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Opened 13 hours ago
#19530 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26100
ChimeraX Version: 1.12.dev202512180555 (2025-12-18 05:55:44 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.12.dev202512180555 (2025-12-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH3.cxs"
Log from Fri Dec 19 14:52:44 2025UCSF ChimeraX version: 1.12.dev202512180555
(2025-12-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường
> Dương/GH30_Cellobiose_boltz.cxs"
Log from Fri Dec 19 09:13:14 2025UCSF ChimeraX version: 1.12.dev202512180555
(2025-12-18)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH30_boltz.cxs"
Log from Thu Dec 18 13:29:25 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.12.dev202512180555 (2025-12-18)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Boltz
> boltz install C:\Users\kieuc/boltz22
Successfully created Boltz Python virtual environment C:\Users\kieuc/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...
C:\Users\kieuc/boltz22\Scripts\python.exe -m pip install
https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Collecting https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
Downloading https://github.com/RBVI/boltz/archive/chimerax_boltz22.zip
\- 2.3 MB 6.1 MB/s 0:00:00
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)
Downloading torch-2.7.1-cp311-cp311-win_amd64.whl.metadata (28 kB)
Requirement already satisfied: numpy<2.0,>=1.26 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\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-2025.9.3-cp311-cp311-win_amd64.whl.metadata (4.3 kB)
Collecting dm-tree==0.1.8 (from boltz==2.2.0)
Downloading dm_tree-0.1.8-cp311-cp311-win_amd64.whl.metadata (2.0 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-2.3.3-cp311-cp311-win_amd64.whl.metadata (19 kB)
Collecting types-requests (from boltz==2.2.0)
Downloading types_requests-2.32.4.20250913-py3-none-any.whl.metadata (2.0 kB)
Collecting einops==0.8.0 (from boltz==2.2.0)
Downloading einops-0.8.0-py3-none-any.whl.metadata (12 kB)
Collecting einx==0.3.0 (from boltz==2.2.0)
Downloading einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)
Collecting fairscale==0.4.13 (from boltz==2.2.0)
Downloading fairscale-0.4.13.tar.gz (266 kB)
\-------------------------------------- 266.3/266.3 kB 2.8 MB/s eta 0:00:00
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'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting mashumaro==3.14 (from boltz==2.2.0)
Downloading mashumaro-3.14-py3-none-any.whl.metadata (114 kB)
\-------------------------------------- 114.4/114.4 kB 6.5 MB/s eta 0:00:00
Collecting modelcif==1.2 (from boltz==2.2.0)
Downloading modelcif-1.2.tar.gz (66 kB)
\---------------------------------------- 66.8/66.8 kB ? eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting wandb==0.18.7 (from boltz==2.2.0)
Downloading wandb-0.18.7-py3-none-win_amd64.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-win_amd64.whl.metadata (2.1 kB)
Collecting biopython==1.84 (from boltz==2.2.0)
Downloading biopython-1.84-cp311-cp311-win_amd64.whl.metadata (13 kB)
Collecting scipy==1.13.1 (from boltz==2.2.0)
Downloading scipy-1.13.1-cp311-cp311-win_amd64.whl.metadata (60 kB)
\---------------------------------------- 60.6/60.6 kB 3.4 MB/s eta 0:00:00
Collecting numba==0.61.0 (from boltz==2.2.0)
Downloading numba-0.61.0-cp311-cp311-win_amd64.whl.metadata (2.8 kB)
Collecting gemmi==0.6.5 (from boltz==2.2.0)
Downloading gemmi-0.6.5-cp311-cp311-win_amd64.whl.metadata (2.3 kB)
Collecting scikit-learn==1.6.1 (from boltz==2.2.0)
Downloading scikit_learn-1.6.1-cp311-cp311-win_amd64.whl.metadata (15 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-0.8.0-py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: setuptools>=46.4.0 in
c:\users\kieuc\boltz22\lib\site-packages (from
chembl_structure_pipeline==1.2.2->boltz==2.2.0) (65.5.0)
Requirement already satisfied: colorama in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from click==8.1.7->boltz==2.2.0)
(0.4.6)
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-2.4.7-py3-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)
Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB)
\-------------------------------------- 117.0/117.0 kB 6.7 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: packaging in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from hydra-
core==1.3.2->boltz==2.2.0) (25.0)
Requirement already satisfied: typing-extensions>=4.1.0 in c:\program
files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from
mashumaro==3.14->boltz==2.2.0) (4.15.0)
Requirement already satisfied: ihm>=1.7 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\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-win_amd64.whl.metadata (5.0 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)
\---------------------------------------- 57.7/57.7 kB ? eta 0:00:00
Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.2.0)
Downloading 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)
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 c:\program
files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from
requests==2.32.3->boltz==2.2.0) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from
requests==2.32.3->boltz==2.2.0) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from
