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Opened 8 days ago
Closed 8 days ago
#19690 closed defect (fixed)
Error running Boltz prediction and submitting feedback
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
Hi,
I received an error while trying to run a Boltz prediction, but when I tried to report this issue I received an "Error while submitting feedback message".
I pasted the contents of the log below-
boltz install /home/xray-alpha/boltz2
Successfully created Boltz Python virtual environment /home/xray-alpha/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...
/home/xray-alpha/boltz2/bin/python -m pip install https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Collecting https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Using cached https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Installing build dependencies: started
boltz install /home/xray-alpha/boltz2
Successfully created Boltz Python virtual environment /home/xray-alpha/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...
/home/xray-alpha/boltz2/bin/python -m pip install https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Collecting https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Using cached https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
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==2.7.1 (from boltz==2.2.0)
Using cached torch-2.7.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (29 kB)
Requirement already satisfied: numpy<2.0,>=1.26 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from boltz==2.2.0) (1.26.4)
Collecting hydra-core==1.3.2 (from boltz==2.2.0)
Using cached hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)
Collecting pytorch-lightning==2.5.0 (from boltz==2.2.0)
Using cached pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB)
Collecting rdkit>=2024.3.2 (from boltz==2.2.0)
Using cached rdkit-2025.9.3-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (4.2 kB)
Collecting dm-tree==0.1.8 (from boltz==2.2.0)
Using cached dm_tree-0.1.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.9 kB)
Collecting requests==2.32.3 (from boltz==2.2.0)
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting pandas>=2.2.2 (from boltz==2.2.0)
Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
Collecting types-requests (from boltz==2.2.0)
Using cached types_requests-2.32.4.20250913-py3-none-any.whl.metadata (2.0 kB)
Collecting einops==0.8.0 (from boltz==2.2.0)
Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)
Collecting einx==0.3.0 (from boltz==2.2.0)
Using cached 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)
Using cached mashumaro-3.14-py3-none-any.whl.metadata (114 kB)
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)
Using cached wandb-0.18.7-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.7 kB)
Collecting click==8.1.7 (from boltz==2.2.0)
Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting pyyaml==6.0.2 (from boltz==2.2.0)
Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting biopython==1.84 (from boltz==2.2.0)
Using cached biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Collecting scipy==1.13.1 (from boltz==2.2.0)
Using cached scipy-1.13.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting numba==0.61.0 (from boltz==2.2.0)
Using cached numba-0.61.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.8 kB)
Collecting gemmi==0.6.5 (from boltz==2.2.0)
Using cached gemmi-0.6.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
Collecting scikit-learn==1.6.1 (from boltz==2.2.0)
Using cached scikit_learn-1.6.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.2.0)
Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl.metadata (3.9 kB)
Collecting cuequivariance_ops_cu12>=0.5.0 (from bo
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==2.7.1 (from boltz==2.2.0)
Using cached torch-2.7.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (29 kB)
Requirement already satisfied: numpy<2.0,>=1.26 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from boltz==2.2.0) (1.26.4)
Collecting hydra-core==1.3.2 (from boltz==2.2.0)
Using cached hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)
Collecting pytorch-lightning==2.5.0 (from boltz==2.2.0)
Using cached pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB)
Collecting rdkit>=2024.3.2 (from boltz==2.2.0)
Using cached rdkit-2025.9.3-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (4.2 kB)
Collecting dm-tree==0.1.8 (from boltz==2.2.0)
Using cached dm_tree-0.1.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.9 kB)
Collecting requests==2.32.3 (from boltz==2.2.0)
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting pandas>=2.2.2 (from boltz==2.2.0)
Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
Collecting types-requests (from boltz==2.2.0)
Using cached types_requests-2.32.4.20250913-py3-none-any.whl.metadata (2.0 kB)
Collecting einops==0.8.0 (from boltz==2.2.0)
Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)
Collecting einx==0.3.0 (from boltz==2.2.0)
Using cached 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)
Using cached mashumaro-3.14-py3-none-any.whl.metadata (114 kB)
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)
