Opened 2 months ago

Closed 2 months ago

#18426 closed defect (can't reproduce)

Boltz-related problems

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.11.dev202508112234 (2025-08-11 22:34:36 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010d

Current thread 0x00001ab4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\core\__main__.py", line 1058 in init
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\core\__main__.py", line 1223 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x80010001

Current thread 0x00001ab4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\boltz\boltz_gui.py", line 800 in _choose_results_directory
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\core\__main__.py", line 1058 in init
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\core\__main__.py", line 1223 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x80010001

Current thread 0x00001ab4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\boltz\boltz_gui.py", line 800 in _choose_results_directory
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\core\__main__.py", line 1058 in init
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\core\__main__.py", line 1223 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: access violation

Current thread 0x00001ab4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\core\__main__.py", line 1058 in init
  File "C:\Program Files\ChimeraX 1.11.dev202508112234\bin\Lib\site-packages\chimerax\core\__main__.py", line 1223 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
===== Log before crash start =====
> ui tool show Boltz

> boltz install C:\Users\xyd/boltz2

Successfully created Boltz Python virtual environment C:\Users\xyd/boltz2.  
Now installing machine learning package torch.  
C:\Users\xyd/boltz2\Scripts\python.exe -m pip install torch --index-url
https://download.pytorch.org/whl/cu126  
Looking in indexes: https://download.pytorch.org/whl/cu126  
  
Collecting torch  
  
Downloading
https://download.pytorch.org/whl/cu126/torch-2.8.0%2Bcu126-cp311-cp311-win_amd64.whl.metadata
(29 kB)  
  
Requirement already satisfied: filelock in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from torch) (3.18.0)  
  
Requirement already satisfied: typing-extensions>=4.10.0 in c:\program
files\chimerax 1.11.dev202508112234\bin\lib\site-packages (from torch)
(4.14.1)  
  
Collecting sympy>=1.13.3 (from torch)  
  
Downloading https://download.pytorch.org/whl/sympy-1.13.3-py3-none-
any.whl.metadata (12 kB)  
  
Requirement already satisfied: networkx in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from torch) (3.3)  
  
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from torch) (3.1.6)  
  
Collecting fsspec (from torch)  
  
Downloading https://download.pytorch.org/whl/fsspec-2024.6.1-py3-none-
any.whl.metadata (11 kB)  
  
Collecting mpmath=1.1.0 (from sympy>=1.13.3->torch)  
  
Downloading https://download.pytorch.org/whl/mpmath-1.3.0-py3-none-any.whl
(536 kB)  
  
\------------------------------------ 536.2/536.2 kB 509.6 kB/s eta 0:00:00  
  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from jinja2->torch) (3.0.2)  
  
Downloading
https://download.pytorch.org/whl/cu126/torch-2.8.0%2Bcu126-cp311-cp311-win_amd64.whl
(2915.5 MB)  
  

QDxgiVSyncService: DXGI Factory is no longer Current  

\---------------------------------------- 2.9/2.9 GB 1.6 MB/s eta 0:00:00  
  

QDxgiVSyncService: DXGI Factory is no longer Current  

Downloading https://download.pytorch.org/whl/sympy-1.13.3-py3-none-any.whl
(6.2 MB)  
  
\---------------------------------------- 6.2/6.2 MB 1.5 MB/s eta 0:00:00  
  
Downloading https://download.pytorch.org/whl/fsspec-2024.6.1-py3-none-any.whl
(177 kB)  
  
\-------------------------------------- 177.6/177.6 kB 972.8 kB/s eta 0:00:00  
  
Installing collected packages: mpmath, sympy, fsspec, torch  
  
Successfully installed fsspec-2024.6.1 mpmath-1.3.0 sympy-1.13.3
torch-2.8.0+cu126  
  
Successfully installed torch.  
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\xyd/boltz2\Scripts\python.exe -m pip install
git+https://github.com/RBVI/boltz@chimerax_boltz2  
Collecting git+https://github.com/RBVI/boltz@chimerax_boltz2  
  
Cloning https://github.com/RBVI/boltz (to revision chimerax_boltz2) to
c:\users\xyd\appdata\local\temp\pip-req-build-xc6a3bb_  
  
Running command git clone --filter=blob:none --quiet
https://github.com/RBVI/boltz 'C:\Users\xyd\AppData\Local\Temp\pip-req-build-
xc6a3bb_'  
  
Running command git checkout -b chimerax_boltz2 --track origin/chimerax_boltz2  
  
branch 'chimerax_boltz2' set up to track 'origin/chimerax_boltz2'.  
  
Switched to a new branch 'chimerax_boltz2'  
  
Resolved https://github.com/RBVI/boltz to commit
6e47badce94c472cd66b543781a3fea9ee9186b9  
  
Installing build dependencies: started  
  
Installing build dependencies: finished with status 'done'  
  
Getting requirements to build wheel: started  
  
Getting requirements to build wheel: finished with status 'done'  
  
Preparing metadata (pyproject.toml): started  
  
Preparing metadata (pyproject.toml): finished with status 'done'  
  
Requirement already satisfied: torch>=2.2 in c:\users\xyd\boltz2\lib\site-
packages (from boltz==2.1.1) (2.8.0+cu126)  
  
Requirement already satisfied: numpy=1.26 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from boltz==2.1.1) (1.26.4)  
  
Collecting hydra-core==1.3.2 (from boltz==2.1.1)  
  
Using cached hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB)  
  
Collecting pytorch-lightning==2.5.0 (from boltz==2.1.1)  
  
Using cached pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB)  
  
Collecting rdkit>=2024.3.2 (from boltz==2.1.1)  
  
Using cached rdkit-2025.3.5-cp311-cp311-win_amd64.whl.metadata (4.2 kB)  
  
Collecting dm-tree==0.1.8 (from boltz==2.1.1)  
  
Using cached dm_tree-0.1.8-cp311-cp311-win_amd64.whl.metadata (2.0 kB)  
  
Collecting requests==2.32.3 (from boltz==2.1.1)  
  
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)  
  
Collecting pandas>=2.2.2 (from boltz==2.1.1)  
  
Using cached pandas-2.3.1-cp311-cp311-win_amd64.whl.metadata (19 kB)  
  
Collecting types-requests (from boltz==2.1.1)  
  
Using cached types_requests-2.32.4.20250809-py3-none-any.whl.metadata (2.0 kB)  
  
Collecting einops==0.8.0 (from boltz==2.1.1)  
  
Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)  
  
