Opened 8 weeks ago

Closed 8 weeks ago

#18794 closed defect (fixed)

Boltz: _each_ligand_predictions: name 'self' is not defined

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202509160050 (2025-09-16 00:50:53 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11.dev202509160050 (2025-09-16)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Boltz

> toolshed show

> boltz install /Users/jcw/boltz22

Successfully created Boltz Python virtual environment /Users/jcw/boltz22.  
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/jcw/boltz22/bin/python -m pip install
git+https://github.com/RBVI/boltz@chimerax_boltz22  
Collecting git+https://github.com/RBVI/boltz@chimerax_boltz22  
  
Cloning https://github.com/RBVI/boltz (to revision chimerax_boltz22) to
/private/var/folders/8z/1q51vsyn6jj352phk_0h9dd80000gn/T/pip-req-build-
eum4h8c2  
  
Running command git clone --filter=blob:none --quiet
https://github.com/RBVI/boltz
/private/var/folders/8z/1q51vsyn6jj352phk_0h9dd80000gn/T/pip-req-build-
eum4h8c2  
  
Running command git checkout -b chimerax_boltz22 --track
origin/chimerax_boltz22  
  
Switched to a new branch 'chimerax_boltz22'  
  
branch 'chimerax_boltz22' set up to track 'origin/chimerax_boltz22'.  
  
Resolved https://github.com/RBVI/boltz to commit
f1638c67006f656dc78fa7062f852077e7016018  
  
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==2.2.0)  
  
Downloading torch-2.8.0-cp311-none-macosx_11_0_arm64.whl.metadata (30 kB)  
  
Requirement already satisfied: numpy<2.0,>=1.26 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from boltz==2.2.0) (1.26.4)  
  
Collecting hydra-core==1.3.2 (from boltz==2.2.0)  
  
Downloading hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)  
  
Collecting pytorch-lightning==2.5.0 (from boltz==2.2.0)  
  
Downloading pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB)  
  
Collecting rdkit>=2024.3.2 (from boltz==2.2.0)  
  
Downloading rdkit-2025.3.6-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.1 kB)  
  
Collecting dm-tree==0.1.8 (from boltz==2.2.0)  
  
Downloading dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl.metadata (1.9 kB)  
  
Collecting requests==2.32.3 (from boltz==2.2.0)  
  
Downloading requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)  
  
Collecting pandas>=2.2.2 (from boltz==2.2.0)  
  
Downloading pandas-2.3.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (91 kB)  
  
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Collecting types-requests (from boltz==2.2.0)  
  
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Downloading einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)  
  
Collecting fairscale==0.4.13 (from boltz==2.2.0)  
  
Using cached fairscale-0.4.13-py3-none-any.whl  
  
Collecting mashumaro==3.14 (from boltz==2.2.0)  
  
Downloading mashumaro-3.14-py3-none-any.whl.metadata (114 kB)  
  
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Collecting modelcif==1.2 (from boltz==2.2.0)  
  
Using cached modelcif-1.2-py3-none-any.whl  
  
Collecting wandb==0.18.7 (from boltz==2.2.0)  
  
Downloading wandb-0.18.7-py3-none-macosx_11_0_arm64.whl.metadata (9.7 kB)  
  
Collecting click==8.1.7 (from boltz==2.2.0)  
  
Downloading click-8.1.7-py3-none-any.whl.metadata (3.0 kB)  
  
Collecting pyyaml==6.0.2 (from boltz==2.2.0)  
  
Downloading PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.1 kB)  
  
Collecting biopython==1.84 (from boltz==2.2.0)  
  
Downloading biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl.metadata (12 kB)  
  
Collecting scipy==1.13.1 (from boltz==2.2.0)  
  
Downloading scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (60 kB)  
  
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Collecting numba==0.61.0 (from boltz==2.2.0)  
  
Downloading numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.7 kB)  
  
Collecting gemmi==0.6.5 (from boltz==2.2.0)  
  
Downloading gemmi-0.6.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.3 kB)  
  
Collecting scikit-learn==1.6.1 (from boltz==2.2.0)  
  
Downloading scikit_learn-1.6.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (31
kB)  
  
Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.2.0)  
  
Downloading chembl_structure_pipeline-1.2.2-py3-none-any.whl.metadata (3.9 kB)  
  