Using cached wandb-0.18.7-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.7 kB)
Collecting click==8.1.7 (from boltz==2.2.0)
Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)
Collecting pyyaml==6.0.2 (from boltz==2.2.0)
Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting biopython==1.84 (from boltz==2.2.0)
Using cached biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
Collecting scipy==1.13.1 (from boltz==2.2.0)
Using cached scipy-1.13.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting numba==0.61.0 (from boltz==2.2.0)
Using cached numba-0.61.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.8 kB)
Collecting gemmi==0.6.5 (from boltz==2.2.0)
Using cached gemmi-0.6.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
Collecting scikit-learn==1.6.1 (from boltz==2.2.0)
Using cached scikit_learn-1.6.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.2.0)
Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl.metadata (3.9 kB)
Collecting cuequivariance_ops_cu12>=0.5.0 (from boltz==2.2.0)
Using cached cuequivariance_ops_cu12-0.8.0-py3-none-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (19 kB)
Collecting cuequivariance_ops_torch_cu12>=0.5.0 (from boltz==2.2.0)
Using cached cuequivariance_ops_torch_cu12-0.8.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (20 kB)
Collecting cuequivariance_torch>=0.5.0 (from boltz==2.2.0)
Using cached cuequivariance_torch-0.8.0-py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: setuptools>=46.4.0 in ./boltz2/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)
Using cached sympy-1.14.0-py3-none-any.whl.metadata (12 kB)
Collecting frozendict (from einx==0.3.0->boltz==2.2.0)
Using cached frozendict-2.4.7-py3-none-any.whl.metadata (23 kB)
Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==2.2.0)
Using cached 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 /usr/lib/ucsf-chimerax/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 /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from mashumaro==3.14->boltz==2.2.0) (4.15.0)
Requirement already satisfied: ihm>=1.7 in /usr/lib/ucsf-chimerax/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)
Using cached llvmlite-0.44.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.8 kB)
Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0)
Using cached fsspec-2025.12.0-py3-none-any.whl.metadata (10 kB)
Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.2.0)
Using cached 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)
Using cached lightning_utilities-0.15.2-py3-none-any.whl.metadata (5.7 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from requests==2.32.3->boltz==2.2.0) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from requests==2.32.3->boltz==2.2.0) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from requests==2.32.3->boltz==2.2.0) (2.6.2)
Requirement already satisfied: certifi>=2017.4.17 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from requests==2.32.3->boltz==2.2.0) (2025.11.12)
Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.2.0)
Using cached joblib-1.5.3-py3-none-any.whl.metadata (5.5 kB)
Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.2.0)
Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Requirement already satisfied: filelock in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from torch==2.7.1->boltz==2.2.0) (3.19.1)
Requirement already satisfied: networkx in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from torch==2.7.1->boltz==2.2.0) (3.3)
Requirement already satisfied: jinja2 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from torch==2.7.1->boltz==2.2.0) (3.1.6)
Collecting nvidia-cuda-nvrtc-cu12==12.6.77 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cuda_nvrtc_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-cuda-runtime-cu12==12.6.77 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cuda_runtime_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-cuda-cupti-cu12==12.6.80 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cuda_cupti_cu12-12.6.80-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cudnn-cu12==9.5.1.17 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cudnn_cu12-9.5.1.17-py3-none-manylinux_2_28_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cublas-cu12==12.6.4.1 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cublas_cu12-12.6.4.1-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-cufft-cu12==11.3.0.4 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cufft_cu12-11.3.0.4-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-curand-cu12==10.3.7.77 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_curand_cu12-10.3.7.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-cusolver-cu12==11.7.1.2 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cusolver_cu12-11.7.1.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cusparse-cu12==12.5.4.2 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cusparse_cu12-12.5.4.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cusparselt-cu12==0.6.3 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cusparselt_cu12-0.6.3-py3-none-manylinux2014_x86_64.whl.metadata (6.8 kB)