requests==2.32.3->boltz==2.2.0) (2.6.2)
Requirement already satisfied: certifi>=2017.4.17 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\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)
Downloading 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)
Downloading threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
Requirement already satisfied: filelock in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from torch==2.7.1->boltz==2.2.0)
(3.19.1)
Requirement already satisfied: networkx in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from torch==2.7.1->boltz==2.2.0)
(3.3)
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from torch==2.7.1->boltz==2.2.0)
(3.1.6)
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 c:\program files\chimerax
1.12.dev202512180555\bin\lib\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)
Downloading protobuf-5.29.5-cp310-abi3-win_amd64.whl.metadata (592 bytes)
Requirement already satisfied: psutil>=5.0.0 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\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)
Downloading sentry_sdk-2.48.0-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-win_amd64.whl.metadata (11 kB)
Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.2.0)
Downloading cuequivariance-0.8.0-py3-none-any.whl.metadata (15 kB)
Requirement already satisfied: python-dateutil>=2.8.2 in c:\program
files\chimerax 1.12.dev202512180555\bin\lib\site-packages (from
pandas>=2.2.2->boltz==2.2.0) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.2.0)
(2025.2)
Requirement already satisfied: tzdata>=2022.7 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.2.0)
(2025.3)
Requirement already satisfied: Pillow in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from
rdkit>=2024.3.2->boltz==2.2.0) (11.3.0)
Requirement already satisfied: six>=1.4.0 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\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 c:\program
files\chimerax 1.12.dev202512180555\bin\lib\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)
Downloading gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)
Requirement already satisfied: msgpack in c:\program files\chimerax
1.12.dev202512180555\bin\lib\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)
Downloading 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)
Downloading opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages (from
jinja2->torch==2.7.1->boltz==2.2.0) (3.0.3)
Requirement already satisfied: aiohappyeyeballs>=2.5.0 in c:\program
files\chimerax 1.12.dev202512180555\bin\lib\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 c:\program files\chimerax
1.12.dev202512180555\bin\lib\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 c:\program files\chimerax
1.12.dev202512180555\bin\lib\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 c:\program files\chimerax
1.12.dev202512180555\bin\lib\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 c:\program
files\chimerax 1.12.dev202512180555\bin\lib\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 c:\program files\chimerax
1.12.dev202512180555\bin\lib\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 c:\program files\chimerax
1.12.dev202512180555\bin\lib\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)
Downloading smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)
Downloading biopython-1.84-cp311-cp311-win_amd64.whl (2.8 MB)
\---------------------------------------- 2.8/2.8 MB 4.6 MB/s eta 0:00:00
Downloading chembl_structure_pipeline-1.2.2-py3-none-any.whl (17 kB)
Downloading click-8.1.7-py3-none-any.whl (97 kB)
\---------------------------------------- 97.9/97.9 kB 5.5 MB/s eta 0:00:00
Downloading dm_tree-0.1.8-cp311-cp311-win_amd64.whl (101 kB)
\---------------------------------------- 101.3/101.3 kB 5.7 MB/s eta 0:00:00
Downloading einops-0.8.0-py3-none-any.whl (43 kB)
\---------------------------------------- 43.2/43.2 kB ? eta 0:00:00
Downloading einx-0.3.0-py3-none-any.whl (102 kB)
\---------------------------------------- 103.0/103.0 kB 5.8 MB/s eta 0:00:00
Downloading gemmi-0.6.5-cp311-cp311-win_amd64.whl (2.3 MB)
\---------------------------------------- 2.3/2.3 MB 5.5 MB/s eta 0:00:00
Downloading hydra_core-1.3.2-py3-none-any.whl (154 kB)
\---------------------------------------- 154.5/154.5 kB 9.6 MB/s eta 0:00:00
Downloading mashumaro-3.14-py3-none-any.whl (92 kB)
\---------------------------------------- 92.2/92.2 kB 5.1 MB/s eta 0:00:00
Downloading numba-0.61.0-cp311-cp311-win_amd64.whl (2.8 MB)
\---------------------------------------- 2.8/2.8 MB 5.5 MB/s eta 0:00:00
Downloading pytorch_lightning-2.5.0-py3-none-any.whl (819 kB)
\---------------------------------------- 819.4/819.4 kB 5.2 MB/s eta 0:00:00
Downloading PyYAML-6.0.2-cp311-cp311-win_amd64.whl (161 kB)
\--------------------------------------- 162.0/162.0 kB 10.1 MB/s eta 0:00:00
Downloading requests-2.32.3-py3-none-any.whl (64 kB)
\---------------------------------------- 64.9/64.9 kB ? eta 0:00:00
Downloading scikit_learn-1.6.1-cp311-cp311-win_amd64.whl (11.1 MB)
\---------------------------------------- 11.1/11.1 MB 5.4 MB/s eta 0:00:00
Downloading scipy-1.13.1-cp311-cp311-win_amd64.whl (46.2 MB)
\---------------------------------------- 46.2/46.2 MB 4.5 MB/s eta 0:00:00