Collecting einx==0.3.0 (from boltz==2.1.1)  
  
Using cached einx-0.3.0-py3-none-any.whl.metadata (6.9 kB)  
  
Collecting fairscale==0.4.13 (from boltz==2.1.1)  
  
Using cached fairscale-0.4.13-py3-none-any.whl  
  
Collecting mashumaro==3.14 (from boltz==2.1.1)  
  
Using cached mashumaro-3.14-py3-none-any.whl.metadata (114 kB)  
  
Collecting modelcif==1.2 (from boltz==2.1.1)  
  
Using cached modelcif-1.2-py3-none-any.whl  
  
Collecting wandb==0.18.7 (from boltz==2.1.1)  
  
Using cached wandb-0.18.7-py3-none-win_amd64.whl.metadata (9.7 kB)  
  
Collecting click==8.1.7 (from boltz==2.1.1)  
  
Using cached click-8.1.7-py3-none-any.whl.metadata (3.0 kB)  
  
Collecting pyyaml==6.0.2 (from boltz==2.1.1)  
  
Using cached PyYAML-6.0.2-cp311-cp311-win_amd64.whl.metadata (2.1 kB)  
  
Collecting biopython==1.84 (from boltz==2.1.1)  
  
Using cached biopython-1.84-cp311-cp311-win_amd64.whl.metadata (13 kB)  
  
Collecting scipy==1.13.1 (from boltz==2.1.1)  
  
Using cached scipy-1.13.1-cp311-cp311-win_amd64.whl.metadata (60 kB)  
  
Collecting numba==0.61.0 (from boltz==2.1.1)  
  
Using cached numba-0.61.0-cp311-cp311-win_amd64.whl.metadata (2.8 kB)  
  
Collecting gemmi==0.6.5 (from boltz==2.1.1)  
  
Using cached gemmi-0.6.5-cp311-cp311-win_amd64.whl.metadata (2.3 kB)  
  
Collecting scikit-learn==1.6.1 (from boltz==2.1.1)  
  
Using cached scikit_learn-1.6.1-cp311-cp311-win_amd64.whl.metadata (15 kB)  
  
Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.1.1)  
  
Using cached chembl_structure_pipeline-1.2.2-py3-none-any.whl.metadata (3.9
kB)  
  
Collecting cuequivariance_torch>=0.5.0 (from boltz==2.1.1)  
  
Using cached cuequivariance_torch-0.6.0-py3-none-any.whl.metadata (15 kB)  
  
Requirement already satisfied: setuptools>=46.4.0 in
c:\users\xyd\boltz2\lib\site-packages (from
chembl_structure_pipeline==1.2.2->boltz==2.1.1) (65.5.0)  
  
Requirement already satisfied: colorama in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from click==8.1.7->boltz==2.1.1)
(0.4.6)  
  
Requirement already satisfied: sympy in c:\users\xyd\boltz2\lib\site-packages
(from einx==0.3.0->boltz==2.1.1) (1.13.3)  
  
Collecting frozendict (from einx==0.3.0->boltz==2.1.1)  
  
Using cached frozendict-2.4.6-py311-none-any.whl.metadata (23 kB)  
  
Collecting omegaconf=2.2 (from hydra-core==1.3.2->boltz==2.1.1)  
  
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==2.1.1)  
  
Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl  
  
Requirement already satisfied: packaging in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from hydra-
core==1.3.2->boltz==2.1.1) (25.0)  
  
Requirement already satisfied: typing-extensions>=4.1.0 in c:\program
files\chimerax 1.11.dev202508112234\bin\lib\site-packages (from
mashumaro==3.14->boltz==2.1.1) (4.14.1)  
  
Requirement already satisfied: ihm>=1.7 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from modelcif==1.2->boltz==2.1.1)
(2.2)  
  
Collecting llvmlite=0.44.0dev0 (from numba==0.61.0->boltz==2.1.1)  
  
Using cached 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==2.1.1)  
  
Downloading tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)  
  
\-------------------------------------- 57.7/57.7 kB 202.7 kB/s eta 0:00:00  
  
Requirement already satisfied: fsspec>=2022.5.0 in
c:\users\xyd\boltz2\lib\site-packages (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1) (2024.6.1)  
  
Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.1.1)  
  
Using cached torchmetrics-1.8.1-py3-none-any.whl.metadata (22 kB)  
  
Collecting lightning-utilities>=0.10.0 (from pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Using cached lightning_utilities-0.15.2-py3-none-any.whl.metadata (5.7 kB)  
  
Requirement already satisfied: charset-normalizer=2 in c:\program
files\chimerax 1.11.dev202508112234\bin\lib\site-packages (from
requests==2.32.3->boltz==2.1.1) (3.4.3)  
  
Requirement already satisfied: idna=2.5 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from
requests==2.32.3->boltz==2.1.1) (3.10)  
  
Requirement already satisfied: urllib3=1.21.1 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from
requests==2.32.3->boltz==2.1.1) (2.5.0)  
  
Requirement already satisfied: certifi>=2017.4.17 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from
requests==2.32.3->boltz==2.1.1) (2025.8.3)  
  
Collecting joblib>=1.2.0 (from scikit-learn==1.6.1->boltz==2.1.1)  
  
Downloading joblib-1.5.1-py3-none-any.whl.metadata (5.6 kB)  
  
Collecting threadpoolctl>=3.1.0 (from scikit-learn==1.6.1->boltz==2.1.1)  
  
Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)  
  
Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==2.1.1)  
  
Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB)  
  
Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==2.1.1)  
  
Downloading gitpython-3.1.45-py3-none-any.whl.metadata (13 kB)  
  
Requirement already satisfied: platformdirs in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from wandb==0.18.7->boltz==2.1.1)
(4.3.8)  
  
Collecting protobuf!=4.21.0,!=5.28.0,=3.19.0 (from
wandb==0.18.7->boltz==2.1.1)  
  
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
1.11.dev202508112234\bin\lib\site-packages (from wandb==0.18.7->boltz==2.1.1)
(7.0.0)  
  
Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==2.1.1)  
  
Using cached sentry_sdk-2.34.1-py2.py3-none-any.whl.metadata (10 kB)  
  
Collecting setproctitle (from wandb==0.18.7->boltz==2.1.1)  
  
Using cached setproctitle-1.3.6-cp311-cp311-win_amd64.whl.metadata (10 kB)  
  
Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.1.1)  
  
Using cached cuequivariance-0.6.0-py3-none-any.whl.metadata (15 kB)  
  
