.1-py3-none-any.whl size=262921 sha256=06e9d2fafb6202a840affbc45fa5f2b4ae118836ab55ff461361af4255c6b020 Stored in directory: /private/var/folders/5y/hlccmqph8xj29d001s70mt7r0000gr/T/pip-ephem-wheel- cache- bjcbav3a/wheels/eb/6b/e8/b8f2318f04e510ea3091105ed50c6e2ff4fa900e16361241f7 Successfully built boltz Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types- requests, tqdm, threadpoolctl, sympy, smmap, setproctitle, sentry-sdk, scipy, rdkit, pyyaml, protobuf, propcache, opt-einsum, multidict, mashumaro, llvmlite, lightning-utilities, joblib, gemmi, fsspec, frozenlist, frozendict, einops, docker-pycreds, click, biopython, attrs, aiohappyeyeballs, yarl, torch, scikit-learn, pandas, omegaconf, numba, modelcif, gitdb, einx, cuequivariance, chembl_structure_pipeline, aiosignal, torchmetrics, hydra- core, gitpython, fairscale, cuequivariance_torch, aiohttp, wandb, pytorch- lightning, boltz Attempting uninstall: scipy Found existing installation: scipy 1.14.0 Not uninstalling scipy at /Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages, outside environment /Users/meng/boltz2 Can't uninstall 'scipy'. No files were found to uninstall. Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.14 aiosignal-1.4.0 antlr4-python3-runtime-4.9.3 attrs-25.3.0 biopython-1.84 boltz-2.1.1 chembl_structure_pipeline-1.2.2 click-8.1.7 cuequivariance-0.5.1 cuequivariance_torch-0.5.1 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0 einx-0.3.0 fairscale-0.4.13 frozendict-2.4.6 frozenlist-1.7.0 fsspec-2025.7.0 gemmi-0.6.5 gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 joblib-1.5.1 lightning-utilities-0.14.3 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.6.3 numba-0.61.0 omegaconf-2.3.0 opt-einsum-3.4.0 pandas-2.3.1 propcache-0.3.2 protobuf-5.29.5 pytorch-lightning-2.5.0 pyyaml-6.0.2 rdkit-2025.3.3 scikit-learn-1.6.1 scipy-1.13.1 sentry-sdk-2.33.2 setproctitle-1.3.6 smmap-5.0.2 sympy-1.14.0 threadpoolctl-3.6.0 torch-2.7.1 torchmetrics-1.8.0 tqdm-4.67.1 types-requests-2.32.4.20250611 wandb-0.18.7 yarl-1.20.1 [notice] A new release of pip is available: 23.1.2 -> 25.1.1 [notice] To update, run: /Users/meng/boltz2/bin/python -m pip install --upgrade pip Downloading Boltz model parameters (4 GB) and chemical component database (1.8 GB) to ~/.boltz /Users/meng/boltz2/bin/python /Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/download_weights_and_ccd.py Downloading the CCD data to /Users/meng/.boltz/mols.tar. This may take a bit of time. You may change the cache directory with the --cache flag. Extracting the CCD data to /Users/meng/.boltz/mols. This may take a bit of time. You may change the cache directory with the --cache flag. Downloading the Boltz-2 weights to /Users/meng/.boltz/boltz2_conf.ckpt. You may change the cache directory with the --cache flag. Downloading the Boltz-2 affinity weights to /Users/meng/.boltz/boltz2_aff.ckpt. You may change the cache directory with the --cache flag. Making CCD atom counts table for 45227 in /Users/meng/.boltz/mols Boltz model parameters and CCD database are installed in ~/.boltz Successfully installed Boltz. > boltz predict protein DDCIKPYGFCSLPILKNGLCCSGACVGVCADLX ligandCcd 12123 name > 1g1p affinity 12123 Running Boltz prediction of protein with 33 residues, 1 ligands 12123 on gpu Using multiple sequence alignment server https://api.colabfold.com Running boltz prediction failed with exit code 0: command: /Users/meng/boltz2/bin/boltz predict /Users/meng/Desktop/boltz_1g1p/1g1p.yaml --use_msa_server --accelerator gpu --no_kernels stdout: Boltz version 2.1.1 Checking input data. Processing 1 inputs with 1 threads. Failed to process /Users/meng/Desktop/boltz_1g1p/1g1p.yaml. Skipping. Error: object of type 'int' has no len(). stderr: 0%| | 0/1 [00:00 1: ^^^^^^^^ TypeError: object of type 'int' has no len() 100%|██████████| 1/1 [00:00<00:00, 8.05it/s] 100%|██████████| 1/1 [00:00<00:00, 8.04it/s] GPU available: True (mps), used: True TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /Users/meng/boltz2/lib/python3.11/site- packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76: Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the `pytorch_lightning` package, due to potential conflicts with other packages in the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the default logger, unless the `tensorboard` or `tensorboardX` packages are found. Please `pip install lightning[extra]` or one of them to enable TensorBoard support by default > pip install lightning[extra] > boltz predict protein DDCIKPYGFCSLPILKNGLCCSGACVGVCADLX ligandCcd 12123 name > 1g1p affinity 12123 Running Boltz prediction of protein with 33 residues, 1 ligands 12123 on gpu Using multiple sequence alignment server https://api.colabfold.com Running boltz prediction failed with exit code 0: command: /Users/meng/boltz2/bin/boltz predict /Users/meng/Desktop/boltz_1g1p_1/1g1p.yaml --use_msa_server --accelerator gpu --no_kernels stdout: Boltz version 2.1.1 Checking input data. Processing 1 inputs with 1 threads. Failed to process /Users/meng/Desktop/boltz_1g1p_1/1g1p.yaml. Skipping. Error: object of type 'int' has no len(). stderr: 0%| | 0/1 [00:00 1: ^^^^^^^^ TypeError: object of type 'int' has no len() 100%|██████████| 1/1 [00:00<00:00, 9.48it/s] 100%|██████████| 1/1 [00:00<00:00, 9.47it/s] GPU available: True (mps), used: True TPU available: False, using: 0 TPU cores HPU available: False, using: 0 HPUs /Users/meng/boltz2/lib/python3.11/site- packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76: Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the `pytorch_lightning` package, due to potential conflicts with other packages in the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the default logger, unless the `tensorboard` or `tensorboardX` packages are found. Please `pip install lightning[extra]` or one of them to enable TensorBoard support by default OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Pro 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: MacBookPro18,1 Model Number: MK1F3LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 11881.121.1 OS Loader Version: 11881.121.1 Software: System Software Overview: System Version: macOS 15.5 (24F74) Kernel Version: Darwin 24.5.0 Time since boot: 6 hours, 49 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 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 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.0 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.10 ChimeraX-AtomicLibrary: 14.1.21 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: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 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umap-learn: 0.5.7 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Structure Prediction fixed all ChimeraX