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Opened 2 months ago
Closed 2 months ago
#18773 closed defect (duplicate)
Boltz progress reporting for dead window
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Prediction | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/vict5/Desktop/chemAI 과제.cxs"
Log from Fri Sep 12 12:26:12 2025UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open Erythromycin
'Erythromycin' has no suffix
> open 1ubq
Summary of feedback from opening 1ubq fetched from pdb
---
note | Fetching compressed mmCIF 1ubq from http://files.rcsb.org/download/1ubq.cif
1ubq title:
Structure of ubiquitin refined At 1.8 angstroms resolution [more info...]
Chain information for 1ubq #1
---
Chain | Description | UniProt
A | UBIQUITIN | UBIQ_HUMAN 1-76
> open Erythromycin
'Erythromycin' has no suffix
> open /Users/vict5/Downloads/ERY.cif
Summary of feedback from opening /Users/vict5/Downloads/ERY.cif
---
warning | No mmCIF models found.
> open /Users/vict5/Desktop/ChimeraX/CCD/ERY.cif
Summary of feedback from opening /Users/vict5/Desktop/ChimeraX/CCD/ERY.cif
---
warning | No mmCIF models found.
> open /Users/vict5/Desktop/ChimeraX/PDB/1v4t.cif
1v4t.cif title:
Crystal structure of human glucokinase [more info...]
Chain information for 1v4t.cif #2
---
Chain | Description | UniProt
A | glucokinase isoform 2 | HXK4_HUMAN 16-465
Non-standard residues in 1v4t.cif #2
---
NA — sodium ion
SO4 — sulfate ion
> hide #1 models
> hide #1 target m
> hide #!2 models
> show #1 models
> show #!2 models
> hide #1 models
> open /Users/vict5/Desktop/ChimeraX/CCD/ERY.cif
Summary of feedback from opening /Users/vict5/Desktop/ChimeraX/CCD/ERY.cif
---
warning | No mmCIF models found.
> open ery fromDatabase ccd
ERY title:
erythromycin A
Opened CCD ERY
> hide #!2 models
> view
> open /Users/vict5/Downloads/ery-rdkit.pdb
> select #3-4/*:*@H*
67 atoms, 1 residue, 1 model selected
> delete sel
> align #3 toAtoms #4
RMSD between 51 atom pairs is 3.502 angstroms
> distance #3:@C7 #4:@C7
Missing or invalid "objects" argument: only initial part "#3" of atom
specifier valid
> distance #3:@C1 #4:@C1
Missing or invalid "objects" argument: only initial part "#3" of atom
specifier valid
Desktop color scheme is dark
Desktop color scheme is light
> show #!2 models
> show #1 models
> hide #3 models
> hide #4 models
> mm#1 to #2
Unknown command: mm#1 to #2
> mmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1v4t.cif, chain A (#2) with 1ubq, chain A (#1), sequence alignment
score = 24.4
RMSD between 13 pruned atom pairs is 0.576 angstroms; (across all 27 pairs:
13.599)
> view
> hide #!2 models
> hide #1 models
> show #3 models
> show #4 models
> view
> ui tool show Boltz
Populating font family aliases took 113 ms. Replace uses of missing font
family "Ui-sans-serif" with one that exists to avoid this cost.
> boltz install /Users/vict5/boltz
Successfully created Boltz Python virtual environment /Users/vict5/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...
/Users/vict5/boltz/bin/python -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
/private/var/folders/5n/xxyvlpq52x531n5z102512n80000gn/T/pip-req-build-
vi1_26ee
Running command git clone --filter=blob:none --quiet
https://github.com/RBVI/boltz
/private/var/folders/5n/xxyvlpq52x531n5z102512n80000gn/T/pip-req-build-
vi1_26ee
Running command git checkout -b chimerax --track origin/chimerax
Switched to a new branch 'chimerax'
branch 'chimerax' set up to track 'origin/chimerax'.