Requirement already satisfied: python-dateutil>=2.8.2 in c:\program
files\chimerax 1.11.dev202508112234\bin\lib\site-packages (from
pandas>=2.2.2->boltz==2.1.1) (2.9.0.post0)  
  
Requirement already satisfied: pytz>=2020.1 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.1.1)
(2025.2)  
  
Requirement already satisfied: tzdata>=2022.7 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from pandas>=2.2.2->boltz==2.1.1)
(2025.2)  
  
Requirement already satisfied: Pillow in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from
rdkit>=2024.3.2->boltz==2.1.1) (10.4.0)  
  
Requirement already satisfied: filelock in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from torch>=2.2->boltz==2.1.1)
(3.18.0)  
  
Requirement already satisfied: networkx in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from torch>=2.2->boltz==2.1.1)
(3.3)  
  
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from torch>=2.2->boltz==2.1.1)
(3.1.6)  
  
Requirement already satisfied: six>=1.4.0 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from docker-
pycreds>=0.4.0->wandb==0.18.7->boltz==2.1.1) (1.17.0)  
  
Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Downloading aiohttp-3.12.15-cp311-cp311-win_amd64.whl.metadata (7.9 kB)  
  
Collecting gitdb=4.0.1 (from
gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.1.1)  
  
Downloading gitdb-4.0.12-py3-none-any.whl.metadata (1.2 kB)  
  
Requirement already satisfied: msgpack in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from
ihm>=1.7->modelcif==1.2->boltz==2.1.1) (1.1.0)  
  
Requirement already satisfied: mpmath=1.1.0 in
c:\users\xyd\boltz2\lib\site-packages (from sympy->einx==0.3.0->boltz==2.1.1)
(1.3.0)  
  
Collecting opt-einsum (from
cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.1.1)  
  
Using cached opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB)  
  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages (from
jinja2->torch>=2.2->boltz==2.1.1) (3.0.2)  
  
Collecting aiohappyeyeballs>=2.5.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Downloading aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)  
  
Collecting aiosignal>=1.4.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Downloading aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)  
  
Collecting attrs>=17.3.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Downloading attrs-25.3.0-py3-none-any.whl.metadata (10 kB)  
  
Collecting frozenlist>=1.1.1 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Downloading frozenlist-1.7.0-cp311-cp311-win_amd64.whl.metadata (19 kB)  
  
Collecting multidict=4.5 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Downloading multidict-6.6.4-cp311-cp311-win_amd64.whl.metadata (5.4 kB)  
  
Collecting propcache>=0.2.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Downloading propcache-0.3.2-cp311-cp311-win_amd64.whl.metadata (12 kB)  
  
Collecting yarl=1.17.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.5.0->boltz==2.1.1)  
  
Downloading yarl-1.20.1-cp311-cp311-win_amd64.whl.metadata (76 kB)  
  
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Collecting smmap=3.0.1 (from
gitdb=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==2.1.1)  
  
Downloading smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB)  
  
Using cached biopython-1.84-cp311-cp311-win_amd64.whl (2.8 MB)  
  
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Using cached dm_tree-0.1.8-cp311-cp311-win_amd64.whl (101 kB)  
  
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Using cached rdkit-2025.3.5-cp311-cp311-win_amd64.whl (23.5 MB)  
  
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Using cached docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)  
  
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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-2.1.1-py3-none-any.whl size=264958
sha256=2c0089ee6915ea5aee0da9d3bac3c69ca97e9378cf016af529a6c9393b151866  
  
Stored in directory: C:\Users\xyd\AppData\Local\Temp\pip-ephem-wheel-
cache-728sgil6\wheels\eb\6b\e8\b8f2318f04e510ea3091105ed50c6e2ff4fa900e16361241f7  
  
Successfully built boltz  
  
Installing collected packages: dm-tree, antlr4-python3-runtime, types-
requests, tqdm, threadpoolctl, smmap, setproctitle, sentry-sdk, scipy,
requests, rdkit, pyyaml, protobuf, propcache, opt-einsum, multidict,
mashumaro, llvmlite, lightning-utilities, joblib, gemmi, frozenlist,
frozendict, einops, docker-pycreds, click, biopython, attrs, aiohappyeyeballs,
yarl, scikit-learn, pandas, omegaconf, numba, modelcif, gitdb, einx,
cuequivariance, chembl_structure_pipeline, aiosignal, torchmetrics, hydra-
core, gitpython, fairscale, cuequivariance_torch, aiohttp, wandb, pytorch-
lightning, boltz  
  
Attempting uninstall: scipy  
  
Found existing installation: scipy 1.14.0  
  
Not uninstalling scipy at c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages, outside environment
C:\Users\xyd\boltz2  
  
Can't uninstall 'scipy'. No files were found to uninstall.  
  
Attempting uninstall: requests  
  
Found existing installation: requests 2.32.4  
  
Not uninstalling requests at c:\program files\chimerax
1.11.dev202508112234\bin\lib\site-packages, outside environment
C:\Users\xyd\boltz2  
  
Can't uninstall 'requests'. No files were found to uninstall.  
  
Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aiosignal-1.4.0
antlr4-python3-runtime-4.9.3 attrs-25.3.0 biopython-1.84 boltz-2.1.1
chembl_structure_pipeline-1.2.2 click-8.1.7 cuequivariance-0.6.0
cuequivariance_torch-0.6.0 dm-tree-0.1.8 docker-pycreds-0.4.0 einops-0.8.0
einx-0.3.0 fairscale-0.4.13 frozendict-2.4.6 frozenlist-1.7.0 gemmi-0.6.5
gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 joblib-1.5.1 lightning-
utilities-0.15.2 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 multidict-6.6.4
numba-0.61.0 omegaconf-2.3.0 opt-einsum-3.4.0 pandas-2.3.1 propcache-0.3.2
protobuf-5.29.5 pytorch-lightning-2.5.0 pyyaml-6.0.2 rdkit-2025.3.5
requests-2.32.3 scikit-learn-1.6.1 scipy-1.13.1 sentry-sdk-2.34.1
setproctitle-1.3.6 smmap-5.0.2 threadpoolctl-3.6.0 torchmetrics-1.8.1
tqdm-4.67.1 types-requests-2.32.4.20250809 wandb-0.18.7 yarl-1.20.1  
  
  
  
[notice] A new release of pip is available: 24.0 -> 25.2  
  
[notice] To update, run: C:\Users\xyd\boltz2\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\xyd/boltz2\Scripts\python.exe C:\Program Files\ChimeraX
1.11.dev202508112234\bin\Lib\site-
packages\chimerax\boltz\download_weights_and_ccd.py  
Downloading the CCD data to C:\Users\xyd\\.boltz\mols.tar. This may take a bit
of time. You may change the cache directory with the --cache flag.  
  