Collecting nvidia-nccl-cu12==2.26.2 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_nccl_cu12-2.26.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.0 kB)
Collecting nvidia-nvtx-cu12==12.6.77 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_nvtx_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-nvjitlink-cu12==12.6.85 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_nvjitlink_cu12-12.6.85-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-cufile-cu12==1.11.1.6 (from torch==2.7.1->boltz==2.2.0)
Using cached nvidia_cufile_cu12-1.11.1.6-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.5 kB)
Collecting triton==3.3.1 (from torch==2.7.1->boltz==2.2.0)
Using cached triton-3.3.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.5 kB)
Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==2.2.0)
Using cached 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-3.1.46-py3-none-any.whl.metadata (13 kB)
Requirement already satisfied: platformdirs in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from wandb==0.18.7->boltz==2.2.0) (4.5.1)
Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from wandb==0.18.7->boltz==2.2.0)
Using cached protobuf-5.29.5-cp38-abi3-manylinux2014_x86_64.whl.metadata (592 bytes)
Requirement already satisfied: psutil>=5.0.0 in /usr/lib/ucsf-chimerax/lib/python3.11/site-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)
Using cached sentry_sdk-2.48.0-py2.py3-none-any.whl.metadata (10 kB)
Collecting setproctitle (from wandb==0.18.7->boltz==2.2.0)
Using cached setproctitle-1.3.7-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (10 kB)
Collecting nvidia-ml-py (from cuequivariance_ops_cu12>=0.5.0->boltz==2.2.0)
Using cached nvidia_ml_py-13.590.44-py3-none-any.whl.metadata (9.8 kB)
Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.2.0)
Using cached cuequivariance-0.8.0-py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: python-dateutil>=2.8.2 in /usr/lib/ucsf-chimerax/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 /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==2.2.0) (2025.2)
Requirement already satisfied: tzdata>=2022.7 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==2.2.0) (2025.3)
Requirement already satisfied: Pillow in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from rdkit>=2024.3.2->boltz==2.2.0) (11.3.0)
Requirement already satisfied: six>=1.4.0 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz==2.2.0) (1.17.0)
Requirement already satisfied: aiohttp!=4.0.0a0,!=4.0.0a1 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (3.13.1)
Collecting gitdb<5,>=4.0.1 (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0)
Using cached gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)
Requirement already satisfied: msgpack in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from ihm>=1.7->modelcif==1.2->boltz==2.2.0) (1.1.1)
Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==2.2.0)
Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
Collecting opt-einsum (from cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.2.0)
Using cached opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)
Requirement already satisfied: MarkupSafe>=2.0 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from jinja2->torch==2.7.1->boltz==2.2.0) (3.0.3)
Requirement already satisfied: aiohappyeyeballs>=2.5.0 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (2.6.1)
Requirement already satisfied: aiosignal>=1.4.0 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (1.4.0)
Requirement already satisfied: attrs>=17.3.0 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (25.4.0)
Requirement already satisfied: frozenlist>=1.1.1 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (1.8.0)
Requirement already satisfied: multidict<7.0,>=4.5 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (6.7.0)
Requirement already satisfied: propcache>=0.2.0 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (0.4.1)
Requirement already satisfied: yarl<2.0,>=1.17.0 in /usr/lib/ucsf-chimerax/lib/python3.11/site-packages (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.5.0->boltz==2.2.0) (1.22.0)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.2.0)
Using cached smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)
Using cached biopython-1.84-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)
Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl (17 kB)
Using cached click-8.1.7-py3-none-any.whl (97 kB)
Using cached dm_tree-0.1.8-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (152 kB)
Using cached einops-0.8.0-py3-none-any.whl (43 kB)
Using cached einx-0.3.0-py3-none-any.whl (102 kB)
Using cached gemmi-0.6.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)
Using cached hydra_core-1.3.2-py3-none-any.whl (154 kB)
Using cached mashumaro-3.14-py3-none-any.whl (92 kB)
Using cached numba-0.61.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (3.8 MB)
Using cached pytorch_lightning-2.5.0-py3-none-any.whl (819 kB)
Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
Using cached requests-2.32.3-py3-none-any.whl (64 kB)
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Using cached scipy-1.13.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (38.6 MB)
Using cached torch-2.7.1-cp311-cp311-manylinux_2_28_x86_64.whl (821.2 MB)