Downloading torch-2.7.1-cp311-cp311-win_amd64.whl (216.1 MB)
\---------------------------------------- 216.1/216.1 MB 1.7 MB/s eta 0:00:00
Downloading wandb-0.18.7-py3-none-win_amd64.whl (15.5 MB)
\---------------------------------------- 15.5/15.5 MB 2.3 MB/s eta 0:00:00
Downloading cuequivariance_torch-0.8.0-py3-none-any.whl (216 kB)
\---------------------------------------- 216.8/216.8 kB 1.7 MB/s eta 0:00:00
Downloading pandas-2.3.3-cp311-cp311-win_amd64.whl (11.3 MB)
\---------------------------------------- 11.3/11.3 MB 1.5 MB/s eta 0:00:00
Downloading rdkit-2025.9.3-cp311-cp311-win_amd64.whl (23.7 MB)
\---------------------------------------- 23.7/23.7 MB 2.2 MB/s eta 0:00:00
Downloading types_requests-2.32.4.20250913-py3-none-any.whl (20 kB)
Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Downloading fsspec-2025.12.0-py3-none-any.whl (201 kB)
\---------------------------------------- 201.4/201.4 kB 2.0 MB/s eta 0:00:00
Downloading gitpython-3.1.45-py3-none-any.whl (208 kB)
\---------------------------------------- 208.2/208.2 kB 2.5 MB/s eta 0:00:00
Downloading joblib-1.5.3-py3-none-any.whl (309 kB)
\---------------------------------------- 309.1/309.1 kB 2.4 MB/s eta 0:00:00
Downloading lightning_utilities-0.15.2-py3-none-any.whl (29 kB)
Downloading llvmlite-0.44.0-cp311-cp311-win_amd64.whl (30.3 MB)
\---------------------------------------- 30.3/30.3 MB 2.8 MB/s eta 0:00:00
Downloading omegaconf-2.3.0-py3-none-any.whl (79 kB)
\---------------------------------------- 79.5/79.5 kB 4.6 MB/s eta 0:00:00
Downloading protobuf-5.29.5-cp310-abi3-win_amd64.whl (434 kB)
\---------------------------------------- 434.8/434.8 kB 3.4 MB/s eta 0:00:00
Downloading sentry_sdk-2.48.0-py2.py3-none-any.whl (414 kB)
\---------------------------------------- 414.6/414.6 kB 3.7 MB/s eta 0:00:00
Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB)
\---------------------------------------- 6.3/6.3 MB 2.5 MB/s eta 0:00:00
Downloading threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
Downloading torchmetrics-1.8.2-py3-none-any.whl (983 kB)
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Downloading tqdm-4.67.1-py3-none-any.whl (78 kB)
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Downloading cuequivariance-0.8.0-py3-none-any.whl (266 kB)
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Downloading frozendict-2.4.7-py3-none-any.whl (16 kB)
Downloading setproctitle-1.3.7-cp311-cp311-win_amd64.whl (13 kB)
Downloading gitdb-4.0.12-py3-none-any.whl (62 kB)
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Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)
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Downloading opt_einsum-3.4.0-py3-none-any.whl (71 kB)
\---------------------------------------- 71.9/71.9 kB 4.1 MB/s eta 0:00:00
Downloading smmap-5.0.2-py3-none-any.whl (24 kB)
Building wheels for collected packages: boltz, fairscale, modelcif,
antlr4-python3-runtime
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=269018
sha256=82e3bcf092870d91ab024996009e2eafbd93fa008661d139448f56053ceaea14
Stored in directory: C:\Users\kieuc\AppData\Local\Temp\pip-ephem-wheel-cache-
_i27jzdy\wheels\26\ba\5c\a8ae06e77eb74d03f129cbbe5d93bfea3b1259fabe4f838af4
Building wheel for fairscale (pyproject.toml): started
Building wheel for fairscale (pyproject.toml): finished with status 'done'
Created wheel for fairscale: filename=fairscale-0.4.13-py3-none-any.whl
size=332216
sha256=32195bf6b96423a04f827ab5233dff6357b218ed3513e75a439b148210b1bcd4
Stored in directory:
c:\users\kieuc\appdata\local\pip\cache\wheels\95\ef\96\5044bde220b2ea299bdc6ec05051e0ef187fad45b341d1c273
Building wheel for modelcif (setup.py): started
Building wheel for modelcif (setup.py): finished with status 'done'
Created wheel for modelcif: filename=modelcif-1.2-py3-none-any.whl size=41204
sha256=141842c3010067f4eafee6bf80ef5380ceafd0220fef1fb8f09963ae31e7c772
Stored in directory:
c:\users\kieuc\appdata\local\pip\cache\wheels\d2\3a\8c\e28cb28a15568d1b1b6163c77c945a5961351340fd15b9b4df
Building wheel for antlr4-python3-runtime (setup.py): started
Building wheel for antlr4-python3-runtime (setup.py): finished with status
'done'
Created wheel for antlr4-python3-runtime:
filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144577
sha256=4b9f7a619903267c03f2bd01c519a479710c43f56c1efb800b835e78a7255cee
Stored in directory:
c:\users\kieuc\appdata\local\pip\cache\wheels\1a\97\32\461f837398029ad76911109f07047fde1d7b661a147c7c56d1
Successfully built boltz fairscale modelcif antlr4-python3-runtime
Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types-
requests, tqdm, threadpoolctl, sympy, smmap, setproctitle, sentry-sdk, scipy,
requests, rdkit, pyyaml, protobuf, opt-einsum, mashumaro, llvmlite, lightning-
utilities, joblib, gemmi, fsspec, frozendict, einops, docker-pycreds, click,
biopython, torch, scikit-learn, pandas, omegaconf, numba, modelcif, gitdb,
einx, cuequivariance, chembl_structure_pipeline, torchmetrics, hydra-core,
gitpython, fairscale, cuequivariance_torch, wandb, pytorch-lightning, boltz
Attempting uninstall: scipy
Found existing installation: scipy 1.14.0
Not uninstalling scipy at c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages, outside environment
C:\Users\kieuc\boltz22
Can't uninstall 'scipy'. No files were found to uninstall.
