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#18611 closed defect (fixed)

Boltz tool: wrapped C/C++ object of type QFrame has been deleted

Reported by:	Mahmoud.ragab@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Structure Prediction	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC)
Description
RuntimeError: wrapped C/C++ object of type QFrame has been deleted Error processing trigger "new frame": RuntimeError: wrapped C/C++ object of type QFrame has been deleted 

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  

> ui tool show Boltz

> boltz install C:\Users\MAHMOUDRAGAB/boltz

Successfully created Boltz Python virtual environment
C:\Users\MAHMOUDRAGAB/boltz.  
Now installing Boltz and required packages from PyPi. This may take tens of of
minutes since Boltz uses many other packages totaling about 1 Gbyte of disk
space including torch, scipy, rdkit, llvmlite, sympy, pandas, numpy, wandb,
numba...  
C:\Users\MAHMOUDRAGAB/boltz\Scripts\python.exe -m pip install
git+https://github.com/RBVI/boltz@chimerax  
Collecting git+https://github.com/RBVI/boltz@chimerax  
  
Cloning https://github.com/RBVI/boltz (to revision chimerax) to
c:\users\mahmoudragab\appdata\local\temp\pip-req-build-md3br9q0  
  
Running command git clone --filter=blob:none --quiet
https://github.com/RBVI/boltz 'C:\Users\MAHMOUDRAGAB\AppData\Local\Temp\pip-
req-build-md3br9q0'  
  
Running command git checkout -b chimerax --track origin/chimerax  
  
branch 'chimerax' set up to track 'origin/chimerax'.  
  
Switched to a new branch 'chimerax'  
  
Resolved https://github.com/RBVI/boltz to commit
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-cp311-win_amd64.whl (241.4 MB)  
  
\------------------------------------ 241.4/241.4 MB 928.6 kB/s eta 0:00:00  
  
Requirement already satisfied: numpy<2.0,>=1.26 in c:\program files\chimerax
1.10\bin\lib\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 1.2 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 1.1 MB/s eta 0:00:00  
  
Collecting rdkit>=2024.3.2 (from boltz==1.0.0)  
  
Downloading rdkit-2025.3.5-cp311-cp311-win_amd64.whl (23.5 MB)  
  
\-------------------------------------- 23.5/23.5 MB 830.5 kB/s eta 0:00:00  
  
Collecting dm-tree==0.1.8 (from boltz==1.0.0)  
  
Downloading dm_tree-0.1.8-cp311-cp311-win_amd64.whl (101 kB)  
  
\-------------------------------------- 101.3/101.3 kB 1.4 MB/s eta 0:00:00  
  
Requirement already satisfied: requests==2.32.3 in c:\program files\chimerax
1.10\bin\lib\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-win_amd64.whl (11.3 MB)  
  
\---------------------------------------- 11.3/11.3 MB 1.4 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 1.1 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 1.2 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 1.2 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 1.0 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 912.2 kB/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-win_amd64.whl (15.5 MB)  
  
\---------------------------------------- 15.5/15.5 MB 1.1 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 1.4 MB/s eta 0:00:00  
  
Collecting pyyaml==6.0.2 (from boltz==1.0.0)  
  
Downloading PyYAML-6.0.2-cp311-cp311-win_amd64.whl (161 kB)  
  
\-------------------------------------- 162.0/162.0 kB 1.2 MB/s eta 0:00:00  
  
Collecting biopython==1.84 (from boltz==1.0.0)  
  
Downloading biopython-1.84-cp311-cp311-win_amd64.whl (2.8 MB)  
  
\---------------------------------------- 2.8/2.8 MB 872.7 kB/s eta 0:00:00  
  
Collecting scipy==1.13.1 (from boltz==1.0.0)  
  
Downloading scipy-1.13.1-cp311-cp311-win_amd64.whl (46.2 MB)  
  
\---------------------------------------- 46.2/46.2 MB 1.3 MB/s eta 0:00:00  
  
Collecting numba==0.61.0 (from boltz==1.0.0)  
  
Downloading numba-0.61.0-cp311-cp311-win_amd64.whl (2.8 MB)  
  
\---------------------------------------- 2.8/2.8 MB 2.1 MB/s eta 0:00:00  
  
Requirement already satisfied: colorama in c:\program files\chimerax
1.10\bin\lib\site-packages (from click==8.1.7->boltz==1.0.0) (0.4.6)  
  
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 1.2 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 887.9 kB/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 1.1 MB/s eta 0:00:00  
  
Preparing metadata (setup.py): started  
  
Preparing metadata (setup.py): finished with status 'done'  
  
Requirement already satisfied: packaging in c:\program files\chimerax
1.10\bin\lib\site-packages (from hydra-core==1.3.2->boltz==1.0.0) (24.2)  
  