QDxgiVSyncService: DXGI Factory is no longer Current  

Extracting the CCD data to C:\Users\xyd\\.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\xyd\\.boltz\boltz2_conf.ckpt. You
may change the cache directory with the --cache flag.  
  
Downloading the Boltz-2 affinity weights to
C:\Users\xyd\\.boltz\boltz2_aff.ckpt. You may change the cache directory with
the --cache flag.  
  

QDxgiVSyncService: DXGI Factory is no longer Current  

Making CCD atom counts table for 45227 in C:\Users\xyd/.boltz/mols  
  
Boltz model parameters and CCD database are installed in ~/.boltz  
Successfully installed Boltz.  

QDxgiVSyncService: DXGI Factory is no longer Current  

> boltz predict protein
> MPGLVDSNPAPPESQEKKPLKPCCACPETKKARDACIIEKGEEHCGHLIEAHKECMRALGFKI ligandSmiles
> CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name Q14061
> resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q14061/affinity device
> gpu affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O
> steering true samples 5

Running Boltz prediction of protein with 63 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using cached multiple sequence alignment
C:\Users\xyd/Downloads/ChimeraX/BoltzMSA\Q14061  
Confidence score 0.83, pTM 0.86, ipTM 0.93, pLDDT 0.80  
Confidence score 0.82, pTM 0.85, ipTM 0.93, pLDDT 0.79  
Confidence score 0.79, pTM 0.83, ipTM 0.89, pLDDT 0.76  
Confidence score 0.78, pTM 0.84, ipTM 0.89, pLDDT 0.76  
Confidence score 0.76, pTM 0.81, ipTM 0.87, pLDDT 0.73  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 4.4 uM, predicted binding probability 0.5  
Boltz prediction completed in 155 seconds (start boltz 10 sec, sequence search
0 sec, load weights 29 sec, structure inference 57 sec, load affinity weights
30 sec, affinity inference 29 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/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q14061/affinity\Q14061_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q14061/affinity\Q14061_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q14061/affinity\Q14061_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q14061/affinity\Q14061_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q14061/affinity\Q14061_model_4.cif
> logInfo false

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> boltz predict protein
> MDQVMQFVEPSRQFVKDSIRLVKRCTKPDRKEFQKIAMATAIGFAIMGFIGFFVKLIHIPINNIIVGG
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> P60059 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P60059 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 68 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  

QDxgiVSyncService: DXGI Factory is no longer Current  

Confidence score 0.72, pTM 0.74, ipTM 0.91, pLDDT 0.67  
Confidence score 0.70, pTM 0.74, ipTM 0.85, pLDDT 0.67  
Confidence score 0.70, pTM 0.72, ipTM 0.90, pLDDT 0.65  
Confidence score 0.68, pTM 0.67, ipTM 0.74, pLDDT 0.66  
Confidence score 0.65, pTM 0.84, ipTM 0.88, pLDDT 0.59  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 0.62 uM, predicted binding probability 0.67  
Boltz prediction completed in 259 seconds (start boltz 9 sec, sequence search
0 sec, load weights 98 sec, structure inference 91 sec, load affinity weights
31 sec, affinity inference 30 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P60059\P60059_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P60059\P60059_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P60059\P60059_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P60059\P60059_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P60059\P60059_model_4.cif
> logInfo false

QDxgiVSyncService: DXGI Factory is no longer Current  

> close

> boltz predict protein
> MPRKIEEIKDFLLTARRKDAKSVKIKKNKDNVKFKVRCSRYLYTLVITDKEKAEKLKQSLPPGLAVKELK
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> P63173 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63173 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 70 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Cannot make a new prediction until the current prediction finishes.  
Confidence score 0.79, pTM 0.94, ipTM 0.88, pLDDT 0.77  
Confidence score 0.78, pTM 0.91, ipTM 0.78, pLDDT 0.78  
Confidence score 0.78, pTM 0.92, ipTM 0.81, pLDDT 0.77  
Confidence score 0.78, pTM 0.92, ipTM 0.79, pLDDT 0.77  
Confidence score 0.77, pTM 0.92, ipTM 0.80, pLDDT 0.77  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 8 uM, predicted binding probability 0.48  
Boltz prediction completed in 297 seconds (start boltz 56 sec, sequence search
0 sec, load weights 119 sec, structure inference 60 sec, load affinity weights
31 sec, affinity inference 29 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63173\P63173_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63173\P63173_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63173\P63173_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63173\P63173_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63173\P63173_model_4.cif
> logInfo false

> close

> boltz predict protein
> MAGQEDPVQREIHQDWANREYIEIITSSIKKIADFLNSFDMSCRSRLATLNEKLTALERRIEYIEARVTKGETLT
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> Q8WUW1 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q8WUW1 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 75 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.79, pTM 0.83, ipTM 0.91, pLDDT 0.76  
Confidence score 0.79, pTM 0.78, ipTM 0.83, pLDDT 0.78  
Confidence score 0.79, pTM 0.83, ipTM 0.92, pLDDT 0.75  
Confidence score 0.77, pTM 0.81, ipTM 0.88, pLDDT 0.74  
Confidence score 0.77, pTM 0.81, ipTM 0.87, pLDDT 0.74  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 1.3 uM, predicted binding probability 0.63  
Boltz prediction completed in 182 seconds (start boltz 9 sec, sequence search
26 sec, load weights 29 sec, structure inference 60 sec, load affinity weights
29 sec, affinity inference 29 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q8WUW1\Q8WUW1_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q8WUW1\Q8WUW1_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q8WUW1\Q8WUW1_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q8WUW1\Q8WUW1_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q8WUW1\Q8WUW1_model_4.cif
> logInfo false

QDxgiVSyncService: DXGI Factory is no longer Current  

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close

Boltz predicted structure is not open.  