Using cached wandb-0.18.7-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.1 MB)
Using cached nvidia_cublas_cu12-12.6.4.1-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (393.1 MB)
Using cached nvidia_cuda_cupti_cu12-12.6.80-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (8.9 MB)
Using cached nvidia_cuda_nvrtc_cu12-12.6.77-py3-none-manylinux2014_x86_64.whl (23.7 MB)
Using cached nvidia_cuda_runtime_cu12-12.6.77-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (897 kB)
Using cached nvidia_cudnn_cu12-9.5.1.17-py3-none-manylinux_2_28_x86_64.whl (571.0 MB)
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Using cached nvidia_cusolver_cu12-11.7.1.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (158.2 MB)
Using cached nvidia_cusparse_cu12-12.5.4.2-py3-none-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (216.6 MB)
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Using cached nvidia_nvjitlink_cu12-12.6.85-py3-none-manylinux2010_x86_64.manylinux_2_12_x86_64.whl (19.7 MB)
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━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 208.6/208.6 kB 7.0 MB/s eta 0:00:00
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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=268988 sha256=eefaa5d735cc5a80a78b8fd98484a0835ac61ac8dc699bcb221941777af150af
Stored in directory: /tmp/pip-ephem-wheel-cache-gjc6xpiu/wheels/26/ba/5c/a8ae06e77eb74d03f129cbbe5d93bfea3b1259fabe4f838af4
Successfully built boltz
Installing collected packages: nvidia-ml-py, nvidia-cusparselt-cu12, mpmath, dm-tree, antlr4-python3-runtime, types-requests, triton, tqdm, threadpoolctl, sympy, smmap, setproctitle, sentry-sdk, scipy, requests, rdkit, pyyaml, protobuf, opt-einsum, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufile-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, mashumaro, llvmlite, lightning-utilities, joblib, gemmi, fsspec, frozendict, einops, docker-pycreds, click, biopython, scikit-learn, pandas, omegaconf, nvidia-cusparse-cu12, nvidia-cufft-cu12, nvidia-cudnn-cu12, numba, modelcif, gitdb, einx, cuequivariance_ops_cu12, cuequivariance, chembl_structure_pipeline, nvidia-cusolver-cu12, hydra-core, gitpython, cuequivariance_torch, cuequivariance_ops_torch_cu12, wandb, torch, torchmetrics, fairscale, pytorch-lightning, boltz
Attempting uninstall: scipy
Found existing installation: scipy 1.14.0
Not uninstalling scipy at /usr/lib/ucsf-chimerax/lib/python3.11/site-packages, outside environment /home/xray-alpha/boltz2
Can't uninstall 'scipy'. No files were found to uninstall.
Attempting uninstall: requests
Found existing installation: requests 2.32.5
Not uninstalling requests at /usr/lib/ucsf-chimerax/lib/python3.11/site-packages, outside environment /home/xray-alpha/boltz2
Can't uninstall 'requests'. No files were found to uninstall.
Attempting uninstall: nvidia-nvjitlink-cu12
Found existing installation: nvidia-nvjitlink-cu12 12.9.86
Not uninstalling nvidia-nvjitlink-cu12 at /usr/lib/ucsf-chimerax/lib/python3.11/site-packages, outside environment /home/xray-alpha/boltz2
Can't uninstall 'nvidia-nvjitlink-cu12'. No files were found to uninstall.
Attempting uninstall: click
Found existing installation: click 8.3.1
Not uninstalling click at /usr/lib/ucsf-chimerax/lib/python3.11/site-packages, outside environment /home/xray-alpha/boltz2
Can't uninstall 'click'. No files were found to uninstall.
ui tool show Log
Successfully installed antlr4-python3-runtime-4.9.3 biopython-1.84 boltz-2.2.0 chembl_structure_pipeline-1.2.2 click-8.1.7 cuequivariance-0.8.0 cuequivariance_ops_cu12-0.8.0 cuequivariance_ops_torch_cu12-0.8.0 cuequivariance_torch-0.8.0 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0 einx-0.3.0 fairscale-0.4.13 frozendict-2.4.7 fsspec-2025.12.0 gemmi-0.6.5 gitdb-4.0.12 gitpython-3.1.46 hydra-core-1.3.2 joblib-1.5.3 lightning-utilities-0.15.2 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 numba-0.61.0 nvidia-cublas-cu12-12.6.4.1 nvidia-cuda-cupti-cu12-12.6.80 nvidia-cuda-nvrtc-cu12-12.6.77 nvidia-cuda-runtime-cu12-12.6.77 nvidia-cudnn-cu12-9.5.1.17 nvidia-cufft-cu12-11.3.0.4 nvidia-cufile-cu12-1.11.1.6 nvidia-curand-cu12-10.3.7.77 nvidia-cusolver-cu12-11.7.1.2 nvidia-cusparse-cu12-12.5.4.2 nvidia-cusparselt-cu12-0.6.3 nvidia-ml-py-13.590.44 nvidia-nccl-cu12-2.26.2 nvidia-nvjitlink-cu12-12.6.85 nvidia-nvtx-cu12-12.6.77 omegaconf-2.3.0 opt-einsum-3.4.0 pandas-2.3.3 protobuf-5.29.5 pytorch-lightning-2.5.0 pyyaml-6.0.2 rdkit-2025.9.3 requests-2.32.3 scikit-learn-1.6.1 scipy-1.13.1 sentry-sdk-2.48.0 setproctitle-1.3.7 smmap-5.0.2 sympy-1.14.0 threadpoolctl-3.6.0 torch-2.7.1 torchmetrics-1.8.2 tqdm-4.67.1 triton-3.3.1 types-requests-2.32.4.20250913 wandb-0.18.7
[notice] A new release of pip is available: 24.0 -> 25.3
[notice] To update, run: /home/xray-alpha/boltz2/bin/python -m pip install --upgrade pip
Downloading Boltz model parameters (4 GB) and chemical component database (1.8 GB) to ~/.boltz
/home/xray-alpha/boltz2/bin/python /usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/boltz/download_weights_and_ccd.py
Boltz model parameters and CCD database are installed in ~/.boltz
Successfully installed Boltz program and neural net weights.