Requirement already satisfied: typing-extensions>=4.1.0 in c:\program
files\chimerax 1.10\bin\lib\site-packages (from mashumaro==3.14->boltz==1.0.0)
(4.14.0)  
  
Requirement already satisfied: ihm>=1.7 in c:\program files\chimerax
1.10\bin\lib\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-win_amd64.whl (30.3 MB)  
  
\---------------------------------------- 30.3/30.3 MB 1.7 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 4.3 MB/s eta 0:00:00  
  
Collecting fsspec[http]>=2022.5.0 (from pytorch-
lightning==2.4.0->boltz==1.0.0)  
  
Downloading fsspec-2025.7.0-py3-none-any.whl (199 kB)  
  
\-------------------------------------- 199.6/199.6 kB 1.7 MB/s eta 0:00:00  
  
Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)  
  
Downloading torchmetrics-1.8.1-py3-none-any.whl (982 kB)  
  
\-------------------------------------- 983.0/983.0 kB 1.8 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 c:\program
files\chimerax 1.10\bin\lib\site-packages (from
requests==2.32.3->boltz==1.0.0) (3.4.2)  
  
Requirement already satisfied: idna<4,>=2.5 in c:\program files\chimerax
1.10\bin\lib\site-packages (from requests==2.32.3->boltz==1.0.0) (3.10)  
  
Requirement already satisfied: urllib3<3,>=1.21.1 in c:\program files\chimerax
1.10\bin\lib\site-packages (from requests==2.32.3->boltz==1.0.0) (2.5.0)  
  
Requirement already satisfied: certifi>=2017.4.17 in c:\program files\chimerax
1.10\bin\lib\site-packages (from requests==2.32.3->boltz==1.0.0) (2025.6.15)  
  
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)  
  
\-------------------------------------- 208.2/208.2 kB 1.8 MB/s eta 0:00:00  
  
Requirement already satisfied: platformdirs in c:\program files\chimerax
1.10\bin\lib\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-cp310-abi3-win_amd64.whl (434 kB)  
  
\-------------------------------------- 434.8/434.8 kB 1.7 MB/s eta 0:00:00  
  
Requirement already satisfied: psutil>=5.0.0 in c:\program files\chimerax
1.10\bin\lib\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-2.35.0-py2.py3-none-any.whl (363 kB)  
  
\-------------------------------------- 363.8/363.8 kB 2.1 MB/s eta 0:00:00  
  
Collecting setproctitle (from wandb==0.18.7->boltz==1.0.0)  
  
Downloading setproctitle-1.3.6-cp311-cp311-win_amd64.whl (12 kB)  
  
Requirement already satisfied: setuptools in
c:\users\mahmoudragab\boltz\lib\site-packages (from
wandb==0.18.7->boltz==1.0.0) (65.5.0)  
  
Requirement already satisfied: python-dateutil>=2.8.2 in c:\program
files\chimerax 1.10\bin\lib\site-packages (from pandas>=2.2.2->boltz==1.0.0)
(2.9.0.post0)  
  
Requirement already satisfied: pytz>=2020.1 in c:\program files\chimerax
1.10\bin\lib\site-packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2)  
  
Requirement already satisfied: tzdata>=2022.7 in c:\program files\chimerax
1.10\bin\lib\site-packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2)  
  
Requirement already satisfied: Pillow in c:\program files\chimerax
1.10\bin\lib\site-packages (from rdkit>=2024.3.2->boltz==1.0.0) (10.4.0)  
  
Requirement already satisfied: filelock in c:\program files\chimerax
1.10\bin\lib\site-packages (from torch>=2.2->boltz==1.0.0) (3.18.0)  
  
Requirement already satisfied: networkx in c:\program files\chimerax
1.10\bin\lib\site-packages (from torch>=2.2->boltz==1.0.0) (3.3)  
  
Requirement already satisfied: jinja2 in c:\program files\chimerax
1.10\bin\lib\site-packages (from torch>=2.2->boltz==1.0.0) (3.1.6)  
  
Requirement already satisfied: six>=1.4.0 in c:\program files\chimerax
1.10\bin\lib\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-win_amd64.whl (453 kB)  
  
\-------------------------------------- 453.3/453.3 kB 2.2 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 1.7 MB/s eta 0:00:00  
  
Requirement already satisfied: msgpack in c:\program files\chimerax
1.10\bin\lib\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 2.1 MB/s eta 0:00:00  
  
Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax
1.10\bin\lib\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 1.7 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-win_amd64.whl (44 kB)  
  
\---------------------------------------- 44.0/44.0 kB 2.1 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-win_amd64.whl (46 kB)  
  
