Opened 3 months ago
Closed 2 months ago
#18342 closed defect (fixed)
PySide6: AttributeError: 'MoleculesTable' object has no attribute 'AdjustToContents'
Reported by: | Owned by: | Zach Pearson | |
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Priority: | normal | Milestone: | |
Component: | Window Toolkit | Version: | |
Keywords: | Cc: | chimerax-programmers | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-15.6-arm64-arm-64bit ChimeraX Version: 1.11.dev202508010600 (2025-08-01 06:00:49 UTC) Description Installed Chimera daily, installed boltz, wanted to add a protein for ligand affinity prediction and this appear: AttributeError: 'MoleculesTable' object has no attribute 'AdjustToContents' File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/item_table.py", line 323, in __init__ self.setSizeAdjustPolicy(self.AdjustToContents) ^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.11.dev202508010600 (2025-08-01) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Boltz > boltz install /Users/amerikachi/boltz2 Successfully created Boltz Python virtual environment /Users/amerikachi/boltz2. Now installing Boltz and required packages from PyPi. This may take tens of of minutes since Boltz uses many other packages totaling about 1 Gbyte of disk space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb, numba... /Users/amerikachi/boltz2/bin/python -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 /private/var/folders/hq/kcw7lmt94s30s264y0cy0z9c0000gs/T/pip-req-build- zxopy5wk Running command git clone --filter=blob:none --quiet https://github.com/RBVI/boltz /private/var/folders/hq/kcw7lmt94s30s264y0cy0z9c0000gs/T/pip-req-build- zxopy5wk Running command git checkout -b chimerax_boltz2 --track origin/chimerax_boltz2 Switched to a new branch 'chimerax_boltz2' branch 'chimerax_boltz2' set up to track 'origin/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' Collecting torch>=2.2 (from boltz==2.1.1) Downloading torch-2.7.1-cp311-none-macosx_11_0_arm64.whl.metadata (29 kB) Requirement already satisfied: numpy<2.0,>=1.26 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from boltz==2.1.1) (1.26.4) Collecting hydra-core==1.3.2 (from boltz==2.1.1) Downloading hydra_core-1.3.2-py3-none-any.whl.metadata (5.5 kB) Collecting pytorch-lightning==2.5.0 (from boltz==2.1.1) Downloading pytorch_lightning-2.5.0-py3-none-any.whl.metadata (21 kB) Collecting rdkit>=2024.3.2 (from boltz==2.1.1) Downloading rdkit-2025.3.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.1 kB) Collecting dm-tree==0.1.8 (from boltz==2.1.1) Downloading dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl.metadata (1.9 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) Downloading pandas-2.3.1-cp311-cp311-macosx_11_0_arm64.whl.metadata (91 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91.2/91.2 kB 700.7 kB/s eta 0:00:00 Collecting types-requests (from boltz==2.1.1) Downloading types_requests-2.32.4.20250611-py3-none-any.whl.metadata (2.1 kB) Collecting einops==0.8.0 (from boltz==2.1.1) Downloading einops-0.8.0-py3-none-any.whl.metadata (12 kB) Collecting einx==0.3.0 (from boltz==2.1.1) Downloading einx-0.3.0-py3-none-any.whl.metadata (6.9 kB) Collecting fairscale==0.4.13 (from boltz==2.1.1) Downloading fairscale-0.4.13.tar.gz (266 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 266.3/266.3 kB 1.6 MB/s eta 0:00:00 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting mashumaro==3.14 (from boltz==2.1.1) Downloading mashumaro-3.14-py3-none-any.whl.metadata (114 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 114.4/114.4 kB 3.1 MB/s eta 0:00:00 Collecting modelcif==1.2 (from boltz==2.1.1) Downloading modelcif-1.2.tar.gz (66 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 66.8/66.8 kB 1.8 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==2.1.1) Downloading wandb-0.18.7-py3-none-macosx_11_0_arm64.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) Downloading PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.1 kB) Collecting biopython==1.84 (from boltz==2.1.1) Downloading biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl.metadata (12 kB) Collecting scipy==1.13.1 (from boltz==2.1.1) Downloading scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (60 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 60.6/60.6 kB 2.1 MB/s eta 0:00:00 Collecting numba==0.61.0 (from boltz==2.1.1) Downloading numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.7 kB) Collecting gemmi==0.6.5 (from boltz==2.1.1) Downloading gemmi-0.6.5-cp311-cp311-macosx_11_0_arm64.whl.metadata (2.3 kB) Collecting scikit-learn==1.6.1 (from boltz==2.1.1) Downloading scikit_learn-1.6.1-cp311-cp311-macosx_12_0_arm64.whl.metadata (31 kB) Collecting chembl_structure_pipeline==1.2.2 (from boltz==2.1.1) Downloading 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) Downloading cuequivariance_torch-0.5.1-py3-none-any.whl.metadata (15 kB) Requirement already satisfied: setuptools>=46.4.0 in /Users/amerikachi/boltz2/lib/python3.11/site-packages (from chembl_structure_pipeline==1.2.2->boltz==2.1.1) (65.5.0) Collecting sympy (from einx==0.3.0->boltz==2.1.1) Downloading sympy-1.14.0-py3-none-any.whl.metadata (12 kB) Collecting frozendict (from einx==0.3.0->boltz==2.1.1) Downloading frozendict-2.4.6-py311-none-any.whl.metadata (23 kB) Collecting omegaconf<2.4,>=2.2 (from hydra-core==1.3.2->boltz==2.1.1) Downloading omegaconf-2.3.0-py3-none-any.whl.metadata (3.9 kB) Collecting antlr4-python3-runtime==4.9.