id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18460 BoltzMSA/index: No such file or directory jacjagoabc@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Attempted to run Boltz prediction. It terminated with error specifying that: File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/boltz/predict.py"", line 272, in _create_yaml_input msa_cache_files = self._msa_cache_files() ^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/boltz/predict.py"", line 303, in _msa_cache_files msa_cache_files = _find_msa_cache_files(protein_seqs, self.msa_cache_dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/boltz/predict.py"", line 691, in _find_msa_cache_files with open(index_path, 'r') as f: ^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '/Users/jacekj/Downloads/ChimeraX/BoltzMSA/index' FileNotFoundError: [Errno 2] No such file or directory: '/Users/jacekj/Downloads/ChimeraX/BoltzMSA/index' File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/boltz/predict.py"", line 691, in _find_msa_cache_files with open(index_path, 'r') as f: ^^^^^^^^^^^^^^^^^^^^^ I manually checked - folder /BoltsMSA/ exists but is empty How do I make Boltz runnung succesfully? Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5es1 format mmcif fromDatabase pdb 5es1 title: Crystal structure of microtubule affinity-regulating kinase 4 catalytic domain In complex with A pyrazolopyrimidine inhibitor [more info...] Chain information for 5es1 #1 --- Chain | Description | UniProt A | MAP/microtubule affinity-regulating kinase 4 | MARK4_HUMAN 41-367 Non-standard residues in 5es1 #1 --- 5RC — ~{N}-[(1~{R},6~{R})-6-azanyl-2,2-bis(fluoranyl)cyclohexyl]-5-ethyl-4-[6-(trifluoromethyl)pyrazolo[1,5-a]pyrimidin-3-yl]thiophene-2-carboxamide > ui tool show Boltz > boltz install /Users/jacekj/boltz Successfully created Boltz Python virtual environment /Users/jacekj/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/jacekj/boltz/bin/python -m pip install git+https://github.com/RBVI/boltz@chimerax Collecting git+https://github.com/RBVI/boltz@chimerax Cloning https://github.com/RBVI/boltz (to revision chimerax) to /private/var/folders/xv/81gtkgsn24xg5lmlbl_jqzg80000gn/T/pip-req- build-26wy61vg Running command git clone --filter=blob:none --quiet https://github.com/RBVI/boltz /private/var/folders/xv/81gtkgsn24xg5lmlbl_jqzg80000gn/T/pip-req- build-26wy61vg Running command git checkout -b chimerax --track origin/chimerax Switched to a new branch 'chimerax' branch 'chimerax' set up to track 'origin/chimerax'. Resolved https://github.com/RBVI/boltz to commit ca6c444937381392e979c1c26db72dce7963e480 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==1.0.0) Using cached torch-2.8.0-cp311-none-macosx_11_0_arm64.whl (73.6 MB) Requirement already satisfied: numpy<2.0,>=1.26 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from boltz==1.0.0) (1.26.4) Collecting hydra-core==1.3.2 (from boltz==1.0.0) Using cached hydra_core-1.3.2-py3-none-any.whl (154 kB) Collecting pytorch-lightning==2.4.0 (from boltz==1.0.0) Using cached pytorch_lightning-2.4.0-py3-none-any.whl (815 kB) Collecting rdkit>=2024.3.2 (from boltz==1.0.0) Using cached rdkit-2025.3.5-cp311-cp311-macosx_11_0_arm64.whl (28.7 MB) Collecting dm-tree==0.1.8 (from boltz==1.0.0) Using cached dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB) Requirement already satisfied: requests==2.32.3 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from boltz==1.0.0) (2.32.3) Collecting pandas>=2.2.2 (from boltz==1.0.0) Using cached pandas-2.3.1-cp311-cp311-macosx_11_0_arm64.whl (10.8 MB) Collecting types-requests (from boltz==1.0.0) Using cached types_requests-2.32.4.20250809-py3-none-any.whl (20 kB) Collecting einops==0.8.0 (from boltz==1.0.0) Using cached einops-0.8.0-py3-none-any.whl (43 kB) Collecting einx==0.3.0 (from boltz==1.0.0) Using cached einx-0.3.0-py3-none-any.whl (102 kB) Collecting fairscale==0.4.13 (from boltz==1.0.0) Using cached fairscale-0.4.13-py3-none-any.whl Collecting mashumaro==3.14 (from boltz==1.0.0) Using cached mashumaro-3.14-py3-none-any.whl (92 kB) Collecting modelcif==1.2 (from boltz==1.0.0) Using cached modelcif-1.2-py3-none-any.whl Collecting wandb==0.18.7 (from boltz==1.0.0) Using cached wandb-0.18.7-py3-none-macosx_11_0_arm64.whl (15.2 MB) Collecting click==8.1.7 (from boltz==1.0.0) Using cached click-8.1.7-py3-none-any.whl (97 kB) Collecting pyyaml==6.0.2 (from boltz==1.0.0) Using cached PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB) Collecting biopython==1.84 (from boltz==1.0.0) Using cached biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB) Collecting scipy==1.13.1 (from boltz==1.0.0) Using cached scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl (30.3 MB) Collecting numba==0.61.0 (from boltz==1.0.0) Using cached numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl (2.8 MB) Collecting sympy (from einx==0.3.0->boltz==1.0.0) Using cached sympy-1.14.0-py3-none-any.whl (6.3 MB) Collecting frozendict (from einx==0.3.0->boltz==1.0.0) 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==1.0.0) 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==1.0.0) Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl Requirement already satisfied: packaging in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from hydra-core==1.3.2->boltz==1.0.0) (24.2) Requirement already satisfied: typing-extensions>=4.1.0 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from mashumaro==3.14->boltz==1.0.0) (4.14.1) Requirement already satisfied: ihm>=1.7 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from modelcif==1.2->boltz==1.0.0) (2.2) Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==1.0.0) Using cached llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl (26.2 MB) Collecting tqdm>=4.57.0 (from pytorch-lightning==2.4.0->boltz==1.0.0) Using cached tqdm-4.67.1-py3-none-any.whl (78 kB) Collecting fsspec[http]>=2022.5.0 (from pytorch- lightning==2.4.0->boltz==1.0.0) Using cached fsspec-2025.7.0-py3-none-any.whl (199 kB) Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz==1.0.0) Using cached torchmetrics-1.8.1-py3-none-any.whl (982 kB) Collecting lightning-utilities>=0.10.0 (from pytorch- lightning==2.4.0->boltz==1.0.0) Using cached lightning_utilities-0.15.2-py3-none-any.whl (29 kB) Requirement already satisfied: charset-normalizer<4,>=2 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==1.0.0) (3.4.2) Requirement already satisfied: idna<4,>=2.5 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==1.0.0) (3.10) Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==1.0.0) (2.5.0) Requirement already satisfied: certifi>=2017.4.17 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==1.0.0) (2023.11.17) Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==1.0.0) 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==1.0.0) Using cached gitpython-3.1.45-py3-none-any.whl (208 kB) Requirement already satisfied: platformdirs in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from wandb==0.18.7->boltz==1.0.0) (4.3.8) Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from wandb==0.18.7->boltz==1.0.0) Using cached protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl (418 kB) Requirement already satisfied: psutil>=5.0.0 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from wandb==0.18.7->boltz==1.0.0) (7.0.0) Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==1.0.0) Downloading sentry_sdk-2.35.0-py2.py3-none-any.whl (363 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 363.8/363.8 kB 8.4 MB/s eta 0:00:00 Collecting setproctitle (from wandb==0.18.7->boltz==1.0.0) Using cached setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl (11 kB) Requirement already satisfied: setuptools in /Users/jacekj/boltz/lib/python3.11/site-packages (from wandb==0.18.7->boltz==1.0.0) (65.5.0) Requirement already satisfied: python-dateutil>=2.8.2 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==1.0.0) (2.9.0.post0) Requirement already satisfied: pytz>=2020.1 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2) Requirement already satisfied: tzdata>=2022.7 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2) Requirement already satisfied: Pillow in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from rdkit>=2024.3.2->boltz==1.0.0) (10.4.0) Requirement already satisfied: filelock in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==1.0.0) (3.18.0) Requirement already satisfied: networkx in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==1.0.0) (3.3) Requirement already satisfied: jinja2 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==1.0.0) (3.1.6) Requirement already satisfied: six>=1.4.0 in /Users/jacekj/Applications/ChimeraX-1.10.1.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==1.0.0) (1.16.0) Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch- lightning==2.4.0->boltz==1.0.0) Using cached aiohttp-3.12.15-cp311-cp311-macosx_11_0_arm64.whl (471 kB) Collecting gitdb<5,>=4.0.1 (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==1.0.0) Using cached gitdb-4.0.12-py3-none-any.whl (62 kB) Requirement already satisfied: msgpack in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ihm>=1.7->modelcif==1.2->boltz==1.0.0) (1.1.0) Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==1.0.0) Using cached mpmath-1.3.0-py3-none-any.whl (536 kB) Requirement already satisfied: MarkupSafe>=2.0 in /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from jinja2->torch>=2.2->boltz==1.0.0) (3.0.2) Collecting aiohappyeyeballs>=2.5.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch- lightning==2.4.0->boltz==1.0.0) 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==2.4.0->boltz==1.0.0) 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==2.4.0->boltz==1.0.0) 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==2.4.0->boltz==1.0.0) 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==2.4.0->boltz==1.0.0) Using cached multidict-6.6.4-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==2.4.0->boltz==1.0.0) 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==2.4.0->boltz==1.0.0) 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==1.0.0) 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-1.0.0-py3-none-any.whl size=150846 sha256=37ade78ebc549b536a14c7e329cadf9606bdc637de59ebb44189586f27426feb Stored in directory: /private/var/folders/xv/81gtkgsn24xg5lmlbl_jqzg80000gn/T/pip-ephem-wheel- cache-0r7cr6fe/wheels/cf/72/1c/bb985c095c0d1f3b385f30452dcb2ac8f404a8439c7b383eef Successfully built boltz Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types- requests, tqdm, sympy, smmap, setproctitle, sentry-sdk, scipy, rdkit, pyyaml, protobuf, propcache, multidict, mashumaro, llvmlite, lightning-utilities, fsspec, frozenlist, frozendict, einops, docker-pycreds, click, biopython, attrs, aiohappyeyeballs, yarl, torch, pandas, omegaconf, numba, modelcif, gitdb, einx, aiosignal, torchmetrics, hydra-core, gitpython, fairscale, aiohttp, wandb, pytorch-lightning, boltz Attempting uninstall: scipy Found existing installation: scipy 1.14.0 Not uninstalling scipy at /Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages, outside environment /Users/jacekj/boltz Can't uninstall 'scipy'. No files were found to uninstall. Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aiosignal-1.4.0 antlr4-python3-runtime-4.9.3 attrs-25.3.0 biopython-1.84 boltz-1.0.0 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-1.7.0 fsspec-2025.7.0 gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 lightning-utilities-0.15.2 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.6.4 numba-0.61.0 omegaconf-2.3.0 pandas-2.3.1 propcache-0.3.2 protobuf-5.29.5 pytorch-lightning-2.4.0 pyyaml-6.0.2 rdkit-2025.3.5 scipy-1.13.1 sentry- sdk-2.35.0 setproctitle-1.3.6 smmap-5.0.2 sympy-1.14.0 torch-2.8.0 torchmetrics-1.8.1 tqdm-4.67.1 types-requests-2.32.4.20250809 wandb-0.18.7 yarl-1.20.1 [notice] A new release of pip is available: 23.1.2 -> 25.2 [notice] To update, run: /Users/jacekj/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/jacekj/boltz/bin/python /Users/jacekj/Applications/ChimeraX-1.10.1.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/jacekj/.boltz/ccd.pkl. You may change the cache directory with the --cache flag. Downloading the model weights to /Users/jacekj/.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. > boltz predict protein /A ligandCcd 5RC name 5es1 device gpu steering true Traceback (most recent call last): File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 511, in _predict self._run_prediction(options = ' '.join(options)) File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py"", line 528, in _run_prediction br = run(self.session, cmd) ^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/jacekj/Applications/ChimeraX-1.10.1.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 ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3221, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/predict.py"", line 63, in boltz_predict br.start(results_directory) File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/predict.py"", line 203, in start yaml = self._create_yaml_input() ^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/predict.py"", line 272, in _create_yaml_input msa_cache_files = self._msa_cache_files() ^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/predict.py"", line 303, in _msa_cache_files msa_cache_files = _find_msa_cache_files(protein_seqs, self.msa_cache_dir) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/predict.py"", line 691, in _find_msa_cache_files with open(index_path, 'r') as f: ^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '/Users/jacekj/Downloads/ChimeraX/BoltzMSA/index' FileNotFoundError: [Errno 2] No such file or directory: '/Users/jacekj/Downloads/ChimeraX/BoltzMSA/index' File ""/Users/jacekj/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/predict.py"", line 691, in _find_msa_cache_files with open(index_path, 'r') as f: ^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 Ultra 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: Mac Studio Model Identifier: Mac14,14 Model Number: Z17Z00074LL/A Chip: Apple M2 Ultra Total Number of Cores: 24 (16 performance and 8 efficiency) Memory: 64 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6 (24G84) Kernel Version: Darwin 24.6.0 Time since boot: 56 minutes, 24 seconds Graphics/Displays: Apple M2 Ultra: Chipset Model: Apple M2 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Studio Display: Display Type: Retina LCD Resolution: 5120 x 2880 Retina Display Serial Number: JGKHYXV56M Display Firmware Version: Version 17.0 (Build 21A329) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No E20: Resolution: 1600 x 900 UI Looks like: 1600 x 900 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported 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: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 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: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 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: 2.2.2 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: 1.1.3 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: 1.2.1 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-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: 1.45.2 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: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 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: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 narwhals: 1.46.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 2.2.6 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: 6.0.1 pluggy: 1.6.0 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 Pygments: 2.18.0 pyKVFinder: 0.8.1 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: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 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 tifffile: 2025.3.13 tinyarray: 1.2.4 tomlkit: 0.13.2 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 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