Resolved https://github.com/RBVI/boltz to commit
ca6c444937381392e979c1c26db72dce7963e480
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==1.0.0)
Downloading torch-2.8.0-cp311-none-macosx_11_0_arm64.whl (73.6 MB)
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Requirement already satisfied: numpy<2.0,>=1.26 in
/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from boltz==1.0.0) (1.26.4)
Collecting hydra-core==1.3.2 (from boltz==1.0.0)
Downloading hydra_core-1.3.2-py3-none-any.whl (154 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 154.5/154.5 kB 3.5 MB/s eta 0:00:00
Collecting pytorch-lightning==2.4.0 (from boltz==1.0.0)
Downloading pytorch_lightning-2.4.0-py3-none-any.whl (815 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 815.2/815.2 kB 4.3 MB/s eta 0:00:00
Collecting rdkit>=2024.3.2 (from boltz==1.0.0)
Downloading rdkit-2025.3.6-cp311-cp311-macosx_11_0_arm64.whl (29.1 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 29.1/29.1 MB 3.9 MB/s eta 0:00:00
Collecting dm-tree==0.1.8 (from boltz==1.0.0)
Downloading dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 110.7/110.7 kB 4.3 MB/s eta 0:00:00
Requirement already satisfied: requests==2.32.3 in
/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from boltz==1.0.0) (2.32.3)
Collecting pandas>=2.2.2 (from boltz==1.0.0)
Downloading pandas-2.3.2-cp311-cp311-macosx_11_0_arm64.whl (10.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.8/10.8 MB 4.0 MB/s eta 0:00:00
Collecting types-requests (from boltz==1.0.0)
Downloading types_requests-2.32.4.20250809-py3-none-any.whl (20 kB)
Collecting einops==0.8.0 (from boltz==1.0.0)
Downloading einops-0.8.0-py3-none-any.whl (43 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.2/43.2 kB 4.1 MB/s eta 0:00:00
Collecting einx==0.3.0 (from boltz==1.0.0)
Downloading einx-0.3.0-py3-none-any.whl (102 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 103.0/103.0 kB 3.8 MB/s eta 0:00:00
Collecting fairscale==0.4.13 (from boltz==1.0.0)
Downloading fairscale-0.4.13.tar.gz (266 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 266.3/266.3 kB 3.8 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Installing backend dependencies: started
Installing backend dependencies: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Collecting mashumaro==3.14 (from boltz==1.0.0)
Downloading mashumaro-3.14-py3-none-any.whl (92 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 92.2/92.2 kB 4.5 MB/s eta 0:00:00
Collecting modelcif==1.2 (from boltz==1.0.0)
Downloading modelcif-1.2.tar.gz (66 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.8/66.8 kB 2.6 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting wandb==0.18.7 (from boltz==1.0.0)
Downloading wandb-0.18.7-py3-none-macosx_11_0_arm64.whl (15.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.2/15.2 MB 3.9 MB/s eta 0:00:00
Collecting click==8.1.7 (from boltz==1.0.0)
Downloading click-8.1.7-py3-none-any.whl (97 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 97.9/97.9 kB 2.9 MB/s eta 0:00:00
Collecting pyyaml==6.0.2 (from boltz==1.0.0)
Downloading PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 172.0/172.0 kB 3.0 MB/s eta 0:00:00
Collecting biopython==1.84 (from boltz==1.0.0)
Downloading biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB 4.1 MB/s eta 0:00:00
Collecting scipy==1.13.1 (from boltz==1.0.0)
Downloading scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl (30.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 30.3/30.3 MB 4.0 MB/s eta 0:00:00
Collecting numba==0.61.0 (from boltz==1.0.0)
Downloading numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl (2.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 4.2 MB/s eta 0:00:00
Collecting sympy (from einx==0.3.0->boltz==1.0.0)
Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.3/6.3 MB 3.8 MB/s eta 0:00:00
Collecting frozendict (from einx==0.3.0->boltz==1.0.0)
Downloading frozendict-2.4.6-py311-none-any.whl (16 kB)
Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==1.0.0)
Downloading omegaconf-2.3.0-py3-none-any.whl (79 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 79.5/79.5 kB 4.4 MB/s eta 0:00:00
Collecting antlr4-python3-runtime==4.9.* (from hydra-
core==1.3.2->boltz==1.0.0)
Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.0/117.0 kB 5.2 MB/s eta 0:00:00