> boltz predict protein
> MAETDPKTVQDLTSVVQTLLQQMQDKFQTMSDQIIGRIDDMSSRIDDLEKNIADLMTQAGVEELESENKIPATQKS
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> O75506 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O75506 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 76 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.74, pTM 0.71, ipTM 0.77, pLDDT 0.73  
Confidence score 0.74, pTM 0.72, ipTM 0.79, pLDDT 0.73  
Confidence score 0.73, pTM 0.68, ipTM 0.71, pLDDT 0.74  
Confidence score 0.72, pTM 0.70, ipTM 0.75, pLDDT 0.72  
Confidence score 0.72, pTM 0.73, ipTM 0.80, pLDDT 0.70  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 3.2 uM, predicted binding probability 0.61  
Boltz prediction completed in 251 seconds (start boltz 9 sec, sequence search
43 sec, load weights 71 sec, structure inference 63 sec, load affinity weights
33 sec, affinity inference 31 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O75506\O75506_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O75506\O75506_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O75506\O75506_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O75506\O75506_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O75506\O75506_model_4.cif
> logInfo false

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> boltz predict protein
> MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFRRPLPKDQQK
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> P33552 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P33552 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 79 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.85, pTM 0.91, ipTM 0.81, pLDDT 0.86  
Confidence score 0.84, pTM 0.90, ipTM 0.82, pLDDT 0.85  
Confidence score 0.84, pTM 0.92, ipTM 0.87, pLDDT 0.83  
Confidence score 0.84, pTM 0.92, ipTM 0.84, pLDDT 0.83  
Confidence score 0.83, pTM 0.92, ipTM 0.85, pLDDT 0.83  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 9.1 uM, predicted binding probability 0.42  
Boltz prediction completed in 414 seconds (start boltz 9 sec, sequence search
0 sec, load weights 109 sec, structure inference 120 sec, load affinity
weights 108 sec, affinity inference 67 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P33552\P33552_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P33552\P33552_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P33552\P33552_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P33552\P33552_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P33552\P33552_model_4.cif
> logInfo false

QDxgiVSyncService: DXGI Factory is no longer Current  

> close

> boltz predict protein
> MNREGAPGKSPEEMYIQQKVRVLLMLRKMGSNLTASEEEFLRTYAGVVNSQLSQLPPHSIDQGAEDVVMAFSRSETEDRRQ
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> Q9NSA3 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NSA3 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 81 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.82, pTM 0.93, ipTM 0.95, pLDDT 0.79  
Confidence score 0.81, pTM 0.93, ipTM 0.95, pLDDT 0.77  
Confidence score 0.80, pTM 0.94, ipTM 0.94, pLDDT 0.76  
Confidence score 0.80, pTM 0.91, ipTM 0.94, pLDDT 0.76  
Confidence score 0.78, pTM 0.95, ipTM 0.95, pLDDT 0.74  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 4.8 uM, predicted binding probability 0.53  
Boltz prediction completed in 331 seconds (start boltz 34 sec, sequence search
14 sec, load weights 80 sec, structure inference 86 sec, load affinity weights
73 sec, affinity inference 44 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NSA3\Q9NSA3_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NSA3\Q9NSA3_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NSA3\Q9NSA3_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NSA3\Q9NSA3_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NSA3\Q9NSA3_model_4.cif
> logInfo false

> close

> boltz predict protein
> MPLAKDLLHPSPEEEKRKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCSTVLCQPTGGKARLTEGCSFRRKQH
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> P42677 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P42677 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 84 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.84, pTM 0.93, ipTM 0.93, pLDDT 0.82  
Confidence score 0.81, pTM 0.92, ipTM 0.90, pLDDT 0.79  
Confidence score 0.80, pTM 0.93, ipTM 0.93, pLDDT 0.77  
Confidence score 0.80, pTM 0.84, ipTM 0.85, pLDDT 0.79  
Confidence score 0.78, pTM 0.86, ipTM 0.84, pLDDT 0.77  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 3.2 uM, predicted binding probability 0.47  
Boltz prediction completed in 381 seconds (start boltz 9 sec, sequence search
0 sec, load weights 104 sec, structure inference 88 sec, load affinity weights
115 sec, affinity inference 63 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P42677\P42677_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P42677\P42677_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P42677\P42677_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P42677\P42677_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P42677\P42677_model_4.cif
> logInfo false

QDxgiVSyncService: DXGI Factory is no longer Current  

> hide #1 models

> hide #2 models

> hide #3 models

> hide #4 models

> close

> boltz predict protein
> MPLARDLLHPSLEEEKKKHKKKRLVQSPNSYFMDVKCPGCYKITTVFSHAQTVVLCVGCSTVLCQPTGGKARLTEGCSFRRKQH
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> Q71UM5 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q71UM5 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 84 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.82, pTM 0.92, ipTM 0.92, pLDDT 0.80  
Confidence score 0.82, pTM 0.86, ipTM 0.88, pLDDT 0.80  
Confidence score 0.77, pTM 0.75, ipTM 0.73, pLDDT 0.78  
Confidence score 0.75, pTM 0.75, ipTM 0.66, pLDDT 0.78  
Confidence score 0.73, pTM 0.81, ipTM 0.79, pLDDT 0.72  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 3.4 uM, predicted binding probability 0.47  
Boltz prediction completed in 231 seconds (start boltz 9 sec, sequence search
0 sec, load weights 85 sec, structure inference 73 sec, load affinity weights
29 sec, affinity inference 31 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q71UM5\Q71UM5_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q71UM5\Q71UM5_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q71UM5\Q71UM5_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q71UM5\Q71UM5_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q71UM5\Q71UM5_model_4.cif
> logInfo false

> boltz predict protein
> MPQYQTWEEFSRAAEKLYLADPMKARVVLKYRHSDGNLCVKVTDDLVCLVYKTDQAQDVKKIEKFHSQLMRLMVAKEARNVTMETE
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> P49458 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P49458 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 86 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  

> close

Confidence score 0.80, pTM 0.90, ipTM 0.88, pLDDT 0.78  
Confidence score 0.80, pTM 0.91, ipTM 0.90, pLDDT 0.77  
Confidence score 0.77, pTM 0.92, ipTM 0.89, pLDDT 0.74  
Confidence score 0.77, pTM 0.91, ipTM 0.88, pLDDT 0.74  
Confidence score 0.75, pTM 0.90, ipTM 0.86, pLDDT 0.72  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 15 uM, predicted binding probability 0.49  
Boltz prediction completed in 423 seconds (start boltz 9 sec, sequence search
0 sec, load weights 107 sec, structure inference 108 sec, load affinity
weights 137 sec, affinity inference 61 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P49458\P49458_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P49458\P49458_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P49458\P49458_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P49458\P49458_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P49458\P49458_model_4.cif
> logInfo false