Attempting uninstall: requests
Found existing installation: requests 2.32.5
Not uninstalling requests at c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages, outside environment
C:\Users\kieuc\boltz22
Can't uninstall 'requests'. No files were found to uninstall.
Attempting uninstall: click
Found existing installation: click 8.3.1
Not uninstalling click at c:\program files\chimerax
1.12.dev202512180555\bin\lib\site-packages, outside environment
C:\Users\kieuc\boltz22
Can't uninstall 'click'. No files were found to uninstall.
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_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-3.1.45 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 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
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: C:\Users\kieuc\boltz22\Scripts\python.exe -m pip
install --upgrade pip
Downloading Boltz model parameters (4 GB) and chemical component database (1.8
GB) to ~/.boltz
C:\Users\kieuc/boltz22\Scripts\python.exe C:\Program Files\ChimeraX
1.12.dev202512180555\bin\Lib\site-
packages\chimerax\boltz\download_weights_and_ccd.py
Downloading the CCD data to C:\Users\kieuc\\.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 C:\Users\kieuc\\.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 C:\Users\kieuc\\.boltz\boltz2_conf.ckpt.
You may change the cache directory with the --cache flag.
Downloading the Boltz-2 affinity weights to
C:\Users\kieuc\\.boltz\boltz2_aff.ckpt. You may change the cache directory
with the --cache flag.
Making CCD atom counts table for 45227 in C:\Users\kieuc/.boltz/mols
Boltz model parameters and CCD database are installed in ~/.boltz
Successfully installed Boltz program and neural net weights.
> boltz predict protein
> SGSGMGSSLEESTINNISKMSPEKRTEFLKKLVDPVDGAGMSLMRLTIGTADFTGRDFYTYYDNVPAADGPDWYNTTGKGFSIQKDIDYNIVSTVKEALKINPNLKLFSSPWTPPGWMKEQTDSSKSYENNDKLIKGGKLSDAHISDAAMYYTRYLEEYAKQGIPIYAMTLQNEPGLQIDYPSCYITPEQEQKLAIAIKADIAKSDVLKGKDIKIWAFDHNFDSGVSFATQALNNDASKSAIDGIAFHDYGGEPTAMTQVHNLFPDHSVNLTERSVWGTTGADRIIQYYRNYAESYNSWVTMLDSNISPEQWTGTPDPTMFVLDANDNNNYWATPEYYITGQFSKFIKPGAVRVDSDYGSSDTVTDVVFKNTDGTLVAVVVNQTDQAQSFKLTSSGAQIFASIPAKNVATYVWKP
> ligandCcd 122 affinity 122
Running Boltz prediction of protein with 415 residues, 1 ligands 122 on cpu
Using multiple sequence alignment server https://api.colabfold.com
Prediction terminated by user
> boltz predict protein
> SGSGMGSSLEESTINNISKMSPEKRTEFLKKLVDPVDGAGMSLMRLTIGTADFTGRDFYTYYDNVPAADGPDWYNTTGKGFSIQKDIDYNIVSTVKEALKINPNLKLFSSPWTPPGWMKEQTDSSKSYENNDKLIKGGKLSDAHISDAAMYYTRYLEEYAKQGIPIYAMTLQNEPGLQIDYPSCYITPEQEQKLAIAIKADIAKSDVLKGKDIKIWAFDHNFDSGVSFATQALNNDASKSAIDGIAFHDYGGEPTAMTQVHNLFPDHSVNLTERSVWGTTGADRIIQYYRNYAESYNSWVTMLDSNISPEQWTGTPDPTMFVLDANDNNNYWATPEYYITGQFSKFIKPGAVRVDSDYGSSDTVTDVVFKNTDGTLVAVVVNQTDQAQSFKLTSSGAQIFASIPAKNVATYVWKP
Running Boltz prediction of protein with 415 residues on cpu
Using cached multiple sequence alignment
C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_1
Confidence score 0.96, pTM 0.96, ipTM 0.00, pLDDT 0.96
Boltz prediction completed in 2793 seconds (start boltz 6 sec, sequence search
0 sec, load weights 41 sec, structure inference 2746 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
> C:\Users\kieuc/Desktop/boltz_2\boltz_results_boltz_2\predictions\boltz_2\boltz_2_model_0.cif
> logInfo false
> boltz predict protein
> SGSGMGSSLEESTINNISKMSPEKRTEFLKKLVDPVDGAGMSLMRLTIGTADFTGRDFYTYYDNVPAADGPDWYNTTGKGFSIQKDIDYNIVSTVKEALKINPNLKLFSSPWTPPGWMKEQTDSSKSYENNDKLIKGGKLSDAHISDAAMYYTRYLEEYAKQGIPIYAMTLQNEPGLQIDYPSCYITPEQEQKLAIAIKADIAKSDVLKGKDIKIWAFDHNFDSGVSFATQALNNDASKSAIDGIAFHDYGGEPTAMTQVHNLFPDHSVNLTERSVWGTTGADRIIQYYRNYAESYNSWVTMLDSNISPEQWTGTPDPTMFVLDANDNNNYWATPEYYITGQFSKFIKPGAVRVDSDYGSSDTVTDVVFKNTDGTLVAVVVNQTDQAQSFKLTSSGAQIFASIPAKNVATYVWKP
> ligandCcd CEL affinity CEL
Running Boltz prediction of protein with 415 residues, 1 ligands CEL on cpu
Using cached multiple sequence alignment
C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_1
> save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH30_boltz.cxs"
——— End of log from Thu Dec 18 13:29:25 2025 ———
> view name session-start
opened ChimeraX session
> ui tool show "Boltz History"
> open
> C:\Users\kieuc/Desktop\boltz_3\boltz_results_boltz_3\predictions\boltz_3\boltz_3_model_0.cif