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: packaging in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from hydra-core==1.3.2->boltz==1.0.0) (24.2)
Requirement already satisfied: typing-extensions>=4.1.0 in
/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from mashumaro==3.14->boltz==1.0.0) (4.14.1)
Requirement already satisfied: ihm>=1.7 in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from modelcif==1.2->boltz==1.0.0) (2.2)
Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==1.0.0)
Downloading llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl (26.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 26.2/26.2 MB 3.8 MB/s eta 0:00:00
Collecting tqdm>=4.57.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)
Downloading tqdm-4.67.1-py3-none-any.whl (78 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 78.5/78.5 kB 4.1 MB/s eta 0:00:00
Collecting fsspec[http]>=2022.5.0 (from pytorch-
lightning==2.4.0->boltz==1.0.0)
Downloading fsspec-2025.9.0-py3-none-any.whl (199 kB)
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Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)
Downloading torchmetrics-1.8.2-py3-none-any.whl (983 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 983.2/983.2 kB 3.4 MB/s eta 0:00:00
Collecting lightning-utilities>=0.10.0 (from pytorch-
lightning==2.4.0->boltz==1.0.0)
Downloading lightning_utilities-0.15.2-py3-none-any.whl (29 kB)
Requirement already satisfied: charset-normalizer<4,>=2 in
/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==1.0.0) (3.4.2)
Requirement already satisfied: idna<4,>=2.5 in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==1.0.0) (3.10)
Requirement already satisfied: urllib3<3,>=1.21.1 in
/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==1.0.0) (2.5.0)
Requirement already satisfied: certifi>=2017.4.17 in
/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from requests==2.32.3->boltz==1.0.0) (2023.11.17)
Collecting docker-pycreds>=0.4.0 (from wandb==0.18.7->boltz==1.0.0)
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==1.0.0)
Downloading gitpython-3.1.45-py3-none-any.whl (208 kB)
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Requirement already satisfied: platformdirs in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from wandb==0.18.7->boltz==1.0.0) (4.3.8)
Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from
wandb==0.18.7->boltz==1.0.0)
Downloading protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl (418 kB)
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Requirement already satisfied: psutil>=5.0.0 in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from wandb==0.18.7->boltz==1.0.0) (7.0.0)
Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==1.0.0)
Downloading sentry_sdk-2.37.1-py2.py3-none-any.whl (368 kB)
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Collecting setproctitle (from wandb==0.18.7->boltz==1.0.0)
Downloading setproctitle-1.3.7-cp311-cp311-macosx_11_0_arm64.whl (13 kB)
Requirement already satisfied: setuptools in
/Users/vict5/boltz/lib/python3.11/site-packages (from
wandb==0.18.7->boltz==1.0.0) (65.5.0)
Requirement already satisfied: python-dateutil>=2.8.2 in
/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==1.0.0) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2)
Requirement already satisfied: tzdata>=2022.7 in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2)
Requirement already satisfied: Pillow in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from rdkit>=2024.3.2->boltz==1.0.0) (10.4.0)
Requirement already satisfied: filelock in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch>=2.2->boltz==1.0.0) (3.18.0)
Requirement already satisfied: networkx in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch>=2.2->boltz==1.0.0) (3.3)
Requirement already satisfied: jinja2 in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from torch>=2.2->boltz==1.0.0) (3.1.6)
Requirement already satisfied: six>=1.4.0 in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from docker-pycreds>=0.4.0->wandb==0.18.7->boltz==1.0.0) (1.16.0)
Collecting aiohttp!=4.0.0a0,!=4.0.0a1 (from fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==1.0.0)
Downloading aiohttp-3.12.15-cp311-cp311-macosx_11_0_arm64.whl (471 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 471.8/471.8 kB 3.5 MB/s eta 0:00:00
