BoltzMSA/index: No such file or directory

[jacjagoabc@…]

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


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    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
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[pett]

Reported by Jacek Jagodzinski

[Tom Goddard]

The way to fix this problem is to delete the directory

~/Downloads/ChimeraX/BoltzMSA

I am not sure how that directory got created without containing a file named "index", because ChimeraX creates the directory and makes the "index" file at the same time. I'll improve the code so that it will work even if the index file does not exist. This directory saves the multiple sequence alignments from your predictions so future predictions on the same proteins don't have to use the MSA server.