> hide #1 models
> close #1
> open 4PTV
4ptv title:
Halothermothrix orenii beta-glucosidase A, thiocellobiose complex [more
info...]
Chain information for 4ptv #1
---
Chain | Description | UniProt
A B | Glycoside hydrolase family 1 | B8CYA8_HALOH 1-451
Non-standard residues in 4ptv #1
---
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)
CS — cesium ion
PE4 — 2-{2-[2-(2-{2-[2-(2-ethoxy-
ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol (polyethylene glycol
PEG4000)
SGC — 4-thio-beta-D-glucopyranose (4-DEOXY-4-THIO-BETA-D-GLUCOPYRANOSE;
4-thio-beta-D-glucose; 4-thio-D-glucose; 4-thio-glucose)
4ptv mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
44 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
7292 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide #1 models
> hide #2 models
> show #1 models
> select :BGC
22 atoms, 22 bonds, 2 residues, 1 model selected
> select :SGC
24 atoms, 24 bonds, 2 residues, 1 model selected
> hide #1 models
> show #2 models
> save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường
> Dương/GH30_Cel_Boltz.pdb"
> open 2O9R
Summary of feedback from opening 2O9R fetched from pdb
---
note | Fetching compressed mmCIF 2o9r from http://files.rcsb.org/download/2o9r.cif
2o9r title:
beta-glucosidase B complexed with thiocellobiose [more info...]
Chain information for 2o9r #3
---
Chain | Description | UniProt
A | Beta-glucosidase B | BGLB_PAEPO 4-448
Non-standard residues in 2o9r #3
---
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)
SGC — 4-thio-beta-D-glucopyranose (4-DEOXY-4-THIO-BETA-D-GLUCOPYRANOSE;
4-thio-beta-D-glucose; 4-thio-D-glucose; 4-thio-glucose)
> ui tool show Boltz
> boltz predict protein #2/A ligandCcd BGC,SGC name boltz_3_model_0.cif
Running Boltz prediction of protein with 415 residues, 2 ligands BGC, SGC on
cpu
Using cached multiple sequence alignment
C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_1
> save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường
> Dương/GH30_Thio_andotherPDBwiththiocellobiose.pdb"
Confidence score 0.92, pTM 0.97, ipTM 0.81, pLDDT 0.95
Boltz prediction completed in 3241 seconds (start boltz 6 sec, sequence search
0 sec, load weights 34 sec, structure inference 3200 sec)
> open
> C:\Users\kieuc/Desktop/boltz_boltz_3_model_0.cif\boltz_results_boltz_3_model_0.cif\predictions\boltz_3_model_0.cif\boltz_3_model_0.cif_model_0.cif
> logInfo false
Matchmaker boltz_3_model_0.cif, chain A (#2) with
boltz_3_model_0.cif_model_0.cif, chain A (#4), sequence alignment score =
2157.8
RMSD between 413 pruned atom pairs is 0.395 angstroms; (across all 415 pairs:
0.429)
> hide #3 models
> hide #2 models
> show #2 models
> hide #4 models
QWindowsWindow::setGeometry: Unable to set geometry 1920x1127+0+35 (frame:
1942x1183-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 557x751 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=858,
y=1183)))
QWindowsWindow::setGeometry: Unable to set geometry 1920x1232+0+35 (frame:
1942x1288-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 557x821 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=858,
y=1288)))
> boltz predict protein #2/A forEachSmilesLigand
> "ligand1,C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C@H](OC([C@@H]([C@H]2O)O)O)CO)O)O)O)O"
> name boltz_3_model_0.cif affinity each
Running Boltz prediction of protein with 415 residues, 1 ligands
C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C@H](OC([C@@H]([C@H]2O)O)O)CO)O)O)O)O
on cpu
Using cached multiple sequence alignment
C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_1
> close #2
> show #4 models
QWindowsWindow::setGeometry: Unable to set geometry 1920x1418+0+35 (frame:
1942x1474-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 557x945 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=858,
y=1474)))
Ligand
C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C@H](OC([C@@H]([C@H]2O)O)O)CO)O)O)O)O
predicted binding affinity 5.4 uM, predicted binding probability 0.47
Boltz prediction completed in 5295 seconds (start boltz 6 sec, sequence search
0 sec, load weights 52 sec, structure inference 3156 sec, load affinity
weights 56 sec, affinity inference 2025 sec)
> open
> C:\Users\kieuc/Desktop/boltz_boltz_3_model_0.cif_1\boltz_results_ligand1\predictions\ligand1\ligand1_model_0.cif
