glClear: invalid framebuffer operation on statusbar expose

[s.lott@…]

The following bug report has been submitted:
Platform:        macOS-26.3-arm64-arm-64bit
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
I wasn't doing anything... 🤷🏻‍♂️

Log:
UCSF ChimeraX version: 1.10 (2025-06-26)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/jlot006/Documents/RNAseHI/Neisseria/apo_structure/Kate_Apo_0711_refine_004_refmac27.pdb

Kate_Apo_0711_refine_004_refmac27.pdb title:  
\--- [more info...]  
  
Chain information for Kate_Apo_0711_refine_004_refmac27.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Non-standard residues in Kate_Apo_0711_refine_004_refmac27.pdb #1  
---  
ACT — (ACT)  
NA — (NA)  
SO4 — (SO4)  
  
229 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> select :tyr

96 atoms, 96 bonds, 8 residues, 1 model selected  

> show sel target ab

> style sel sphere

Changed 96 atom styles  

> style sel stick

Changed 96 atom styles  

> color sel lime

> select clear

> style stick

Changed 2510 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> style sphere

Changed 2510 atom styles  

> style sphere

Changed 2510 atom styles  

> style stick

Changed 2510 atom styles  

> hide surfaces

> hide cartoons

> hide atoms

> show cartoons

> select :trp

196 atoms, 210 bonds, 14 residues, 1 model selected  

> style sel stick

Changed 196 atom styles  

> show sel atoms

> color sel hot pink

> select :A

Nothing selected  

> select :all.a

Expected an objects specifier or a keyword  

> select chain a

Expected an objects specifier or a keyword  

> select :.A

Expected an objects specifier or a keyword  

> select /A

1082 atoms, 1104 bonds, 1 pseudobond, 139 residues, 2 models selected  

> hide sel atoms

> hide sel cartoons

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> select add #1.1

1082 atoms, 1104 bonds, 2 pseudobonds, 139 residues, 3 models selected  

> select subtract #1.1

1082 atoms, 1104 bonds, 1 pseudobond, 139 residues, 2 models selected  

> select add #1.1

1082 atoms, 1104 bonds, 2 pseudobonds, 139 residues, 3 models selected  

> select subtract #1.1

1082 atoms, 1104 bonds, 1 pseudobond, 139 residues, 2 models selected  

> select add #1.2

1082 atoms, 1104 bonds, 2 pseudobonds, 139 residues, 2 models selected  

> select subtract #1.2

1082 atoms, 1104 bonds, 139 residues, 1 model selected  

> hide #1.2 models

> select ::name="ASP"

125 atoms, 113 bonds, 16 residues, 1 model selected  

> style sel stick

Changed 125 atom styles  

> show sel atoms

> hide sel atoms

> show sel atoms

[Repeated 1 time(s)]

> show (sel-residues & sidechain) target ab

> hide sel atoms

> show (sel-residues & sidechain) target ab

> select add #1.2

125 atoms, 113 bonds, 2 pseudobonds, 16 residues, 2 models selected  

> select subtract #1.2

125 atoms, 113 bonds, 16 residues, 1 model selected  

> show #1.2 models

> select add #1.2

125 atoms, 113 bonds, 2 pseudobonds, 16 residues, 2 models selected  

> select subtract #1.2

125 atoms, 113 bonds, 16 residues, 1 model selected  

> ui tool show Boltz

> boltz install /Users/jlot006/boltz

Successfully created Boltz Python virtual environment /Users/jlot006/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/jlot006/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/mz/p2r_565j1y19w67c2j7lf_d00000gs/T/pip-req-build-
_z8n1tet  
  
Running command git clone --filter=blob:none --quiet
https://github.com/RBVI/boltz
/private/var/folders/mz/p2r_565j1y19w67c2j7lf_d00000gs/T/pip-req-build-
_z8n1tet  
  
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-2.12.0-cp311-cp311-macosx_14_0_arm64.whl (88.0 MB)  
  
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Requirement already satisfied: numpy<2.0,>=1.26 in
/Applications/ChimeraX-1.10.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)  
  
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Collecting pytorch-lightning==2.4.0 (from boltz==1.0.0)  
  
Downloading pytorch_lightning-2.4.0-py3-none-any.whl (815 kB)  
  
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Collecting rdkit>=2024.3.2 (from boltz==1.0.0)  
  
Downloading rdkit-2026.3.1-cp311-cp311-macosx_11_0_arm64.whl (29.9 MB)  
  