boltz predict protein /B ligandCcd CA(2),ZN ligandSmiles [N-]=[N+]=N[C@@](O[C@@]([H])([C@]1(O)[H])N2C=NC(C(C(OC)=N3)=CN=C3N)=C2)([C@](O)1[H])COP(O)(OP(O)(OP(O)(O)=O)=O)=O name SARS_CoV_2 NSP14 affinity [N-]=[N+]=N[C@@](O[C@@]([H])([C@]1(O)[H])N2C=NC(C(C(OC)=N3)=CN=C3N)=C2)([C@](O)1[H])COP(O)(OP(O)(OP(O)(O)=O)=O)=O steering true samples 2
Expected a keyword
boltz predict protein /B ligandCcd CA(2),ZN ligandSmiles [N-]=[N+]=N[C@@](O[C@@]([H])([C@]1(O)[H])N2C=NC(C(C(OC)=N3)=CN=C3N)=C2)([C@](O)1[H])COP(O)(OP(O)(OP(O)(O)=O)=O)=O name SARS_CoV_2 NSP14 steering true samples 2
Expected a keyword
boltz predict protein /B ligandCcd CA(2),ZN ligandSmiles [N-]=[N+]=N[C@@](O[C@@]([H])([C@]1(O)[H])N2C=NC(C(C(OC)=N3)=CN=C3N)=C2)([C@](O)1[H])COP(O)(OP(O)(OP(O)(O)=O)=O)=O name nsp14 steering true samples 2
Running Boltz prediction of protein with 527 residues, 4 ligands CA (2), ZN, [N-]=[N+]=N[C@@](O[C@@]([H])([C@]1(O)[H])N2C=NC(C(C(OC)=N3)=CN=C3N)=C2)([C@](O)1[H])COP(O)(OP(O)(OP(O)(O)=O)=O)=O on cpu
Using multiple sequence alignment server https://api.colabfold.com <https://api.colabfold.com/>
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/boltz/predict.py", line 751, in _check_process_completion
self._process_completed(stdout, stderr)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/boltz/predict.py", line 826, in _process_completed
f.write(stdout)
UnicodeEncodeError: 'ascii' codec can't encode characters in position 715-724: ordinal not in range(128)
Error processing trigger "new frame":
UnicodeEncodeError: 'ascii' codec can't encode characters in position 715-724: ordinal not in range(128)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/boltz/predict.py", line 826, in _process_completed
f.write(stdout)
See log for complete Python traceback.
