The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.10rc202505150242 (2025-05-15 02:42:12 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 0x000008d0 (most recent call first):
File "C:\Program Files\ChimeraX 1.10rc202505150242\bin\Lib\site-packages\chimerax\ui\gui.py", line 368 in event_loop
File "C:\Program Files\ChimeraX 1.10rc202505150242\bin\Lib\site-packages\chimerax\core\__main__.py", line 1057 in init
File "C:\Program Files\ChimeraX 1.10rc202505150242\bin\Lib\site-packages\chimerax\core\__main__.py", line 1220 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202505150242 (2025-05-15)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Boltz
> boltz install C:\Users\shing/boltz
Successfully created Boltz Python virtual environment C:\Users\shing/boltz.
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\shing/boltz\Scripts\python.exe -m pip install
git+https://github.com/RBVI/boltz@chimerax
Collecting git+https://github.com/RBVI/boltz@chimerax
Cloning https://github.com/RBVI/boltz (to revision chimerax) to
c:\users\shing\appdata\local\temp\pip-req-build-kx34perf
Running command git clone --filter=blob:none --quiet
https://github.com/RBVI/boltz 'C:\Users\shing\AppData\Local\Temp\pip-req-
build-kx34perf'
Running command git checkout -b chimerax --track origin/chimerax
branch 'chimerax' set up to track 'origin/chimerax'.
Switched to a new branch 'chimerax'
Resolved https://github.com/RBVI/boltz to commit
0ac2d0db5c18661b5027d88fbadf9b78c96c751e
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting torch>=2.2 (from boltz==0.4.1)
Downloading torch-2.7.0-cp311-cp311-win_amd64.whl (212.5 MB)
\------------------------------------- 212.5/212.5 MB 20.5 MB/s eta 0:00:00
Collecting numpy==1.26.3 (from boltz==0.4.1)
Downloading numpy-1.26.3-cp311-cp311-win_amd64.whl (15.8 MB)
\--------------------------------------- 15.8/15.8 MB 81.8 MB/s eta 0:00:00
Collecting hydra-core==1.3.2 (from boltz==0.4.1)
Downloading hydra_core-1.3.2-py3-none-any.whl (154 kB)
\---------------------------------------- 154.5/154.5 kB ? eta 0:00:00
Collecting pytorch-lightning==2.4.0 (from boltz==0.4.1)
Downloading pytorch_lightning-2.4.0-py3-none-any.whl (815 kB)
\------------------------------------- 815.2/815.2 kB 53.7 MB/s eta 0:00:00
Collecting rdkit>=2024.3.2 (from boltz==0.4.1)
Downloading rdkit-2025.3.2-cp311-cp311-win_amd64.whl (22.7 MB)
\--------------------------------------- 22.7/22.7 MB 72.5 MB/s eta 0:00:00
Collecting dm-tree==0.1.8 (from boltz==0.4.1)
Downloading dm_tree-0.1.8-cp311-cp311-win_amd64.whl (101 kB)
\---------------------------------------- 101.3/101.3 kB ? eta 0:00:00
Requirement already satisfied: requests==2.32.3 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from boltz==0.4.1) (2.32.3)
Collecting pandas>=2.2.2 (from boltz==0.4.1)
Downloading pandas-2.2.3-cp311-cp311-win_amd64.whl (11.6 MB)
\--------------------------------------- 11.6/11.6 MB 81.8 MB/s eta 0:00:00
Collecting types-requests (from boltz==0.4.1)
Downloading types_requests-2.32.0.20250515-py3-none-any.whl (20 kB)
Collecting einops==0.8.0 (from boltz==0.4.1)
Downloading einops-0.8.0-py3-none-any.whl (43 kB)
\---------------------------------------- 43.2/43.2 kB ? eta 0:00:00
Collecting einx==0.3.0 (from boltz==0.4.1)
Downloading einx-0.3.0-py3-none-any.whl (102 kB)
\-------------------------------------- 103.0/103.0 kB 6.2 MB/s eta 0:00:00
Collecting fairscale==0.4.13 (from boltz==0.4.1)
Downloading fairscale-0.4.13.tar.gz (266 kB)
\---------------------------------------- 266.3/266.3 kB ? 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==0.4.1)
Downloading mashumaro-3.14-py3-none-any.whl (92 kB)