QDxgiVSyncService: DXGI Factory is no longer Current  

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close

> boltz predict protein
> MCDRKAVIKNADMSEEMQQDSVECATQALEKYNIEKDIAAHIKKEFDKKYNPTWHCIVGRNFGSYVTHETKHFIYFYLGQVAILLFKSG
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> P63167 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63167 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 89 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.90, pTM 0.96, ipTM 0.93, pLDDT 0.89  
Confidence score 0.88, pTM 0.96, ipTM 0.93, pLDDT 0.87  
Confidence score 0.87, pTM 0.96, ipTM 0.93, pLDDT 0.85  
Confidence score 0.86, pTM 0.95, ipTM 0.92, pLDDT 0.85  
Confidence score 0.86, pTM 0.95, ipTM 0.91, pLDDT 0.85  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 5.9 uM, predicted binding probability 0.4  
Boltz prediction completed in 170 seconds (start boltz 9 sec, sequence search
0 sec, load weights 29 sec, structure inference 65 sec, load affinity weights
29 sec, affinity inference 33 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63167\P63167_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63167\P63167_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63167\P63167_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63167\P63167_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P63167\P63167_model_4.cif
> logInfo false

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close #4

> close

> boltz predict protein
> MACPLDQAIGLLVAIFHKYSGREGDKHTLSKKELKELIQKELTIGSKLQDAEIARLMEDLDRNKDQEVNFQEYVTFLGALALIYNEALKG
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> P06703 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P06703 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 90 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.87, pTM 0.94, ipTM 0.94, pLDDT 0.85  
Confidence score 0.85, pTM 0.94, ipTM 0.92, pLDDT 0.83  
Confidence score 0.84, pTM 0.94, ipTM 0.92, pLDDT 0.81  
Confidence score 0.82, pTM 0.93, ipTM 0.90, pLDDT 0.79  
Confidence score 0.81, pTM 0.93, ipTM 0.90, pLDDT 0.79  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 13 uM, predicted binding probability 0.44  
Boltz prediction completed in 388 seconds (start boltz 9 sec, sequence search
25 sec, load weights 107 sec, structure inference 97 sec, load affinity
weights 87 sec, affinity inference 56 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P06703\P06703_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P06703\P06703_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P06703\P06703_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P06703\P06703_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P06703\P06703_model_4.cif
> logInfo false

> hide #2 models

> hide #3 models

> select add #1

742 atoms, 752 bonds, 91 residues, 1 model selected  

> select subtract #1

Nothing selected  

> hide #4 models

> hide #5 models

> close #1

> close

> boltz predict protein
> MDPLRAQQLAAELEVEMMADMYNRMTSACHRKCVPPHYKEAELSKGESVCLDRCVSKYLDIHERMGKKLTELSMQDEELMKRVQQSSGPA
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> P62072 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P62072 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 90 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.84, pTM 0.92, ipTM 0.96, pLDDT 0.81  
Confidence score 0.81, pTM 0.90, ipTM 0.95, pLDDT 0.78  
Confidence score 0.81, pTM 0.87, ipTM 0.96, pLDDT 0.77  
Confidence score 0.81, pTM 0.86, ipTM 0.95, pLDDT 0.77  
Confidence score 0.78, pTM 0.87, ipTM 0.94, pLDDT 0.74  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 13 uM, predicted binding probability 0.62  
Boltz prediction completed in 346 seconds (start boltz 9 sec, sequence search
27 sec, load weights 80 sec, structure inference 85 sec, load affinity weights
87 sec, affinity inference 54 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P62072\P62072_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P62072\P62072_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P62072\P62072_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P62072\P62072_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P62072\P62072_model_4.cif
> logInfo false

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close #3

> close

> boltz predict protein
> MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPTDIPVVCLESDNGNIMIQKHDGITVAVHKMAS
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> O43504 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43504 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 91 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.92, pTM 0.96, ipTM 0.95, pLDDT 0.92  
Confidence score 0.92, pTM 0.96, ipTM 0.96, pLDDT 0.92  
Confidence score 0.92, pTM 0.95, ipTM 0.95, pLDDT 0.92  
Confidence score 0.92, pTM 0.96, ipTM 0.95, pLDDT 0.91  
Confidence score 0.92, pTM 0.96, ipTM 0.96, pLDDT 0.91  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 5.6 uM, predicted binding probability 0.37  
Boltz prediction completed in 1434 seconds (start boltz 8 sec, sequence search
1126 sec, load weights 74 sec, structure inference 101 sec, load affinity
weights 83 sec, affinity inference 42 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43504\O43504_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43504\O43504_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43504\O43504_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43504\O43504_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43504\O43504_model_4.cif
> logInfo false

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close #2

> close

> boltz predict protein
> MTELETAMGMIIDVFSRYSGSEGSTQTLTKGELKVLMEKELPGFLQSGKDKDAVDKLLKDLDANGDAQVDFSEFIVFVAAITSACHKYFEKAGLK
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> P25815 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P25815 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 95 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.85, pTM 0.90, ipTM 0.81, pLDDT 0.86  
Confidence score 0.84, pTM 0.90, ipTM 0.85, pLDDT 0.84  
Confidence score 0.82, pTM 0.89, ipTM 0.79, pLDDT 0.83  
Confidence score 0.81, pTM 0.90, ipTM 0.81, pLDDT 0.81  
Confidence score 0.80, pTM 0.88, ipTM 0.77, pLDDT 0.81  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 17 uM, predicted binding probability 0.39  
Boltz prediction completed in 350 seconds (start boltz 8 sec, sequence search
0 sec, load weights 111 sec, structure inference 101 sec, load affinity
weights 73 sec, affinity inference 52 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P25815\P25815_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P25815\P25815_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P25815\P25815_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P25815\P25815_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/P25815\P25815_model_4.cif
> logInfo false

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close #5

> close

> boltz predict protein
> MAEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPTE
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> Q9NP97 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NP97 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 96 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.87, pTM 0.95, ipTM 0.91, pLDDT 0.86  
Confidence score 0.86, pTM 0.94, ipTM 0.89, pLDDT 0.86  
Confidence score 0.86, pTM 0.93, ipTM 0.87, pLDDT 0.86  
Confidence score 0.82, pTM 0.93, ipTM 0.85, pLDDT 0.82  
Confidence score 0.82, pTM 0.93, ipTM 0.84, pLDDT 0.81  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 7 uM, predicted binding probability 0.47  
Boltz prediction completed in 419 seconds (start boltz 8 sec, sequence search
0 sec, load weights 118 sec, structure inference 107 sec, load affinity
weights 122 sec, affinity inference 60 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NP97\Q9NP97_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NP97\Q9NP97_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NP97\Q9NP97_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NP97\Q9NP97_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9NP97\Q9NP97_model_4.cif
> logInfo false