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/bug_reporter/tool.py", line 264, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields, timeout=10, ssl=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/webservices/post_form.py", line 43, in post_multipart_formdata
h.request('POST', url, body=body, headers=headers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1303, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1349, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1298, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1058, in _send_output
self.send(msg)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 996, in send
self.connect()
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1468, in connect
super().connect()
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 962, in connect
self.sock = self._create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/socket.py", line 863, in create_connection
raise exceptions[0]
File "/usr/lib/ucsf-chimerax/lib/python3.11/socket.py", line 848, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/bug_reporter/tool.py", line 264, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields, timeout=10, ssl=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/webservices/post_form.py", line 43, in post_multipart_formdata
h.request('POST', url, body=body, headers=headers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1303, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1349, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1298, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1058, in _send_output
self.send(msg)
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 996, in send
self.connect()
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 1468, in connect
super().connect()
File "/usr/lib/ucsf-chimerax/lib/python3.11/http/client.py", line 962, in connect
self.sock = self._create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/socket.py", line 863, in create_connection
raise exceptions[0]
File "/usr/lib/ucsf-chimerax/lib/python3.11/socket.py", line 848, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
______________________________________________________________________________
Gathered information:
OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3
OpenGL renderer: Mesa Intel(R) UHD Graphics 770 (ADL-S GT1)
OpenGL vendor: Intel
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 12th Gen Intel(R) Core(TM) i9-12900
Cache Size: 30720 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 12Gi 10Gi 1.1Gi 39Gi 49Gi
Swap: 2.0Gi 0.0Ki 2.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation AlderLake-S GT1 [8086:4680] (rev 0c)
Subsystem: Dell AlderLake-S GT1 [1028:0a9f]
Kernel driver in use: i915
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
autocommand: 2.2.2
babel: 2.17.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.11.12
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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-Clipper: 0.23.0
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
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: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
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: 1.15.2
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: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
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: 1.3.3
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: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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-OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3
OpenGL renderer: Mesa Intel(R) UHD Graphics 770 (ADL-S GT1)
OpenGL vendor: Intel
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 12th Gen Intel(R) Core(TM) i9-12900
Cache Size: 30720 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 12Gi 10Gi 1.1Gi 39Gi 49Gi
Swap: 2.0Gi 0.0Ki 2.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation AlderLake-S GT1 [8086:4680] (rev 0c)
Subsystem: Dell AlderLake-S GT1 [1028:0a9f]
Kernel driver in use: i915
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
autocommand: 2.2.2
babel: 2.17.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.11.12
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
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-Clipper: 0.23.0
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
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: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
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-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
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: 1.15.2
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: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
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: 1.3.3
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: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
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: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
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
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
inflect: 7.3.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jaraco.collections: 5.1.0
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
more-itertools: 10.3.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
packaging: 24.2
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: 4.5.1
platformdirs: 4.2.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
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
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
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: 3.2.5
pyproject_hooks: 1.2.0
PyQt6: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
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
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomli: 2.0.1
tornado: 6.5.4
traitlets: 5.14.3
typeguard: 4.3.0
typing-inspection: 0.4.2
typing_extensions: 4.15.0
typing_extensions: 4.12.2
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
zipp: 3.19.2
WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
inflect: 7.3.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jaraco.collections: 5.1.0
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
more-itertools: 10.3.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
packaging: 24.2
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: 4.5.1
platformdirs: 4.2.2
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
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
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
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: 3.2.5
pyproject_hooks: 1.2.0
PyQt6: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.0.0
roman-numerals-py: 4.0.0
rpds-py: 0.30.0
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
sse-starlette: 3.0.4
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomli: 2.0.1
tornado: 6.5.4
traitlets: 5.14.3
typeguard: 4.3.0
typing-inspection: 0.4.2
typing_extensions: 4.15.0
typing_extensions: 4.12.2
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
zipp: 3.19.2
Platform: Linux-6.8.0-65-generic-x86_64-with-glibc2.35
ChimeraX version: 1.11 (2025-12-17 06:45:39 UTC)
Thanks,
Ryan Slack, PhD
Associate Research Scientist
Sarafianos Laboratory
Department of Pediatrics, Emory University School of Medicine
Email: ryan.slack@emory.edu <mailto:ryan.slack@emory.edu>
Address: 1760 Haygood Dr NE E497, Atlanta, GA 30322
Change History (2)
comment:1 by , 8 days ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
comment:2 by , 8 days ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Sorry that our ChimeraX bug reporting web service was down due to a server problem.
The error with Boltz is because apparently on your Linux system the default file encoding for text files written by Python is ASCII instead of the standard UTF-8. The error happened because the Boltz output included some non-ascii text and attempted to write it to a file. I've improved the ChimeraX Boltz code so that it always writes the output in utf-8 encoding even if the default on your operating system is to write ascii. That will be in tomorrow's daily build.