* (from hydra- core==1.3.2->boltz==2.1.1) Downloading antlr4-python3-runtime-4.9.3.tar.gz (117 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 117.0/117.0 kB 2.7 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Requirement already satisfied: packaging in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from hydra-core==1.3.2->boltz==2.1.1) (24.2) Requirement already satisfied: typing-extensions>=4.1.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from mashumaro==3.14->boltz==2.1.1) (4.14.1) Requirement already satisfied: ihm>=1.7 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from modelcif==1.2->boltz==2.1.1) (2.2) Collecting llvmlite<0.45,>=0.44.0dev0 (from numba==0.61.0->boltz==2.1.1) Downloading llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl.metadata (4.8 kB) Collecting tqdm>=4.57.0 (from pytorch-lightning==2.5.0->boltz==2.1.1) Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB) Collecting fsspec>=2022.5.0 (from fsspec[http]>=2022.5.0->pytorch- lightning==2.5.0->boltz==2.1.1) Downloading fsspec-2025.7.0-py3-none-any.whl.metadata (12 kB) Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.5.0->boltz==2.1.1) Downloading torchmetrics-1.8.0-py3-none-any.whl.metadata (21 kB) Collecting lightning-utilities>=0.10.0 (from pytorch- lightning==2.5.0->boltz==2.1.1) Downloading lightning_utilities-0.15.0-py3-none-any.whl.metadata (5.7 kB) Requirement already satisfied: charset-normalizer<4,>=2 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==2.1.1) (3.4.2) Requirement already satisfied: idna<4,>=2.5 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==2.1.1) (3.10) Requirement already satisfied: urllib3<3,>=1.21.1 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==2.1.1) (2.5.0) Requirement already satisfied: certifi>=2017.4.17 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from requests==2.32.3->boltz==2.1.1) (2025.7.14) 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) Downloading docker_pycreds-0.4.0-py2.py3-none-any.whl.metadata (1.8 kB) Collecting gitpython!=3.1.29,>=1.0.0 (from wandb==0.18.7->boltz==2.1.1) Downloading gitpython-3.1.45-py3-none-any.whl.metadata (13 kB) Requirement already satisfied: platformdirs in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from wandb==0.18.7->boltz==2.1.1) (4.3.8) Collecting protobuf!=4.21.0,!=5.28.0,<6,>=3.19.0 (from wandb==0.18.7->boltz==2.1.1) Downloading protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl.metadata (592 bytes) Requirement already satisfied: psutil>=5.0.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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) Downloading sentry_sdk-2.34.1-py2.py3-none-any.whl.metadata (10 kB) Collecting setproctitle (from wandb==0.18.7->boltz==2.1.1) Downloading setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl.metadata (10 kB) Collecting cuequivariance (from cuequivariance_torch>=0.5.0->boltz==2.1.1) Downloading cuequivariance-0.5.1-py3-none-any.whl.metadata (15 kB) Requirement already satisfied: python-dateutil>=2.8.2 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==2.1.1) (2.9.0.post0) Requirement already satisfied: pytz>=2020.1 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==2.1.1) (2025.2) Requirement already satisfied: tzdata>=2022.7 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from pandas>=2.2.2->boltz==2.1.1) (2025.2) Requirement already satisfied: Pillow in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from rdkit>=2024.3.2->boltz==2.1.1) (10.4.0) Requirement already satisfied: filelock in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==2.1.1) (3.18.0) Requirement already satisfied: networkx in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==2.1.1) (3.3) Requirement already satisfied: jinja2 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from torch>=2.2->boltz==2.1.1) (3.1.6) Requirement already satisfied: six>=1.4.0 in /Applications/ChimeraX_Daily.