Collecting cuequivariance_torch>=0.5.0 (from boltz==2.2.0)  
  
Downloading cuequivariance_torch-0.6.1-py3-none-any.whl.metadata (15 kB)  
  
Requirement already satisfied: setuptools>=46.4.0 in
/Users/jcw/boltz22/lib/python3.11/site-packages (from
chembl_structure_pipeline==1.2.2->boltz==2.2.0) (65.5.0)  
  
Collecting sympy (from einx==0.3.0->boltz==2.2.0)  
  
Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB)  
  
Collecting frozendict (from einx==0.3.0->boltz==2.2.0)  
  
Downloading frozendict-2.4.6-py311-none-any.whl.metadata (23 kB)  
  
Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==2.2.0)  
  
Downloading omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB)  
  
Collecting antlr4-python3-runtime==4.9.* (from hydra-
core==1.3.2->boltz==2.2.0)  
  
Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl  
  
Requirement already satisfied: packaging in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from hydra-core==1.3.2->boltz==2.2.0) (25.0)  
  
Requirement already satisfied: typing-extensions>=4.1.0 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from mashumaro==3.14->boltz==2.2.0) (4.15.0)  
  
Requirement already satisfied: ihm>=1.7 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from modelcif==1.2->boltz==2.2.0) (2.2)  
  
Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==2.2.0)  
  
Downloading llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.8
kB)  
  
Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)  
  
Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)  
  
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Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Downloading fsspec-2025.9.0-py3-none-any.whl.metadata (10 kB)  
  
Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)  
  
Downloading torchmetrics-1.8.2-py3-none-any.whl.metadata (22 kB)  
  
Collecting lightning-utilities>=0.10.0 (from pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
Downloading lightning_utilities-0.15.2-py3-none-any.whl.metadata (5.7 kB)  
  
Requirement already satisfied: charset-normalizer<4,>=2 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (3.4.3)  
  
Requirement already satisfied: idna<4,>=2.5 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (3.10)  
  
Requirement already satisfied: urllib3<3,>=1.21.1 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (2.5.0)  
  
Requirement already satisfied: certifi>=2017.4.17 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==2.2.0) (2025.7.14)  
  
Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.2.0)  
  
Downloading joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB)  
  
Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.2.0)  
  
Downloading threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)  
  
Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==2.2.0)  
  
Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB)  
  
Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==2.2.0)  
  
Downloading gitpython-3.1.45-py3-none-any.whl.metadata (13 kB)  
  
Requirement already satisfied: platformdirs in
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packages (from wandb==0.18.7->boltz==2.2.0) (4.4.0)  
  
Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from
wandb==0.18.7->boltz==2.2.0)  
  
Downloading protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl.metadata (592
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Requirement already satisfied: psutil>=5.0.0 in
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packages (from wandb==0.18.7->boltz==2.2.0) (7.0.0)  
  
Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==2.2.0)  
  
Downloading sentry_sdk-2.38.0-py2.py3-none-any.whl.metadata (10 kB)  
  
Collecting setproctitle (from wandb==0.18.7->boltz==2.2.0)  
  
Downloading setproctitle-1.3.7-cp311-cp311-macosx_11_0_arm64.whl.metadata (10
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Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.2.0)  
  
Downloading cuequivariance-0.6.1-py3-none-any.whl.metadata (15 kB)  
  
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/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==2.2.0) (2.9.0.post0)  
  
Requirement already satisfied: pytz>=2020.1 in
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Requirement already satisfied: tzdata>=2022.7 in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==2.2.0) (2025.2)  
  
Requirement already satisfied: Pillow in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from rdkit>=2024.3.2->boltz==2.2.0) (11.3.0)  
  
Requirement already satisfied: filelock in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch>=2.2->boltz==2.2.0) (3.19.1)  
  
Requirement already satisfied: networkx in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
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packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz==2.2.0) (1.17.0)  
  
Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)  
  
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Collecting gitdb<5,>=4.0.1 (from
gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0)  
  
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Requirement already satisfied: msgpack in
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
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Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==2.2.0)  
  
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Collecting aiohappyeyeballs>=2.5.0 (from
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Collecting multidict<7.0,>=4.5 (from
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Downloading propcache-0.3.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (12 kB)  
  