> logInfo false
> hide #2 models
> hide #4 models
> show #2 models
> save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH3-cellobiose-
> Boltz.pdb"
> close #4
> rename #2 GH30-Cellulobio.cif
> rename #2 GH30-Cellulobiose.cif
> save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường
> Dương/GH30_Cellobiose_boltz.cxs"
——— End of log from Fri Dec 19 09:13:14 2025 ———
> view name session-start
opened ChimeraX session
> hide #2 models
> show #1 models
> select ~sel & ##selected
7785 atoms, 7580 bonds, 1313 residues, 1 model selected
> select clear
> show #3 models
> hide #1 models
> ui tool show "Boltz History"
> open
Missing or invalid "fileNames" argument: Expected a file name
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2585, in <lambda>
self.ui_area.contextMenuEvent = lambda e, *, self=self:
self.show_context_menu(e)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2759, in show_context_menu
_show_context_menu(event, self.tool_window.tool_instance, self.tool_window,
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2809, in _show_context_menu
fill_cb(menu, pos.x(), pos.y())
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\boltz\history.py", line 190, in fill_context_menu
if self._results_table:
^^^^^^^^^^^^^^^^^^^
AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table'
AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table'
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\boltz\history.py", line 190, in fill_context_menu
if self._results_table:
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2585, in <lambda>
self.ui_area.contextMenuEvent = lambda e, *, self=self:
self.show_context_menu(e)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2759, in show_context_menu
_show_context_menu(event, self.tool_window.tool_instance, self.tool_window,
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2809, in _show_context_menu
fill_cb(menu, pos.x(), pos.y())
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\boltz\history.py", line 190, in fill_context_menu
if self._results_table:
^^^^^^^^^^^^^^^^^^^
AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table'
AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table'
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\boltz\history.py", line 190, in fill_context_menu
if self._results_table:
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show Boltz
> open
> C:\Users\kieuc/Desktop\boltz_Gh3_cellobiose\boltz_results_Gh3_cellobiose\predictions\Gh3_cellobiose\Gh3_cellobiose_model_0.cif
> ui tool show Matchmaker
> matchmaker #2 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Gh3_cellobiose_model_0.cif, chain A (#4) with
GH30-Cellulobiose.cif, chain A (#2), sequence alignment score = 95
RMSD between 10 pruned atom pairs is 1.373 angstroms; (across all 325 pairs:
28.468)
> matchmaker #2 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Gh3_cellobiose_model_0.cif, chain A (#4) with
GH30-Cellulobiose.cif, chain A (#2), sequence alignment score = 95
RMSD between 10 pruned atom pairs is 1.373 angstroms; (across all 325 pairs:
28.468)
> ui tool show Matchmaker
> matchmaker #2 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Gh3_cellobiose_model_0.cif, chain A (#4) with
GH30-Cellulobiose.cif, chain A (#2), sequence alignment score = 95
RMSD between 10 pruned atom pairs is 1.373 angstroms; (across all 325 pairs:
28.468)
> matchmaker #2 to #4
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker Gh3_cellobiose_model_0.cif, chain A (#4) with
GH30-Cellulobiose.cif, chain A (#2), sequence alignment score = 95
RMSD between 10 pruned atom pairs is 1.373 angstroms; (across all 325 pairs:
28.468)
> ui tool show Matchmaker
> matchmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4ptv, chain A (#1) with Gh3_cellobiose_model_0.cif, chain A (#4),
sequence alignment score = 121.4
RMSD between 21 pruned atom pairs is 1.094 angstroms; (across all 379 pairs:
30.950)
> matchmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 4ptv, chain A (#1) with Gh3_cellobiose_model_0.cif, chain A (#4),
sequence alignment score = 121.4
RMSD between 21 pruned atom pairs is 1.094 angstroms; (across all 379 pairs:
30.950)
> show #1 models
> hide #3 models
> select #3/A
