failure trying to run boltz-2

[Elaine Meng]

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)  
  
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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)  
  
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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)  
  
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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)  
  
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Requirement already satisfied: setuptools>=46.4.0 in
/Users/meng/boltz2/lib/python3.11/site-packages (from
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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
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Requirement already satisfied: ihm>=1.7 in
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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)  
  
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Collecting lightning-utilities>=0.10.0 (from pytorch-
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Using cached lightning_utilities-0.14.3-py3-none-any.whl (28 kB)  
  
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Requirement already satisfied: urllib3<3,>=1.21.1 in
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Requirement already satisfied: certifi>=2017.4.17 in
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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)  
  
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Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.1.1)  
  
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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)  
  
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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)  
  
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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)  
  
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Collecting setproctitle (from wandb==0.18.7->boltz==2.1.1)  
  
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Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-
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Requirement already satisfied: msgpack in
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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)  
  
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Collecting aiosignal>=1.4.0 (from
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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<?, ?it/s]Traceback (most recent call last):  
File "/Users/meng/boltz2/lib/python3.11/site-packages/boltz/main.py", line
505, in process_input  
target = parse_yaml(path, ccd, mol_dir, boltz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/meng/boltz2/lib/python3.11/site-
packages/boltz/data/parse/yaml.py", line 68, in parse_yaml  
return parse_boltz_schema(name, data, ccd, mol_dir, boltz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/meng/boltz2/lib/python3.11/site-
packages/boltz/data/parse/schema.py", line 1182, in parse_boltz_schema  
if affinity and len(seq) > 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<?, ?it/s]Traceback (most recent call last):  
File "/Users/meng/boltz2/lib/python3.11/site-packages/boltz/main.py", line
505, in process_input  
target = parse_yaml(path, ccd, mol_dir, boltz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/meng/boltz2/lib/python3.11/site-
packages/boltz/data/parse/yaml.py", line 68, in parse_yaml  
return parse_boltz_schema(name, data, ccd, mol_dir, boltz2)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/meng/boltz2/lib/python3.11/site-
packages/boltz/data/parse/schema.py", line 1182, in parse_boltz_schema  
if affinity and len(seq) > 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
    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: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202507240055
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7
    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: 2.14
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    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: 1.0.1
    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: 1.15.1
    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: 1.1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.4
    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: 1.5.2
    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: 2.17.2
    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: 1.47
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.1
    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: 7.9.2
    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
    joblib: 1.5.0
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    llvmlite: 0.44.0
    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: 1.39.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numba: 0.61.2
    numexpr: 2.11.0
    numpy: 2.2.5
    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: 0.8.0
    pynmrstar: 3.3.5
    pynndescent: 0.5.13
    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
    scikit-learn: 1.6.1
    scipy: 1.14.0
    setuptools: 78.1.1
    sfftk-rw: 0.8.1
    six: 1.16.0
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    sortedcontainers: 2.4.0
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    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
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    stack-data: 0.6.3
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    widgetsnbextension: 4.0.14

[Tom Goddard]

You are a pro at finding bugs. This boltz error is because your CCD code is a number. Apparenlty the YAML input files if it sees 12123 parses as an integer but if it sees 1212A it parses as a string. I'll fix it my putting quotes around the CCD name in the YAML file. For now you can test with a non-numeric CCD code.

[Tom Goddard]

Fixed.

I fixed the quoting of the CCD code in the YAML boltz input file. But then I get the message that Boltz does not know CCD 12123 and the message suggests I look up the smiles string for that code on RCSB. When I do that I find there is no CCD "12123". So I'm not sure where you got that 12123 code. Maybe you were using a PubChem CID code. That is not supported by Boltz. CCD codes are assigned by the PDB. It would be possible for ChimeraX to support PubChem CID codes and it could look up the equivalent SMILES string to pass to Boltz. Not sure if the PubChem CID codes are a well-used way of specifying ligands.

[Elaine Meng]

Oops my bad!! Yes I was thinking PubChem ID -- I incorrectly "remembered" it was one way to do it, undoubtedly from using some other tool like Build Structure. Sorry about that.

[Tom Goddard]

The way to use a PubChem ligand would be to get its SMILES string from the PubChem page. For example,

boltz predict protein DDCIKPYGFCSLPILKNGLCCSGACVGVCADLX ligandSmiles CC(=O)NC1=CC(=CC=C1)Br name 1g1p affinity CC(=O)NC1=CC(=CC=C1)Br

Interestingly this prediction gives a conformation nothing like PDB 1g1p.

[Elaine Meng]

Might be nice to allow specifying a ligand as a current model number.  Then one could pubchem fetch (and even modify the structure with Build Structure) before running Boltz.

[Elaine Meng]

I guess that would be too difficult if you have to back-convert it to one of the other choices before submitting to boltz. Also maybe nice to check if a specified CCD actually exists, but likewise perhaps not feasible.

[Tom Goddard]

Unfortunately Boltz does not accept ligands input as a structure, only as a CCD code or SMILES string. The reason is that it adds a bunch of info like bond order using RDKit. It could do that directly from a structure. Some contributor has contributed Boltz code to make it accept a ligand structure, convert to a SMILES string, then derive all the meta-data with that. But that code has not been accepted, possibly because conversion to and from SMILES is treacherous, with stereo-centers being especially problematic.

You can specify a ligand using an atom specifier with the ChimeraX boltz predict command (e.g. "boltz predict protein #1/A ligands #1:GTP") but it will use the residue 3 or 5 letter code (CCD code), not the actual structure.

[Tom Goddard]

I agree that allowing ChimeraX Boltz to accept a ligand structure would be very nice and I have for months planned on implementing that, probably by modifying the Boltz code myself. Have not got to it, nor have I even had time to look at the contributed code that supposedly does it. A number of people requested it in the Boltz github issues.

[Tom Goddard]

ChimeraX does check if the CCD codes exist but only after it runs Boltz and receives an error. Then it will give an easy to understand error message. In your case Boltz hit the parsing error because of the integer/string issue so you didn't get the non-existent CCD error. I could check the validity of the CCD code before running Boltz but that slows down the prediction as it looks for the code, so I chose to check only when Boltz gives an error.

[Tom Goddard]

Here is the error that your CCD 12123 gives in ChimeraX after my fix today:

"Your Boltz installation does not have a molecular structure for PDB chemical component dictionary code 12123 either because that code is new or is mistyped. You can try specifying that ligand using a SMILES string from ​https://www.rcsb.org/ligand/12123 instead of using its CCD code."