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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)  
  
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Requirement already satisfied: requests==2.32.3 in
/Applications/ChimeraX-1.10.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-3.0.3-cp311-cp311-macosx_11_0_arm64.whl (9.9 MB)  
  
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Collecting types-requests (from boltz==1.0.0)  
  
Downloading types_requests-2.33.0.20260513-py3-none-any.whl (21 kB)  
  
Collecting einops==0.8.0 (from boltz==1.0.0)  
  
Downloading einops-0.8.0-py3-none-any.whl (43 kB)  
  
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Collecting einx==0.3.0 (from boltz==1.0.0)  
  
Downloading einx-0.3.0-py3-none-any.whl (102 kB)  
  
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Collecting fairscale==0.4.13 (from boltz==1.0.0)  
  
Downloading fairscale-0.4.13.tar.gz (266 kB)  
  
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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)  
  
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Collecting modelcif==1.2 (from boltz==1.0.0)  
  
Downloading modelcif-1.2.tar.gz (66 kB)  
  
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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)  
  
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Collecting click==8.1.7 (from boltz==1.0.0)  
  
Downloading click-8.1.7-py3-none-any.whl (97 kB)  
  
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Collecting pyyaml==6.0.2 (from boltz==1.0.0)  
  
Downloading PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB)  
  
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Collecting biopython==1.84 (from boltz==1.0.0)  
  
Downloading biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB)  
  
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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)  
  
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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)  
  
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Collecting sympy (from einx==0.3.0->boltz==1.0.0)  
  
Downloading sympy-1.14.0-py3-none-any.whl (6.3 MB)  
  
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Collecting frozendict (from einx==0.3.0->boltz==1.0.0)  
  
Downloading frozendict-2.4.7-py3-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)  
  
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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)  
  
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Preparing metadata (setup.py): started  
  
Preparing metadata (setup.py): finished with status 'done'  
  
Requirement already satisfied: packaging in
/Applications/ChimeraX-1.10.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages (from mashumaro==3.14->boltz==1.0.0) (4.14.0)  
  
Requirement already satisfied: ihm>=1.7 in
/Applications/ChimeraX-1.10.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)  
  
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Collecting tqdm>=4.57.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)  
  
Downloading tqdm-4.67.3-py3-none-any.whl (78 kB)  
  
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Collecting fsspec[http]>=2022.5.0 (from pytorch-
lightning==2.4.0->boltz==1.0.0)  
  
Downloading fsspec-2026.4.0-py3-none-any.whl (203 kB)  
  
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Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)  
  
Downloading torchmetrics-1.9.0-py3-none-any.whl (983 kB)  
  
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Collecting lightning-utilities>=0.10.0 (from pytorch-
lightning==2.4.0->boltz==1.0.0)  
  
Downloading lightning_utilities-0.15.3-py3-none-any.whl (31 kB)  
  
Requirement already satisfied: charset-normalizer<4,>=2 in
/Applications/ChimeraX-1.10.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.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.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.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-3.1.50-py3-none-any.whl (212 kB)  
  
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Requirement already satisfied: platformdirs in
/Applications/ChimeraX-1.10.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-5.29.6-cp38-abi3-macosx_10_9_universal2.whl (418 kB)  
  
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Requirement already satisfied: psutil>=5.0.0 in
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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-2.60.0-py3-none-any.whl (475 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/jlot006/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
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packages (from pandas>=2.2.2->boltz==1.0.0) (2.9.0.post0)  
  
Requirement already satisfied: Pillow in
/Applications/ChimeraX-1.10.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.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>=2.5.1 in
/Applications/ChimeraX-1.10.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.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.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-3.13.5-cp311-cp311-macosx_11_0_arm64.whl (501 kB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 501.7/501.7 kB 6.8 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)  
  
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Requirement already satisfied: msgpack in
/Applications/ChimeraX-1.10.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 9.3 MB/s eta 0:00:00  
  
Requirement already satisfied: MarkupSafe>=2.0 in
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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-26.1.0-py3-none-any.whl (67 kB)  
  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 67.5/67.5 kB 7.5 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-1.8.0-cp311-cp311-macosx_11_0_arm64.whl (50 kB)  
  
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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-6.7.1-cp311-cp311-macosx_11_0_arm64.whl (44 kB)  
  
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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-0.5.2-cp311-cp311-macosx_11_0_arm64.whl (52 kB)  
  