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==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-macosx_11_0_arm64.whl.metadata (7.7 kB) Collecting gitdb<5,>=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 /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages (from ihm>=1.7->modelcif==1.2->boltz==2.1.1) (1.1.0) Collecting mpmath<1.4,>=1.1.0 (from sympy->einx==0.3.0->boltz==2.1.1) Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB) Collecting opt-einsum (from cuequivariance->cuequivariance_torch>=0.5.0->boltz==2.1.1) Downloading opt_einsum-3.4.0-py3-none-any.whl.metadata (6.3 kB) Requirement already satisfied: MarkupSafe>=2.0 in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/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-macosx_11_0_arm64.whl.metadata (18 kB) Collecting multidict<7.0,>=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-6.6.3-cp311-cp311-macosx_11_0_arm64.whl.metadata (5.3 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-macosx_11_0_arm64.whl.metadata (12 kB) Collecting yarl<2.0,>=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-macosx_11_0_arm64.whl.metadata (73 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 73.9/73.9 kB 2.2 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==2.1.1) Downloading smmap-5.0.2-py3-none-any.whl.metadata (4.3 kB) Downloading biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.7/2.7 MB 3.8 MB/s eta 0:00:00 Downloading chembl_structure_pipeline-1.2.2-py3-none-any.whl (17 kB) Using cached click-8.1.7-py3-none-any.whl (97 kB) Downloading dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 110.7/110.7 kB 2.7 MB/s eta 0:00:00 Downloading einops-0.8.0-py3-none-any.whl (43 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 43.2/43.2 kB 657.9 kB/s eta 0:00:00 Downloading einx-0.3.0-py3-none-any.whl (102 kB) 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eta 0:00:00 Downloading sentry_sdk-2.34.1-py2.py3-none-any.whl (357 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 357.7/357.7 kB 6.0 MB/s eta 0:00:00 Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.3/6.3 MB 11.1 MB/s eta 0:00:00 Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB) Downloading torchmetrics-1.8.0-py3-none-any.whl (981 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 981.9/981.9 kB 12.6 MB/s eta 0:00:00 Using cached tqdm-4.67.1-py3-none-any.whl (78 kB) Downloading cuequivariance-0.5.1-py3-none-any.whl (126 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 126.2/126.2 kB 1.7 MB/s eta 0:00:00 Downloading frozendict-2.4.6-py311-none-any.whl (16 kB) Downloading setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl (11 kB) Downloading aiohttp-3.12.15-cp311-cp311-macosx_11_0_arm64.whl (471 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 471.8/471.8 kB 9.8 MB/s eta 0:00:00 Downloading gitdb-4.0.12-py3-none-any.whl (62 kB) 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yarl-1.20.1-cp311-cp311-macosx_11_0_arm64.whl (89 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 89.8/89.8 kB 953.7 kB/s eta 0:00:00 Building wheels for collected packages: boltz, fairscale, modelcif, antlr4-python3-runtime Building wheel for boltz (pyproject.toml): started Building wheel for boltz (pyproject.toml): finished with status 'done' Created wheel for boltz: filename=boltz-2.1.1-py3-none-any.whl size=262921 sha256=34bb9c41c50e686b10f3d3e0d89beb31d29b3955181d018c13361378941fa5e9 Stored in directory: /private/var/folders/hq/kcw7lmt94s30s264y0cy0z9c0000gs/T/pip-ephem-wheel- cache- he38gow8/wheels/eb/6b/e8/b8f2318f04e510ea3091105ed50c6e2ff4fa900e16361241f7 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=2d458139c7febbb49dfcc5eaf30eacecacda3a973ee10c28d67224732948560a Stored in directory: /Users/amerikachi/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=c4915f07582b72aa4349ae15a02cc06b3e731e9a13d878d38558b56a3e8330b2 Stored in directory: /Users/amerikachi/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=38cd5b1248154d5d0eee3cfb17e88b864cb23e2291b25783ef8a4a3105afa101 Stored in directory: /Users/amerikachi/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, threadpoolctl, sympy, smmap, setproctitle, sentry-sdk, scipy, requests, rdkit, pyyaml, protobuf, propcache, opt-einsum, multidict, mashumaro, llvmlite, lightning-utilities, joblib, gemmi, fsspec, frozenlist, frozendict, einops, docker-pycreds, click, biopython, attrs, aiohappyeyeballs, yarl, torch, 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 /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages, outside environment /Users/amerikachi/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 /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages, outside environment /Users/amerikachi/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-0.5.1 cuequivariance_torch-0.5.1 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-2025.7.0 gemmi-0.6.5 gitdb-4.0.12 gitpython-3.1.45 hydra-core-1.3.2 joblib-1.5.1 lightning-utilities-0.15.0 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.6.3 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 sympy-1.14.0 threadpoolctl-3.6.0 torch-2.7.1 torchmetrics-1.8.0 tqdm-4.67.1 types- requests-2.32.4.20250611 wandb-0.18.7 yarl-1.20.1 [notice] A new release of pip is available: 24.0 -> 25.2 [notice] To update, run: /Users/amerikachi/boltz2/bin/python -m pip install --upgrade pip Downloading Boltz model parameters (4 GB) and chemical component database (1.8 GB) to ~/.boltz /Users/amerikachi/boltz2/bin/python /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/download_weights_and_ccd.py Downloading the CCD data to /Users/amerikachi/.boltz/mols.tar. This may take a bit of time. You may change the cache directory with the --cache flag. Extracting the CCD data to /Users/amerikachi/.