\---------------------------------------- 92.2/92.2 kB 5.5 MB/s eta 0:00:00
Collecting modelcif==1.2 (from boltz==0.4.1)
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==0.4.1)
Downloading wandb-0.18.7-py3-none-win_amd64.whl (15.5 MB)
\--------------------------------------- 15.5/15.5 MB 81.8 MB/s eta 0:00:00
Collecting click==8.1.7 (from boltz==0.4.1)
Downloading click-8.1.7-py3-none-any.whl (97 kB)
\---------------------------------------- 97.9/97.9 kB 5.5 MB/s eta 0:00:00
Collecting pyyaml==6.0.2 (from boltz==0.4.1)
Downloading PyYAML-6.0.2-cp311-cp311-win_amd64.whl (161 kB)
\---------------------------------------- 162.0/162.0 kB ? eta 0:00:00
Collecting biopython==1.84 (from boltz==0.4.1)
Downloading biopython-1.84-cp311-cp311-win_amd64.whl (2.8 MB)
\---------------------------------------- 2.8/2.8 MB 89.7 MB/s eta 0:00:00
Collecting scipy==1.13.1 (from boltz==0.4.1)
Downloading scipy-1.13.1-cp311-cp311-win_amd64.whl (46.2 MB)
\--------------------------------------- 46.2/46.2 MB 59.4 MB/s eta 0:00:00
Requirement already satisfied: colorama in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from click==8.1.7->boltz==0.4.1)
(0.4.6)
Collecting sympy (from einx==0.3.0->boltz==0.4.1)
Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB)
\---------------------------------------- 6.3/6.3 MB 79.6 MB/s eta 0:00:00
Collecting frozendict (from einx==0.3.0->boltz==0.4.1)
Downloading frozendict-2.4.6-py311-none-any.whl (16 kB)
Collecting omegaconf=2.2 (from hydra-core==1.3.2->boltz==0.4.1)
Downloading omegaconf-2.3.0-py3-none-any.whl (79 kB)
\---------------------------------------- 79.5/79.5 kB ? eta 0:00:00
Collecting antlr4-python3-runtime==4.9.* (from hydra-
core==1.3.2->boltz==0.4.1)
Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB)
\---------------------------------------- 117.0/117.0 kB ? 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
1.10rc202505150242\bin\lib\site-packages (from hydra-
core==1.3.2->boltz==0.4.1) (24.2)
Requirement already satisfied: typing-extensions>=4.1.0 in c:\program
files\chimerax 1.10rc202505150242\bin\lib\site-packages (from
mashumaro==3.14->boltz==0.4.1) (4.13.2)
Requirement already satisfied: ihm>=1.7 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from modelcif==1.2->boltz==0.4.1)
(2.2)
Collecting tqdm>=4.57.0 (from pytorch-lightning==2.4.0->boltz==0.4.1)
Downloading tqdm-4.67.1-py3-none-any.whl (78 kB)
\---------------------------------------- 78.5/78.5 kB ? eta 0:00:00
Collecting fsspec[http]>=2022.5.0 (from pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading fsspec-2025.3.2-py3-none-any.whl (194 kB)
\------------------------------------- 194.4/194.4 kB 11.5 MB/s eta 0:00:00
Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz==0.4.1)
Downloading torchmetrics-1.7.1-py3-none-any.whl (961 kB)
\---------------------------------------- 961.5/961.5 kB ? eta 0:00:00
Collecting lightning-utilities>=0.10.0 (from pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading lightning_utilities-0.14.3-py3-none-any.whl (28 kB)
Requirement already satisfied: charset-normalizer=2 in c:\program
files\chimerax 1.10rc202505150242\bin\lib\site-packages (from
requests==2.32.3->boltz==0.4.1) (3.4.2)
Requirement already satisfied: idna=2.5 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from requests==2.32.3->boltz==0.4.1)
(3.10)
Requirement already satisfied: urllib3=1.21.1 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from requests==2.32.3->boltz==0.4.1)
(2.4.0)
Requirement already satisfied: certifi>=2017.4.17 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from requests==2.32.3->boltz==0.4.1)
(2025.4.26)
Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==0.4.1)
Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl (9.0 kB)
Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==0.4.1)
Downloading GitPython-3.1.44-py3-none-any.whl (207 kB)
\---------------------------------------- 207.6/207.6 kB ? eta 0:00:00
Requirement already satisfied: platformdirs in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from wandb==0.18.7->boltz==0.4.1)
(4.3.8)
Collecting protobuf!=4.21.0,!=5.28.0,=3.19.0 (from
wandb==0.18.7->boltz==0.4.1)
Downloading protobuf-5.29.4-cp310-abi3-win_amd64.whl (434 kB)
\---------------------------------------- 434.5/434.5 kB ? eta 0:00:00
Requirement already satisfied: psutil>=5.0.0 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from wandb==0.18.7->boltz==0.4.1)
(7.0.0)
Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==0.4.1)
Downloading sentry_sdk-2.28.0-py2.py3-none-any.whl (341 kB)
\------------------------------------- 341.7/341.7 kB 20.7 MB/s eta 0:00:00
Collecting setproctitle (from wandb==0.18.7->boltz==0.4.1)
Downloading setproctitle-1.3.6-cp311-cp311-win_amd64.whl (12 kB)
Requirement already satisfied: setuptools in c:\users\shing\boltz\lib\site-
packages (from wandb==0.18.7->boltz==0.4.1) (65.5.0)
Requirement already satisfied: python-dateutil>=2.8.2 in c:\program
files\chimerax 1.10rc202505150242\bin\lib\site-packages (from
pandas>=2.2.2->boltz==0.4.1) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from pandas>=2.2.2->boltz==0.4.1)
(2025.2)
Requirement already satisfied: tzdata>=2022.7 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from pandas>=2.2.2->boltz==0.4.1)
(2025.2)
Requirement already satisfied: Pillow in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from rdkit>=2024.3.2->boltz==0.4.1)
(10.4.0)
Requirement already satisfied: filelock in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from torch>=2.2->boltz==0.4.1)
(3.18.0)
Requirement already satisfied: networkx in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from torch>=2.2->boltz==0.4.1) (3.3)
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from torch>=2.2->boltz==0.4.1)
(3.1.6)
Requirement already satisfied: six>=1.4.0 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from docker-
pycreds>=0.4.0->wandb==0.18.7->boltz==0.4.1) (1.16.0)
Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading aiohttp-3.11.18-cp311-cp311-win_amd64.whl (443 kB)
\------------------------------------- 443.7/443.7 kB 27.1 MB/s eta 0:00:00
Collecting gitdb=4.0.1 (from
gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==0.4.1)
Downloading gitdb-4.0.12-py3-none-any.whl (62 kB)
\---------------------------------------- 62.8/62.8 kB ? eta 0:00:00
Requirement already satisfied: msgpack in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from
ihm>=1.7->modelcif==1.2->boltz==0.4.1) (1.1.0)
Collecting mpmath=1.1.0 (from sympy->einx==0.3.0->boltz==0.4.1)
Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)
\---------------------------------------- 536.2/536.2 kB ? eta 0:00:00
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages (from
jinja2->torch>=2.2->boltz==0.4.1) (3.0.2)
Collecting aiohappyeyeballs>=2.3.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
Collecting aiosignal>=1.1.2 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading aiosignal-1.3.2-py2.py3-none-any.whl (7.6 kB)
Collecting attrs>=17.3.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading attrs-25.3.0-py3-none-any.whl (63 kB)
\---------------------------------------- 63.8/63.8 kB ? eta 0:00:00
Collecting frozenlist>=1.1.1 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading frozenlist-1.6.0-cp311-cp311-win_amd64.whl (120 kB)