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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-1.23.0-cp311-cp311-macosx_11_0_arm64.whl (85 kB)  
  
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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-5.0.3-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=6cf3d9748331e41e66236c9890f59585cd5b11c6b54769af5d5ac51ff5f87b51  
  
Stored in directory:
/private/var/folders/mz/p2r_565j1y19w67c2j7lf_d00000gs/T/pip-ephem-wheel-
cache-
pcw0cl0x/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=332207
sha256=e81cb5afaaccec89b1f02655adc2eb32a4df55b63217ebed497098cbf63f7fc2  
  
Stored in directory:
/Users/jlot006/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=9ce1031bfa88980ff758ea72f9bc24911520e823284a0b565302a4ff96eae869  
  
Stored in directory:
/Users/jlot006/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=97a42b91c3cb25940d7e4f2f92ea35c4aba6db9636bfceee2aabbd398192f2a3  
  
Stored in directory:
/Users/jlot006/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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages, outside environment /Users/jlot006/boltz  
  
Can't uninstall 'scipy'. No files were found to uninstall.  
  
Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.13.5 aiosignal-1.4.0
antlr4-python3-runtime-4.9.3 attrs-26.1.0 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-2.4.7 frozenlist-1.8.0 fsspec-2026.4.0
gitdb-4.0.12 gitpython-3.1.50 hydra-core-1.3.2 lightning-utilities-0.15.3
llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.7.1
numba-0.61.0 omegaconf-2.3.0 pandas-3.0.3 propcache-0.5.2 protobuf-5.29.6
pytorch-lightning-2.4.0 pyyaml-6.0.2 rdkit-2026.3.1 scipy-1.13.1 sentry-
sdk-2.60.0 setproctitle-1.3.7 smmap-5.0.3 sympy-1.14.0 torch-2.12.0
torchmetrics-1.9.0 tqdm-4.67.3 types-requests-2.33.0.20260513 wandb-0.18.7
yarl-1.23.0  
  
  
  
[notice] A new release of pip is available: 23.1.2 -> 26.1.1  
  
[notice] To update, run: /Users/jlot006/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/jlot006/boltz/bin/python
/Applications/ChimeraX-1.10.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/jlot006/.boltz/ccd.pkl. You may
change the cache directory with the --cache flag.  
  
Downloading the model weights to /Users/jlot006/.boltz/boltz1_conf.ckpt. You
may change the cache directory with the --cache flag.  
  

> ui tool show AlphaFold

> alphafold predict #1/A

Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.  
Running AlphaFold prediction  

> select :.A

Expected an objects specifier or a keyword  

> select :.A

Expected an objects specifier or a keyword  

> select :.A

Expected an objects specifier or a keyword  

> select :.A

Expected an objects specifier or a keyword  
Running AlphaFold prediction  
AlphaFold prediction finished  
Results in /Users/jlot006/Downloads/ChimeraX/AlphaFold/prediction_1  

> open /Users/jlot006/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb

AlphaFold prediction matching Kate_Apo_0711_refine_004_refmac27.pdb #1/A  
---  
Chain| RMSD| Length| Seen| % Id  
A | 1.85 | 138 | 138 | 100   
  
Cannot make a prediction until Boltz installation finishes.  
Boltz model parameters and CCD database are installed in ~/.boltz  
Successfully installed Boltz.  
No Boltz prediction has been run.  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event  
self.status(self._last_message, self._last_color)  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status  
r.draw_background()  
File
"/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Max
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 Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14Z000TLX/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 Performance and 2 Efficiency)
      Memory: 32 GB
      System Firmware Version: 13822.81.10
      OS Loader Version: 13822.81.10

Software:

    System Software Overview:

      System Version: macOS 26.3 (25D125)
      Kernel Version: Darwin 25.3.0
      Time since boot: 36 days, 21 hours, 44 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 4
      Displays:
        2352:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          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
    auditwheel: 6.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.5.0
    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: 14.1.18
    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-Clipper: 0.25.2
    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
    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: 1.1.2
    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: 1.2.1
    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: 7.9.1
    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: 4.58.4
    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: 4.4.4
    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
    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: 8.4.1
    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: 4.14.0
    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

[Eric Pettersen]

Reported by Shaun

[Tom Goddard]

This ChimeraX error on Mac is caused by a Qt window toolkit bug. We put a work-around in the current ChimeraX 1.12 release candidate and daily build.