Collecting gitdb<5,>=4.0.1 (from
gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==1.0.0)
Downloading gitdb-4.0.12-py3-none-any.whl (62 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 4.2 MB/s eta 0:00:00
Requirement already satisfied: msgpack in /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from ihm>=1.7->modelcif==1.2->boltz==1.0.0) (1.1.0)
Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==1.0.0)
Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 4.4 MB/s eta 0:00:00
Requirement already satisfied: MarkupSafe>=2.0 in
/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from jinja2->torch>=2.2->boltz==1.0.0) (3.0.2)
Collecting aiohappyeyeballs>=2.5.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==1.0.0)
Downloading aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
Collecting aiosignal>=1.4.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==1.0.0)
Downloading aiosignal-1.4.0-py3-none-any.whl (7.5 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==1.0.0)
Downloading attrs-25.3.0-py3-none-any.whl (63 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 63.8/63.8 kB 2.9 MB/s 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==1.0.0)
Downloading frozenlist-1.7.0-cp311-cp311-macosx_11_0_arm64.whl (47 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.1/47.1 kB 3.2 MB/s eta 0:00:00
Collecting multidict<7.0,>=4.5 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==1.0.0)
Downloading multidict-6.6.4-cp311-cp311-macosx_11_0_arm64.whl (44 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.3/44.3 kB 2.5 MB/s eta 0:00:00
Collecting propcache>=0.2.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==1.0.0)
Downloading propcache-0.3.2-cp311-cp311-macosx_11_0_arm64.whl (43 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.5/43.5 kB 2.8 MB/s eta 0:00:00
Collecting yarl<2.0,>=1.17.0 (from
aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-
lightning==2.4.0->boltz==1.0.0)
Downloading yarl-1.20.1-cp311-cp311-macosx_11_0_arm64.whl (89 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.8/89.8 kB 4.1 MB/s eta 0:00:00
Collecting smmap<6,>=3.0.1 (from
gitdb<5,>=4.0.1->gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==1.0.0)
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-1.0.0-py3-none-any.whl size=150846
sha256=a64a965fbd3677a16b2a54e532e2b79d1c7076a5887ff7c9e052c0896d1a5de4
Stored in directory:
/private/var/folders/5n/xxyvlpq52x531n5z102512n80000gn/T/pip-ephem-wheel-
cache-
hx_dypna/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=332208
sha256=1f7c2cbd6164866bcbf48b263ce888dd79b90a0e1b1b7fbf9b15e767572c0d23
Stored in directory:
/Users/vict5/Library/Caches/pip/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=41181
sha256=3e000878b8866f7d0a6751506cc6541079beb321f22c632beae4f867ecd21005
Stored in directory:
/Users/vict5/Library/Caches/pip/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=144555
sha256=d1d04fddaeaf44894d1407fc19ccf54d48a9e9ff9d0a1ff3a7513d5987347a0d
Stored in directory:
/Users/vict5/Library/Caches/pip/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, scipy, rdkit, pyyaml,
protobuf, propcache, multidict, mashumaro, llvmlite, lightning-utilities,
fsspec, frozenlist, frozendict, einops, docker-pycreds, click, biopython,
attrs, aiohappyeyeballs, yarl, torch, pandas, omegaconf, numba, modelcif,
gitdb, einx, aiosignal, torchmetrics, hydra-core, gitpython, fairscale,
aiohttp, wandb, pytorch-lightning, boltz
Attempting uninstall: scipy
Found existing installation: scipy 1.14.0
Not uninstalling scipy at /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/vict5/boltz
Can't uninstall 'scipy'. 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-1.0.0
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-1.7.0 fsspec-2025.9.0
gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 lightning-utilities-0.15.2
llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.6.4
numba-0.61.0 omegaconf-2.3.0 pandas-2.3.2 propcache-0.3.2 protobuf-5.29.5
pytorch-lightning-2.4.0 pyyaml-6.0.2 rdkit-2025.3.6 scipy-1.13.1 sentry-
sdk-2.37.1 setproctitle-1.3.7 smmap-5.0.2 sympy-1.14.0 torch-2.8.0
torchmetrics-1.8.2 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: 23.1.2 -> 25.2
[notice] To update, run: /Users/vict5/boltz/bin/python -m pip install
--upgrade pip
Successfully installed Boltz.