\-------------------------------------- 120.9/120.9 kB 6.9 MB/s eta 0:00:00
Collecting multidict=4.5 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading multidict-6.4.3-cp311-cp311-win_amd64.whl (38 kB)
Collecting propcache>=0.2.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading propcache-0.3.1-cp311-cp311-win_amd64.whl (45 kB)
\---------------------------------------- 45.2/45.2 kB ? eta 0:00:00
Collecting yarl=1.17.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==0.4.1)
Downloading yarl-1.20.0-cp311-cp311-win_amd64.whl (93 kB)
\---------------------------------------- 93.4/93.4 kB ? eta 0:00:00
Collecting smmap=3.0.1 (from
gitdb=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==0.4.1)
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-0.4.1-py3-none-any.whl size=139914
sha256=fd63d733df8685533deee6c16824a06443638543cf298df345bdc2eaf2abba1b
Stored in directory: C:\Users\shing\AppData\Local\Temp\pip-ephem-wheel-cache-
dm1n12z9\wheels\cf\72\1c\bb985c095c0d1f3b385f30452dcb2ac8f404a8439c7b383eef
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=332215
sha256=2570a60065b42803110e9bb44a771f9eb703543d6a38538abc02e9c38cac3388
Stored in directory:
c:\users\shing\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=fda2b892ce7b7c4f09d531ebcafe5e5acc66980da9c90d6398825574f373c9eb
Stored in directory:
c:\users\shing\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=8195e6f39b05d91f6270f1347f8f7271fa739d5e7516bac5878ff196b634af14
Stored in directory:
c:\users\shing\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, sympy, smmap, setproctitle, sentry-sdk, pyyaml, protobuf,
propcache, numpy, multidict, mashumaro, lightning-utilities, fsspec,
frozenlist, frozendict, einops, docker-pycreds, click, attrs,
aiohappyeyeballs, yarl, torch, scipy, rdkit, pandas, omegaconf, modelcif,
gitdb, einx, biopython, aiosignal, torchmetrics, hydra-core, gitpython,
fairscale, aiohttp, wandb, pytorch-lightning, boltz
Attempting uninstall: numpy
Found existing installation: numpy 1.26.4
Not uninstalling numpy at c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages, outside environment
C:\Users\shing\boltz
Can't uninstall 'numpy'. No files were found to uninstall.
Attempting uninstall: scipy
Found existing installation: scipy 1.14.0
Not uninstalling scipy at c:\program files\chimerax
1.10rc202505150242\bin\lib\site-packages, outside environment
C:\Users\shing\boltz
Can't uninstall 'scipy'. No files were found to uninstall.
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
chimerax-bundlebuilder 1.5.1 requires numpy==1.26.4, but you have numpy 1.26.3
which is incompatible.
chimerax-bundlebuilder 1.5.1 requires setuptools==78.1.0, but you have
setuptools 65.5.0 which is incompatible.
Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.11.18 aiosignal-1.3.2
antlr4-python3-runtime-4.9.3 attrs-25.3.0 biopython-1.84 boltz-0.4.1
click-8.1.7 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-1.6.0 fsspec-2025.3.2
gitdb-4.0.12 gitpython-3.1.44 hydra-core-1.3.2 lightning-utilities-0.14.3
mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.4.3 numpy-1.26.3
omegaconf-2.3.0 pandas-2.2.3 propcache-0.3.1 protobuf-5.29.4 pytorch-
lightning-2.4.0 pyyaml-6.0.2 rdkit-2025.3.2 scipy-1.13.1 sentry-sdk-2.28.0
setproctitle-1.3.6 smmap-5.0.2 sympy-1.14.0 torch-2.7.0 torchmetrics-1.7.1
tqdm-4.67.1 types-requests-2.32.0.20250515 wandb-0.18.7 yarl-1.20.0
[notice] A new release of pip is available: 23.1.2 -> 25.1.1
[notice] To update, run: C:\Users\shing\boltz\Scripts\python.exe -m pip
install --upgrade pip
Successfully installed Boltz.