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Collecting smmap<6,>=3.0.1 (from
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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-2.2.0-py3-none-any.whl size=268910
sha256=b5c2132f896d2009f3b6a4a7ec7de0bb63fdba9659f4f54ff7917961ce7a9083  
  
Stored in directory:
/private/var/folders/8z/1q51vsyn6jj352phk_0h9dd80000gn/T/pip-ephem-wheel-
cache-1h8i0g1v/wheels/a2/57/a2/680a7866e1b7f1dc290112e8f82241f58511d33c66a8818e3d  
  
Successfully built boltz  
  
Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types-
requests, tqdm, threadpoolctl, sympy, smmap, setproctitle, sentry-sdk, scipy,
requests, 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
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/jcw/boltz22  
  
Can't uninstall 'scipy'. No files were found to uninstall.  
  
Attempting uninstall: requests  
  
Found existing installation: requests 2.32.4  
  
Not uninstalling requests at
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/jcw/boltz22  
  
Can't uninstall 'requests'. 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-2.2.0
chembl_structure_pipeline-1.2.2 click-8.1.7 cuequivariance-0.6.1
cuequivariance_torch-0.6.1 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-2025.9.0
gemmi-0.6.5 gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 joblib-1.5.2
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 opt-einsum-3.4.0
pandas-2.3.2 propcache-0.3.2 protobuf-5.29.5 pytorch-lightning-2.5.0
pyyaml-6.0.2 rdkit-2025.3.6 requests-2.32.3 scikit-learn-1.6.1 scipy-1.13.1
sentry-sdk-2.38.0 setproctitle-1.3.7 smmap-5.0.2 sympy-1.14.0
threadpoolctl-3.6.0 torch-2.8.0 torchmetrics-1.8.2 tqdm-4.67.1 types-
requests-2.32.4.20250913 wandb-0.18.7 yarl-1.20.1  
  
  
  
[notice] A new release of pip is available: 24.0 -> 25.2  
  
[notice] To update, run: /Users/jcw/boltz22/bin/python -m pip install
--upgrade pip  
  
Downloading Boltz model parameters (4 GB) and chemical component database (1.8
GB) to ~/.boltz  
/Users/jcw/boltz22/bin/python
/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/download_weights_and_ccd.py  
Making CCD atom counts table for 45227 in /Users/jcw/.boltz/mols  
  
Boltz model parameters and CCD database are installed in ~/.boltz  
Successfully installed Boltz program and neural net weights.  
Boltz does not have CCD code 8x7 in its CCD database ~/.boltz/ccd.pkl. You
could instead try to include that ligand using a SMILES string.  

> boltz predict protein
> >sp|P30291|299-569Wee1kinasedomainFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVL
> ligandSmiles
> AZD1775/8X7CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(cc4)N5CCN(CC5)C)C(=O)N2CC=C)O
> affinity
> AZD1775/8X7CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(cc4)N5CCN(CC5)C)C(=O)N2CC=C)O
> steering true

Invalid "protein" argument: Sequences argument
">sp|P30291|299-569Wee1kinasedomainFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVL"
is not a chain specifier, alignment id, UniProt id, or sequence characters  

> boltz predict protein
> FHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVL
> ligandSmiles
> CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(cc4)N5CCN(CC5)C)C(=O)N2CC=C)O name
> AZD1775_Wee1 affinity
> CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(cc4)N5CCN(CC5)C)C(=O)N2CC=C)O steering
> true

Running Boltz prediction of protein with 271 residues, 1 ligands
CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(cc4)N5CCN(CC5)C)C(=O)N2CC=C)O on gpu  
Using cached multiple sequence alignment
/Users/jcw/Downloads/ChimeraX/BoltzMSA/azd1775  
Confidence score 0.93, pTM 0.95, ipTM 0.98, pLDDT 0.92  
Ligand CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(cc4)N5CCN(CC5)C)C(=O)N2CC=C)O
predicted binding affinity 0.006 uM, predicted binding probability 0.86  
Boltz prediction completed in 2491 seconds (start boltz 5 sec, sequence search
0 sec, load weights 12 sec, structure inference 372 sec, load affinity weights
14 sec, affinity inference 2088 sec)  
Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.  