3755 atoms, 3737 bonds, 575 residues, 1 model selected
> hide #1 models
> hide #4 models
> show #4 models
> show #1 models
> select #1/B
3853 atoms, 3778 bonds, 627 residues, 1 model selected
> delete #1/B
> delete #1/D
> hide #1 models
> select add #4
4307 atoms, 4378 bonds, 567 residues, 1 model selected
> close #1
> close #2
> close #3
QWindowsWindow::setGeometry: Unable to set geometry 1920x1115+0+35 (frame:
1942x1171-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1094+0+34 (frame: 1942x1150-11-11) margins: 11, 45,
11, 11 minimum size: 557x743 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=858,
y=1171)))
> boltz predict protein /A ligandSmiles
> C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)OC2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)OC3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O)O
> name Gh3_laminarin.cif
Running Boltz prediction of protein with 566 residues, 1 ligands
C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)OC2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)OC3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O)O
on cpu
Using cached multiple sequence alignment
C:\Users\kieuc/Downloads/ChimeraX/BoltzMSA\boltz_4
> open 6SZ6
Summary of feedback from opening 6SZ6 fetched from pdb
---
notes | Fetching compressed mmCIF 6sz6 from http://files.rcsb.org/download/6sz6.cif
Fetching CCD BMA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif
Fetching CCD MAN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif
Fetching CCD NAG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/NAG/NAG.cif
6sz6 title:
Chaetomium thermophilum beta-glucosidase [more info...]
Chain information for 6sz6 #1
---
Chain | Description | UniProt
A | Beta-glucosidase | A6YRT4_9PEZI 32-867
Non-standard residues in 6sz6 #1
---
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
6820 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show Matchmaker
> matchmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6sz6, chain A (#1) with Gh3_cellobiose_model_0.cif, chain A (#4),
sequence alignment score = 632.3
RMSD between 241 pruned atom pairs is 0.997 angstroms; (across all 492 pairs:
9.752)
> matchmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 6sz6, chain A (#1) with Gh3_cellobiose_model_0.cif, chain A (#4),
sequence alignment score = 632.3
RMSD between 241 pruned atom pairs is 0.997 angstroms; (across all 492 pairs:
9.752)
> select clear
> hide #1 models
> show #1 models
> hide #4 models
> open 3zyz
Summary of feedback from opening 3zyz fetched from pdb
---
notes | Fetching compressed mmCIF 3zyz from http://files.rcsb.org/download/3zyz.cif
Fetching CCD GOL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif
Fetching CCD PEG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/PEG/PEG.cif
3zyz title:
Crystal structure of a glycoside hydrolase family 3 beta-glucosidase, Bgl1
from Hypocrea jecorina at 2.1A resolution. [more info...]
Chain information for 3zyz #2
---
Chain | Description | UniProt
A | BETA-D-GLUCOSIDE GLUCOHYDROLASE | Q12715_TRIRE 1-713
Non-standard residues in 3zyz #2
---
BGC — beta-D-glucopyranose (beta-D-glucose; D-glucose; glucose)
GOL — glycerol (glycerin; propane-1,2,3-triol)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
PEG — di(hydroxyethyl)ether
56 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #1 models
> open 2X40
Summary of feedback from opening 2X40 fetched from pdb
---
notes | Fetching compressed mmCIF 2x40 from http://files.rcsb.org/download/2x40.cif
Fetching CCD BR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/BR/BR.cif
2x40 title:
Structure of beta-glucosidase 3B from Thermotoga neapolitana in complex with
glycerol [more info...]
Chain information for 2x40 #3
---
Chain | Description | UniProt
A | BETA-GLUCOSIDASE | Q0GC07_THENN 1-721
Non-standard residues in 2x40 #3
---
BR — bromide ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
2x40 mmCIF Assemblies
---
1| author_and_software_defined_assembly
5660 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide #2 models
> open "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường
> Dương/GH3_fold_2025_09_27_06_25/fold_2025_09_27_06_25_model_0.cif"
Chain information for fold_2025_09_27_06_25_model_0.cif #5
---
Chain | Description
A | .