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close #2

> close

> boltz predict protein
> MAAEPLTELEESIETVVTTFFTFARQEGRKDSLSVNEFKELVTQQLPHLLKDVGSLDEKMKSLDVNQDSELKFNEYWRLIGELAKEIRKKKDLKIRKK
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> Q99584 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q99584 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 98 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.88, pTM 0.89, ipTM 0.87, pLDDT 0.88  
Confidence score 0.86, pTM 0.91, ipTM 0.89, pLDDT 0.85  
Confidence score 0.84, pTM 0.86, ipTM 0.77, pLDDT 0.85  
Confidence score 0.83, pTM 0.86, ipTM 0.80, pLDDT 0.84  
Confidence score 0.80, pTM 0.86, ipTM 0.77, pLDDT 0.81  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 25 uM, predicted binding probability 0.42  
Boltz prediction completed in 294 seconds (start boltz 8 sec, sequence search
0 sec, load weights 73 sec, structure inference 88 sec, load affinity weights
77 sec, affinity inference 44 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q99584\Q99584_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q99584\Q99584_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q99584\Q99584_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q99584\Q99584_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q99584\Q99584_model_4.cif
> logInfo false

> close

> boltz predict protein
> MAAAAASRGVGAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFGQETNVPLNNFSADQVTRALENVLSGKA
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> O43678 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43678 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 99 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.92, pTM 0.93, ipTM 0.97, pLDDT 0.91  
Confidence score 0.92, pTM 0.92, ipTM 0.96, pLDDT 0.91  
Confidence score 0.92, pTM 0.91, ipTM 0.97, pLDDT 0.91  
Confidence score 0.90, pTM 0.95, ipTM 0.97, pLDDT 0.88  
Confidence score 0.90, pTM 0.91, ipTM 0.95, pLDDT 0.88  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 8.1 uM, predicted binding probability 0.43  
Boltz prediction completed in 207 seconds (start boltz 8 sec, sequence search
29 sec, load weights 31 sec, structure inference 68 sec, load affinity weights
32 sec, affinity inference 33 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43678\O43678_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43678\O43678_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43678\O43678_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43678\O43678_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/O43678\O43678_model_4.cif
> logInfo false

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close

> boltz predict protein
> MEEASEGGGNDRVRNLQSEVEGVKNIMTQNVERILARGENLEHLRNKTEDLEATSEHFKTTSQKVARKFWWKNVKMIVLICVIVFIIILFIVLFATGAFS
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> Q9BV40 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BV40 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 100 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.76, pTM 0.65, ipTM 0.87, pLDDT 0.73  
Confidence score 0.75, pTM 0.68, ipTM 0.95, pLDDT 0.70  
Confidence score 0.75, pTM 0.69, ipTM 0.94, pLDDT 0.70  
Confidence score 0.74, pTM 0.65, ipTM 0.88, pLDDT 0.70  
Confidence score 0.70, pTM 0.64, ipTM 0.89, pLDDT 0.65  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 7.2 uM, predicted binding probability 0.55  
Boltz prediction completed in 333 seconds (start boltz 8 sec, sequence search
28 sec, load weights 73 sec, structure inference 92 sec, load affinity weights
82 sec, affinity inference 44 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BV40\Q9BV40_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BV40\Q9BV40_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BV40\Q9BV40_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BV40\Q9BV40_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BV40\Q9BV40_model_4.cif
> logInfo false

> close

> boltz predict protein
> MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> Q9BW61 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BW61 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 102 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  
Confidence score 0.64, pTM 0.70, ipTM 0.86, pLDDT 0.59  
Confidence score 0.59, pTM 0.64, ipTM 0.66, pLDDT 0.57  
Confidence score 0.57, pTM 0.62, ipTM 0.63, pLDDT 0.55  
Confidence score 0.56, pTM 0.51, ipTM 0.61, pLDDT 0.55  
Confidence score 0.55, pTM 0.54, ipTM 0.62, pLDDT 0.54  
Ligand CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O predicted
binding affinity 8 uM, predicted binding probability 0.57  
Boltz prediction completed in 349 seconds (start boltz 8 sec, sequence search
0 sec, load weights 74 sec, structure inference 96 sec, load affinity weights
120 sec, affinity inference 49 sec)  

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BW61\Q9BW61_model_0.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BW61\Q9BW61_model_1.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BW61\Q9BW61_model_2.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BW61\Q9BW61_model_3.cif
> logInfo false

> open
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9BW61\Q9BW61_model_4.cif
> logInfo false

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> close

> boltz predict protein
> MHRKKVDNRIRILIENGVAERQRSLFVVVGDRGKDQVVILHHMLSKATVKARPSVLWCYKKELGFSSHRKKRMRQLQKKIKNGTLNIKQDDPFELFIAATNIRYCYYNETHKILGNTFGMCVLQDFEALTPNLLARTVETVEGGGLVVILLRTMNSLKQLYTVTMDVHSRYRTEAHQDVVGRFNERFILSLASCKKCLVIDDQLNILPISSHVATMEALPPQTPDESLGPSDLELRELKESLQDTQPVGVLVDCCKTLDQAKAVLKFIEGISEKTLRSTVALTAARGRGKSAALGLAIAGAVAFGYSNIFVTSPSPDNLHTLFEFVFKGFDALQYQEHLDYEIIQSLNPEFNKAVIRVNVFREHRQTIQYIHPADAVKLGQAELVVIDEAAAIPLPLVKSLLGPYLVFMASTINGYEGTGRSLSLKLIQQLRQQSAQSQVSTTAENKTTTTARLASARTLYEVSLQESIRYAPGDAVEKWLNDLLCLDCLNITRIVSGCPLPEACELYYVNRDTLFCYHKASEVFLQRLMALYVASHYKNSPNDLQMLSDAPAHHLFCLLPPVPPTQNALPEVLAVIQVCLEGEISRQSILNSLSRGKKASGDLIPWTVSEQFQDPDFGGLSGGRVVRIAVHPDYQGMGYGSRALQLLQMYYEGRFPCLEEKVLETPQEIHTVSSEAVSLLEEVITPRKDLPPLLLKLNERPAERLDYLGVSYGLTPRLLKFWKRAGFVPVYLRQTPNDLTGEHSCIMLKTLTDEDEADQGGWLAAFWKDFRRRFLALLSYQFSTFSPSLALNIIQNRNMGKPAQPALSREELEALFLPYDLKRLEMYSRNMVDYHLIMDMIPAISRIYFLNQLGDLALSAAQSALLLGIGLQHKSVDQLEKEIELPSGQLMGLFNRIIRKVVKLFNEVQEKAIEEQMVAAKDVVMEPTMKTLSDDLDEAAKEFQEKHKKEVGKLKSMDLSEYIIRGDDEEWNEVLNKAGPNASIISLKSDKKRKLEAKQEPKQSKKLKNRETKNKKDMKLKRKK
> ligandSmiles CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O name
> Q9H0A0 resultsDirectory
> C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9H0A0 device gpu
> affinity CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O steering
> true samples 5