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 /Users/amerikachi/.boltz/boltz2_conf.ckpt. You may change the cache directory with the --cache flag. Downloading the Boltz-2 affinity weights to /Users/amerikachi/.boltz/boltz2_aff.ckpt. You may change the cache directory with the --cache flag. Making CCD atom counts table for 45227 in /Users/amerikachi/.boltz/mols Boltz model parameters and CCD database are installed in ~/.boltz Successfully installed Boltz. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py", line 280, in _add_molecule self._molecules_table = mt = MoleculesTable(parent, comps) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py", line 1005, in __init__ ItemTable.__init__(self, parent = parent, allow_user_sorting = False, auto_multiline_headers = False) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_table.py", line 323, in __init__ self.setSizeAdjustPolicy(self.AdjustToContents) ^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'MoleculesTable' object has no attribute 'AdjustToContents' AttributeError: 'MoleculesTable' object has no attribute 'AdjustToContents' File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_table.py", line 323, in __init__ self.setSizeAdjustPolicy(self.AdjustToContents) ^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py", line 280, in _add_molecule self._molecules_table = mt = MoleculesTable(parent, comps) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py", line 1005, in __init__ ItemTable.__init__(self, parent = parent, allow_user_sorting = False, auto_multiline_headers = False) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_table.py", line 323, in __init__ self.setSizeAdjustPolicy(self.AdjustToContents) ^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'MoleculesTable' object has no attribute 'AdjustToContents' AttributeError: 'MoleculesTable' object has no attribute 'AdjustToContents' File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_table.py", line 323, in __init__ self.setSizeAdjustPolicy(self.AdjustToContents) ^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py", line 280, in _add_molecule self._molecules_table = mt = MoleculesTable(parent, comps) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/boltz/boltz_gui.py", line 1005, in __init__ ItemTable.__init__(self, parent = parent, allow_user_sorting = False, auto_multiline_headers = False) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_table.py", line 323, in __init__ self.setSizeAdjustPolicy(self.AdjustToContents) ^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'MoleculesTable' object has no attribute 'AdjustToContents' AttributeError: 'MoleculesTable' object has no attribute 'AdjustToContents' File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/widgets/item_table.py", line 323, in __init__ self.setSizeAdjustPolicy(self.AdjustToContents) ^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PySide6 6.9.1, Qt 6.9.1 Qt runtime version: 6.9.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AU00299LL/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6 (24G84) Kernel Version: Darwin 24.6.0 Time since boot: 1 hour, 11 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 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: 4.13.4 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2025.7.14 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: 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: 1.60.10 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: 1.5.1 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: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.dev202508010600 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: 1.9.1 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: 2.15 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.1 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-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: 1.47 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.1 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 contourpy: 1.3.3 coverage: 7.10.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.2 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: 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 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: 25.2 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 PySide6: 6.9.1 PySide6_Addons: 6.9.1 PySide6_Essentials: 6.9.1 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: 2.32.4 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 shiboken6: 6.9.1 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: 6.5.1 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 , 3 months ago
Cc: | added |
---|---|
Component: | Unassigned → Window Toolkit |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → PySide6: AttributeError: 'MoleculesTable' object has no attribute 'AdjustToContents' |
comment:2 by , 2 months ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
Fixed with new qtshim that promotes enums on PySide6 like it does for PyQt6. Use a newer daily build which uses PyQt6 or use the techpreview that has the new qtshim.
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