> open
> /Users/jcw/Desktop/boltz_AZD1775_Wee1/boltz_results_AZD1775_Wee1/predictions/AZD1775_Wee1/AZD1775_Wee1_model_0.cif
> logInfo false

> log metadata #1

Metadata for AZD1775_Wee1_model_0.cif #1  
---  
Title | .  
Non-standard residue | LIG1 — (LIG1)  
  
> log chains #1

Chain information for AZD1775_Wee1_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> log metadata #1

Metadata for AZD1775_Wee1_model_0.cif #1  
---  
Title | .  
Non-standard residue | LIG1 — (LIG1)  
  
> log chains #1

Chain information for AZD1775_Wee1_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> view clip false

> show target m

> select add #1

2181 atoms, 2232 bonds, 272 residues, 1 model selected  

> select subtract #1

Nothing selected  

> hide #1 models

> show #1 models

> boltz predict protein
> FHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVL
> forEachSmilesLigand
> "A1A1S,CC(=O)N1c2cnc(nc2N(C[C@H]1c3c(cccc3Cl)Cl)C)Nc4ccc(cc4)N5CCN(CC5)C,A1A1T,C[C@@H](c1cccs1)c2c(c3cnc(nc3n2C)Nc4cnn(c4)C5CCN(CC5)C)C#N,A1A1R,CN1CCC(CC1)n2cc(cn2)c3cc4c5c(cnc4[nH]3)C(=O)N(CN5C)c6c(cccc6Cl)Cl"
> name Wee1_ steering true

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 587, in _predict  
self._run_prediction(options = ' '.join(options))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 604, in _run_prediction  
br = run(self.session, cmd)  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 69, in boltz_predict  
predictions = _each_ligand_predictions(for_each_ligand, molecular_components,
predict_affinity, align_to)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 197, in _each_ligand_predictions  
affinity = self._predict_affinity  
^^^^  
NameError: name 'self' is not defined  
  
NameError: name 'self' is not defined  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 197, in _each_ligand_predictions  
affinity = self._predict_affinity  
^^^^  
  
See log for complete Python traceback.  
  

> boltz predict protein
> FHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVL
> forEachSmilesLigand
> "A1A1S,CC(=O)N1c2cnc(nc2N(C[C@H]1c3c(cccc3Cl)Cl)C)Nc4ccc(cc4)N5CCN(CC5)C,A1A1T,C[C@@H](c1cccs1)c2c(c3cnc(nc3n2C)Nc4cnn(c4)C5CCN(CC5)C)C#N,A1A1R,CN1CCC(CC1)n2cc(cn2)c3cc4c5c(cnc4[nH]3)C(=O)N(CN5C)c6c(cccc6Cl)Cl"
> name Wee1_ steering true

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 587, in _predict  
self._run_prediction(options = ' '.join(options))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 604, in _run_prediction  
br = run(self.session, cmd)  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.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
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 69, in boltz_predict  
predictions = _each_ligand_predictions(for_each_ligand, molecular_components,
predict_affinity, align_to)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 197, in _each_ligand_predictions  
affinity = self._predict_affinity  
^^^^  
NameError: name 'self' is not defined  
  
NameError: name 'self' is not defined  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/predict.py", line 197, in _each_ligand_predictions  
affinity = self._predict_affinity  
^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3B/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 5 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: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        PL2290:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          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: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.8.0
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0.2
    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: 1.60.16
    ChimeraX-AtomicLibrary: 14.2
    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: 1.6.0
    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.dev202509160050
    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: 1.7.1
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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: 2.17.1
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.3.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    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-Scenes: 0.2.1
    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: 2.17.2
    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: 1.48.2
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.3.3
    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: 0.2.3
    contourpy: 1.3.3
    coverage: 7.10.6
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.3
    debugpy: 1.8.16
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.59.2
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2025.4.15
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.7
    jedi: 0.19.2
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.1
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.5
    matplotlib-inline: 0.1.7
    msgpack: 1.1.1
    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: 2.12.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.4.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.4
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 8.4.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    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: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.15.0
    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

Change History (2)

comment:1 by Eric Pettersen, 8 weeks ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Boltz: _each_ligand_predictions: name 'self' is not defined

comment:2 by Tom Goddard, 8 weeks ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Predicting for multiple ligands with Boltz without predicting affinity gave this error due to a typo. Surprisingly I must not have tested predicting multi-ligand without affinity.

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