Downloading Boltz model parameters (3.3 GB) and chemical component database
(330 MB) to ~/.boltz
C:\Users\shing/boltz\Scripts\python.exe C:\Program Files\ChimeraX
1.10rc202505150242\bin\Lib\site-
packages\chimerax\boltz\download_weights_and_ccd.py
Downloading the CCD dictionary to C:\Users\shing\\.boltz\ccd.pkl. You may
change the cache directory with the --cache flag.
Downloading the model weights to C:\Users\shing\\.boltz\boltz1_conf.ckpt. You
may change the cache directory with the --cache flag.
Boltz model parameters and CCD database are installed in ~/.boltz
Successfully installed Boltz.
> boltz predict protein
> SDPPLVFHWVPFIGSTITYGIDPYKFFFSCREKYGDVFTFILLGKKTTVCLGTKGNDFILNGKLKDVNAEEIYSPLTTPVFGKDVVYDCPNSKLMEQKKFVKYGLTTSALQSYVTLIAAETRQFFDRNNPHKKFASTSGTIDLPPALAELTIYTASRSLQGKEVREGFDSSFADLYHYLDMGFTPINFMLPWAPLPQNRRRDYAQKKMSETYMSIIQKRRESKTGEHEEDMIHNLMQCKYKDGNAIPDKEIAHMMIALLMAGQHSSSATESWITLRLASRPDIQDELLQEQKDMLGVNADGSIKELTYANLSKLTLLNQVVKETLRIHAPIHSILRKVKSPMPIEGTAYVIPTTHTLLAAPGTTSRMDEHFPDCLHWEPHRWDESPSEKYKHLSPTTALGSIAEEKEDYGYGLVSKGAASPYLPFGAGRHRCIGEQFAYVQLQTITATMVRDFKFYNVDGSDNVVGTDYSSLFSRPLSPAVVKWERR
> ligandCcd HEM ligandSmiles CC1(CCC(C1(CN2C=NC=N2)O)CC3=CC=C(C=C3)Cl)C name
> ZtCYP51_MCZ
Running Boltz prediction of protein with 487 residues, 2 ligands
CC1(CCC(C1(CN2C=NC=N2)O)CC3=CC=C(C=C3)Cl)C, HEM on cpu
Using multiple sequence alignment server https://api.colabfold.com
Please cite Boltz-1 Democratizing Biomolecular Interaction Modeling. BioRxiv
https://doi.org/10.1101/2024.11.19.624167 if you use these predictions.
> ui windowfill toggle
Prediction terminated by user
> boltz predict protein
> SDPPLVFHWVPFIGSTITYGIDPYKFFFSCREKYGDVFTFILLGKKTTVCLGTKGNDFILNGKLKDVNAEEIYSPLTTPVFGKDVVYDCPNSKLMEQKKFVKYGLTTSALQSYVTLIAAETRQFFDRNNPHKKFASTSGTIDLPPALAELTIYTASRSLQGKEVREGFDSSFADLYHYLDMGFTPINFMLPWAPLPQNRRRDYAQKKMSETYMSIIQKRRESKTGEHEEDMIHNLMQCKYKDGNAIPDKEIAHMMIALLMAGQHSSSATESWITLRLASRPDIQDELLQEQKDMLGVNADGSIKELTYANLSKLTLLNQVVKETLRIHAPIHSILRKVKSPMPIEGTAYVIPTTHTLLAAPGTTSRMDEHFPDCLHWEPHRWDESPSEKYKHLSPTTALGSIAEEKEDYGYGLVSKGAASPYLPFGAGRHRCIGEQFAYVQLQTITATMVRDFKFYNVDGSDNVVGTDYSSLFSRPLSPAVVKWERR
> ligandCcd HEM ligandSmiles CC1(CCC(C1(CN2C=NC=N2)O)CC3=CC=C(C=C3)Cl)C name
> ZtCYP51_MCZ device gpu
Running Boltz prediction of protein with 487 residues, 2 ligands
CC1(CCC(C1(CN2C=NC=N2)O)CC3=CC=C(C=C3)Cl)C, HEM on gpu
Using multiple sequence alignment server https://api.colabfold.com
Attempted to run Boltz on the GPU but no supported GPU device could be found.