Running Boltz prediction of protein with 1025 residues, 1 ligands
CC(C)(CCC1=C2C(=C(C=C1O)O)C(=O)C(=C(O2)C3=CC=C(C=C3)OC)O)O on gpu  
Using multiple sequence alignment server https://api.colabfold.com  

Device loss detected in Present()  

Running boltz prediction failed with exit code 1:  
command:  
C:\Users\xyd/boltz2\Scripts\boltz.exe predict
C:/Users/xyd/Desktop/NAT10/PELSA/Wu/chimeraX_boltz_2/Q9H0A0\Q9H0A0.yaml
--use_msa_server --use_potentials --accelerator gpu --no_kernels
--diffusion_samples 5  
stdout:  
Boltz version 2.1.1  
Checking input data.  
Processing 1 inputs with 1 threads.  
Generating MSA for
C:\Users\xyd\Desktop\NAT10\PELSA\Wu\chimeraX_boltz_2\Q9H0A0\Q9H0A0.yaml with 1
protein entities.  
Running structure prediction for 1 input.  
Predicting: | | 0/? [00:00", line 198, in _run_module_as_main  
File "", line 88, in _run_code  
File "C:\Users\xyd\boltz2\Scripts\boltz.exe\\__main__.py", line 7, in   
File "C:\Users\xyd\boltz2\Lib\site-packages\click\core.py", line 1157, in
__call__  
return self.main(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\xyd\boltz2\Lib\site-packages\click\core.py", line 1078, in main  
rv = self.invoke(ctx)  
^^^^^^^^^^^^^^^^  
File "C:\Users\xyd\boltz2\Lib\site-packages\click\core.py", line 1688, in
invoke  
return _process_result(sub_ctx.command.invoke(sub_ctx))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\xyd\boltz2\Lib\site-packages\click\core.py", line 1434, in
invoke  
return ctx.invoke(self.callback, **ctx.params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\xyd\boltz2\Lib\site-packages\click\core.py", line 783, in
invoke  
return __callback(*args, **kwargs)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\xyd\boltz2\Lib\site-packages\boltz\main.py", line 1219, in
predict  
trainer.predict(  
File "C:\Users\xyd\boltz2\Lib\site-
packages\pytorch_lightning\trainer\trainer.py", line 859, in predict  
return call._call_and_handle_interrupt(  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\xyd\boltz2\Lib\site-
packages\pytorch_lightning\trainer\call.py", line 68, in
_call_and_handle_interrupt  
trainer._teardown()  
File "C:\Users\xyd\boltz2\Lib\site-
packages\pytorch_lightning\trainer\trainer.py", line 1005, in _teardown  
self.strategy.teardown()  
File "C:\Users\xyd\boltz2\Lib\site-
packages\pytorch_lightning\strategies\strategy.py", line 536, in teardown  
self.lightning_module.cpu()  
File "C:\Users\xyd\boltz2\Lib\site-
packages\lightning_fabric\utilities\device_dtype_mixin.py", line 82, in cpu  
return super().cpu()  
^^^^^^^^^^^^^  
File "C:\Users\xyd\boltz2\Lib\site-packages\torch\nn\modules\module.py", line
1150, in cpu  
return self._apply(lambda t: t.cpu())  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\xyd\boltz2\Lib\site-packages\torch\nn\modules\module.py", line
928, in _apply  
module._apply(fn)  
File "C:\Users\xyd\boltz2\Lib\site-packages\torchmetrics\metric.py", line 891,
in _apply  
this._defaults[key] = fn(value)  
^^^^^^^^^  
File "C:\Users\xyd\boltz2\Lib\site-packages\torch\nn\modules\module.py", line
1150, in   
return self._apply(lambda t: t.cpu())  
^^^^^^^  
torch.AcceleratorError: CUDA error: unknown error  
CUDA kernel errors might be asynchronously reported at some other API call, so
the stacktrace below might be incorrect.  
For debugging consider passing CUDA_LAUNCH_BLOCKING=1  
Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.  
  
  

Device loss detected in Present()  

QQuickWidget: failed to create resized output texture of size 1665x1002  

QQuickWidget: failed to create resized depth/stencil buffer of size 1665x1002  

Device loss detected in ResizeBuffers()  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.11.dev202508112234 (2025-08-11)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 580.97
OpenGL renderer: NVIDIA GeForce RTX 3070 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: zh_CN.cp936
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.1
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: Raider GE67HX 12UGS
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 34,046,783,488
MaxProcessMemory: 137,438,953,344
CPU: 24 12th Gen Intel(R) Core(TM) i9-12900HX
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.4
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.8.3
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.3
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.11
    ChimeraX-AtomicLibrary: 14.1.21
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11.dev202508112234
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.17
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.5.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.3
    ChimeraX-ProfileGrids: 1.1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.4
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.48
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.2.2
    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
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.10.3
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.2
    debugpy: 1.8.16
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 5.3.1
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    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: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.3.8
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.1
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.1
    PyQt6_sip: 13.10.2
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pywin32: 310
    pyzmq: 27.0.1
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.7.5
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.2
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 2 months ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Boltz-related problems

comment:2 by Tom Goddard, 2 months ago

Resolution: → can't reproduce
Status: assigned → closed

Have seen this apparent loss of GPU OpenGL context several times, only on Windows. Also in this bug report after the Device loss message boltz torch failed, probably related to not having GPU access. Maybe these errors mean there was a GPU error or overheating and connections to the GPU are lost. Don't know. Nvidia 3070 Ti.

Device loss detected in Present()
QQuickWidget: failed to create resized output texture of size 1665x1002
QQuickWidget: failed to create resized depth/stencil buffer of size 1665x1002
Device loss detected in ResizeBuffers()

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