Computing secondary structure
> hide #5 models
Confidence score 0.97, pTM 0.97, ipTM 0.97, pLDDT 0.97
Boltz prediction completed in 6389 seconds (start boltz 7 sec, sequence search
0 sec, load weights 36 sec, structure inference 6347 sec)
> open
> C:\Users\kieuc/Desktop/boltz_Gh3_laminarin\boltz_results_Gh3_laminarin\predictions\Gh3_laminarin\Gh3_laminarin_model_0.cif
> logInfo false
> open 8VA3
Summary of feedback from opening 8VA3 fetched from pdb
---
notes | Fetching compressed mmCIF 8va3 from http://files.rcsb.org/download/8va3.cif
Fetching CCD EPE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/EPE/EPE.cif
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif
Fetching CCD PGE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/PGE/PGE.cif
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif
8va3 title:
Crystal structure of CapGH3b enzyme retrieved from capybara gut metagenome
[more info...]
Chain information for 8va3 #7
---
Chain | Description
A B | Glycoside hydrolase family 3
Non-standard residues in 8va3 #7
---
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)
GOL — glycerol (glycerin; propane-1,2,3-triol)
MG — magnesium ion
NA — sodium ion
PEG — di(hydroxyethyl)ether
PGE — triethylene glycol
PO4 — phosphate ion
43 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
11824 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> close #3
> hide #!7 models
> save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường
> Dương/Gh3_laminarin1_boltz.pdb"
> close #1
> close #2
> show #!7 models
> hide #6 models
> select #7/B
6635 atoms, 6096 bonds, 7 pseudobonds, 1425 residues, 3 models selected
> delete #7/B
> show #5 models
> ui tool show Matchmaker
> matchmaker #5 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8va3, chain A (#7) with fold_2025_09_27_06_25_model_0.cif, chain A
(#5), sequence alignment score = 1149.7
RMSD between 432 pruned atom pairs is 0.940 angstroms; (across all 547 pairs:
4.765)
> matchmaker #5 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8va3, chain A (#7) with fold_2025_09_27_06_25_model_0.cif, chain A
(#5), sequence alignment score = 1149.7
RMSD between 432 pruned atom pairs is 0.940 angstroms; (across all 547 pairs:
4.765)
> mmaker #4,5,6 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8va3, chain A (#7) with Gh3_cellobiose_model_0.cif, chain A (#4),
sequence alignment score = 1142.8
RMSD between 443 pruned atom pairs is 0.951 angstroms; (across all 551 pairs:
5.421)
Matchmaker 8va3, chain A (#7) with fold_2025_09_27_06_25_model_0.cif, chain A
(#5), sequence alignment score = 1149.7
RMSD between 432 pruned atom pairs is 0.940 angstroms; (across all 547 pairs:
4.765)
Matchmaker 8va3, chain A (#7) with Gh3_laminarin_model_0.cif, chain A (#6),
sequence alignment score = 1139.2
RMSD between 426 pruned atom pairs is 0.951 angstroms; (across all 550 pairs:
4.769)
> hide #5 models
> show #6 models
> hide #6 models
> show #4 models
> hide #4 models
> save "C:/Users/kieuc/Dropbox/1 Choi lab/Students/Hường Dương/GH3.cxs"
——— End of log from Fri Dec 19 14:52:44 2025 ———
> view name session-start
opened ChimeraX session
> hide #!7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #4 models
> close session
> ui tool show "Boltz History"
Confidence score 0.93, pTM 0.96, ipTM 0.85, pLDDT 0.95
Boltz prediction completed in 4766 seconds (start boltz 60 sec, sequence
search 0 sec, load weights 151 sec, structure inference 4555 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
> C:\Users\kieuc/Desktop/boltz_GH30-xylan_1\boltz_results_GH30-xylan\predictions\GH30-xylan\GH30-xylan_model_0.cif
> logInfo false
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2585, in <lambda>
self.ui_area.contextMenuEvent = lambda e, *, self=self:
self.show_context_menu(e)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2759, in show_context_menu
_show_context_menu(event, self.tool_window.tool_instance, self.tool_window,
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\ui\gui.py", line 2809, in _show_context_menu
fill_cb(menu, pos.x(), pos.y())
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\boltz\history.py", line 190, in fill_context_menu
if self._results_table:
^^^^^^^^^^^^^^^^^^^
AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table'
AttributeError: 'BoltzHistoryPanel' object has no attribute '_results_table'
File "C:\Program Files\ChimeraX 1.12.dev202512180555\bin\Lib\site-
packages\chimerax\boltz\history.py", line 190, in fill_context_menu
if self._results_table:
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 32.0.101.7077
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows
Manufacturer: Dell Inc.
Model: XPS 13 9310
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 34,052,284,416
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1195G7 @ 2.90GHz
OSLanguage: en-US
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
babel: 2.17.0
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: 1.61.5
ChimeraX-AtomicLibrary: 14.2.2
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: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12.dev202512180555
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: 1.8
ChimeraX-Label: 1.3
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: 2.7.12
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: 1.7
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: 1.50
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
comtypes: 1.4.11
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
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
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
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
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
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
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-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: 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
pywin32: 311
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: 4.1.0
roman-numerals-py: 4.1.0
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
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2025.3
urllib3: 2.6.2
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
WMI: 1.5.1
yarl: 1.22.0
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