To avoid this error specify the compute device as "cpu" in the ChimeraX Boltz
options panel, or using the ChimeraX boltz command "device cpu" option. Boltz
supports Nvidia GPUs with CUDA and Mac M series GPUs. On Windows the Boltz
installation installs torch with no GPU support, so using Nvidia GPUs on
Windows requires reinstalling gpu-enabled torch with Boltz which we plan to
support in the future.
> boltz predict protein
> SDPPLVFHWVPFIGSTITYGIDPYKFFFSCREKYGDVFTFILLGKKTTVCLGTKGNDFILNGKLKDVNAEEIYSPLTTPVFGKDVVYDCPNSKLMEQKKFVKYGLTTSALQSYVTLIAAETRQFFDRNNPHKKFASTSGTIDLPPALAELTIYTASRSLQGKEVREGFDSSFADLYHYLDMGFTPINFMLPWAPLPQNRRRDYAQKKMSETYMSIIQKRRESKTGEHEEDMIHNLMQCKYKDGNAIPDKEIAHMMIALLMAGQHSSSATESWITLRLASRPDIQDELLQEQKDMLGVNADGSIKELTYANLSKLTLLNQVVKETLRIHAPIHSILRKVKSPMPIEGTAYVIPTTHTLLAAPGTTSRMDEHFPDCLHWEPHRWDESPSEKYKHLSPTTALGSIAEEKEDYGYGLVSKGAASPYLPFGAGRHRCIGEQFAYVQLQTITATMVRDFKFYNVDGSDNVVGTDYSSLFSRPLSPAVVKWERR
> ligandCcd HEM ligandSmiles CC1(CCC(C1(CN2C=NC=N2)O)CC3=CC=C(C=C3)Cl)C name
> ZtCYP51_MCZ device cpu
Running Boltz prediction of protein with 487 residues, 2 ligands
CC1(CCC(C1(CN2C=NC=N2)O)CC3=CC=C(C=C3)Cl)C, HEM on cpu
Using multiple sequence alignment server https://api.colabfold.com
Boltz prediction completed in 1879 seconds
> open C:\Users\shing/Desktop/boltz_ZtCYP51_MCZ_2\ZtCYP51_MCZ_model_0.cif
> logInfo false
Summary of feedback from opening
C:\Users\shing/Desktop/boltz_ZtCYP51_MCZ_2\ZtCYP51_MCZ_model_0.cif
---
notes | Fetching CCD HEM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/HEM/HEM.cif
Fetching CCD LIG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/LIG/LIG.cif
> color bfactor #1 palette alphafold
3945 atoms, 489 residues, atom bfactor range 51.7 to 98.8
> ui windowfill toggle
> set bgColor white
> set bgColor #ffffff00
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10rc202505150242 (2025-05-15)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 528.89
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: ja_JP.cp65001
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows
Manufacturer: HP
Model: HP Z4 G4 Workstation
OS: Microsoft Windows 10 Pro for Workstations (Build 19045)
Memory: 188,692,598,784
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Xeon(R) W-2245 CPU @ 3.90GHz
OSLanguage: ja-JP
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
auditwheel: 6.3.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.3.3
build: 1.2.2.post1
certifi: 2025.4.26
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.3
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.6
ChimeraX-AtomicLibrary: 14.1.18
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.6
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10rc202505150242
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
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
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: 1.14.1
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
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: 1.5.1
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: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.45.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.10
contourpy: 1.3.2
coverage: 7.8.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.14
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.58.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.13.0
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: 5.7.2
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.4
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.5.0
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
pyelftools: 0.32
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: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.3.5
pytest-cov: 6.1.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pywin32: 310
pyzmq: 26.4.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
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: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.13.2
tzdata: 2025.2
urllib3: 2.4.0
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Was after running some Boltz predictions, but not necessarily related.