Downloading Boltz model parameters (3.3 GB) and chemical component database
(330 MB) to ~/.boltz
/Users/vict5/boltz/bin/python /Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/download_weights_and_ccd.py
Downloading the CCD dictionary to /Users/vict5/.boltz/ccd.pkl. You may change
the cache directory with the --cache flag.
Traceback (most recent call last):
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1348, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1286, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1332, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1281, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1041, in _send_output
self.send(msg)
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 979, in send
self.connect()
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1458, in connect
self.sock = self._context.wrap_socket(self.sock,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py",
line 517, in wrap_socket
return self.sslsocket_class._create(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py",
line 1075, in _create
self.do_handshake()
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py",
line 1346, in do_handshake
self._sslobj.do_handshake()
ConnectionResetError: [Errno 54] Connection reset by peer
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/download_weights_and_ccd.py", line 30, in <module>
download_weights_and_ccd()
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/download_weights_and_ccd.py", line 11, in
download_weights_and_ccd
download(Path(data_path))
File "/Users/vict5/boltz/lib/python3.11/site-
packages/lightning_utilities/core/rank_zero.py", line 41, in wrapped_fn
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/Users/vict5/boltz/lib/python3.11/site-packages/boltz/main.py", line
118, in download
urllib.request.urlretrieve(CCD_URL, str(ccd)) # noqa: S310
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 241, in urlretrieve
with contextlib.closing(urlopen(url, data)) as fp:
^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 216, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 519, in open
response = self._open(req, data)
^^^^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 536, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 496, in _call_chain
result = func(*args)
^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1391, in https_open
return self.do_open(http.client.HTTPSConnection, req,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1351, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 54] Connection reset by peer>
Downloading Boltz model parameters and CCD database to ~/.boltz or creating
CCD atom counts file failed.
> boltz install /Users/vict5/boltz
You must install Boltz into a new or empty directory. The directory
/Users/vict5/boltz already exists and is not empty.
> save "/Users/vict5/Desktop/chemAI 과제.cxs"
——— End of log from Fri Sep 12 12:26:12 2025 ———
> view name session-start
opened ChimeraX session
Traceback (most recent call last):
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/boltz/boltz_gui.py", line 572, in _report_progress
if not self.tool_window.shown:
^^^^^^^^^^^^^^^^^^^^^^
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2343, in shown
return self.__toolkit.shown
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'shown'
Error processing trigger "new frame":
AttributeError: 'NoneType' object has no attribute 'shown'
File "/Applications/ChimeraX-1.10.1
2.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2343, in shown
return self.__toolkit.shown
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Air
Model Identifier: Mac16,12
Model Number: MC6U4KH/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 7일 2시간 47분
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
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: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
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: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
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: 2.2.2
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: 1.1.3
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: 1.2.1
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: 1.45.2
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
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
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: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
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
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
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: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
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: 6.5.1
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
Change History (2)
comment:1 by , 2 months ago
| Component: | Unassigned → Structure Prediction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Boltz progress reporting for dead window |
comment:2 by , 2 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Was fixed several weeks ago in daily build. Boltz GUI closed (in this case by opening a new session) while run was in progress.
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Seems like this is fixed in the current code