\---------------------------------------- 46.0/46.0 kB 2.2 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-win_amd64.whl (41 kB)  
  
\---------------------------------------- 41.5/41.5 kB 2.0 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-win_amd64.whl (86 kB)  
  
\---------------------------------------- 86.7/86.7 kB 1.6 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=152119
sha256=62aa0ebdc5fdd11d10c988509005470d516ca2b1d35454af425c90e3411966bb  
  
Stored in directory: C:\Users\MAHMOUDRAGAB\AppData\Local\Temp\pip-ephem-wheel-
cache-511q3ajt\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=332216
sha256=ff1fd62df71b5a08087b344edb1b563fe7e7db69608a1e7a2387c264e4ab28f9  
  
Stored in directory:
c:\users\mahmoudragab\appdata\local\pip\cache\wheels\95\ef\96\5044bde220b2ea299bdc6ec05051e0ef187fad45b341d1c273  
  
Building wheel for modelcif (setup.py): started  
  
Building wheel for modelcif (setup.py): finished with status 'done'  
  
Created wheel for modelcif: filename=modelcif-1.2-py3-none-any.whl size=41204
sha256=a0ccb3978507d15afb225302950599cd13012bf72165ceb7ee2c1f3c5f7ec028  
  
Stored in directory:
c:\users\mahmoudragab\appdata\local\pip\cache\wheels\d2\3a\8c\e28cb28a15568d1b1b6163c77c945a5961351340fd15b9b4df  
  
Building wheel for antlr4-python3-runtime (setup.py): started  
  
Building wheel for antlr4-python3-runtime (setup.py): finished with status
'done'  
  
Created wheel for antlr4-python3-runtime:
filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144577
sha256=a90c50ac98c4d149190c2c2a2b9705c5559b4cbf63b18b76a6fdfcfdc8cab2e4  
  
Stored in directory:
c:\users\mahmoudragab\appdata\local\pip\cache\wheels\1a\97\32\461f837398029ad76911109f07047fde1d7b661a147c7c56d1  
  
Successfully built boltz fairscale modelcif antlr4-python3-runtime  
  
Installing collected packages: mpmath, dm-tree, antlr4-python3-runtime, types-
requests, tqdm, sympy, smmap, setproctitle, sentry-sdk, 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 c:\program files\chimerax 1.10\bin\lib\site-
packages, outside environment C:\Users\MAHMOUDRAGAB\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-2025.7.0
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-2025.3.5 scipy-1.13.1 sentry-
sdk-2.35.0 setproctitle-1.3.6 smmap-5.0.2 sympy-1.14.0 torch-2.8.0
torchmetrics-1.8.1 tqdm-4.67.1 types-requests-2.32.4.20250809 wandb-0.18.7
yarl-1.20.1  
  
  
  
[notice] A new release of pip is available: 23.1.2 -> 25.2  
  
[notice] To update, run: C:\Users\MAHMOUDRAGAB\boltz\Scripts\python.exe -m pip
install --upgrade pip  
  
Successfully installed Boltz.  
Downloading Boltz model parameters (3.3 GB) and chemical component database
(330 MB) to ~/.boltz  
C:\Users\MAHMOUDRAGAB/boltz\Scripts\python.exe C:\Program Files\ChimeraX
1.10\bin\Lib\site-packages\chimerax\boltz\download_weights_and_ccd.py  
Downloading the CCD dictionary to C:\Users\MAHMOUDRAGAB\\.boltz\ccd.pkl. You
may change the cache directory with the --cache flag.  
  
Downloading the model weights to
C:\Users\MAHMOUDRAGAB\\.boltz\boltz1_conf.ckpt. You may change the cache
directory with the --cache flag.  
  

> open 1err format mmcif fromDatabase pdb

1err title:  
Human estrogen receptor ligand-binding domain In complex with raloxifene [more
info...]  
  
Chain information for 1err #1  
---  
Chain | Description | UniProt  
A B | ESTROGEN RECEPTOR | ESR1_HUMAN 301-553  
  
Non-standard residues in 1err #1  
---  
RAL — raloxifene  
  
63 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close session

> ui tool show Boltz

Boltz model parameters and CCD database are installed in ~/.boltz  
Successfully installed Boltz.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\boltz\install.py", line 264, in _log_queued_lines  
self._finished()  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\boltz\install.py", line 270, in _finished  
self._finished_callback(success)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\boltz\install.py", line 208, in
_finished_download_weights_and_ccd  
self._finished('download weights and ccd', success)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\boltz\install.py", line 225, in _finished  
self.finished_callback(success)  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\boltz\boltz_gui.py", line 792, in _boltz_install_finished  
layout = self._button_row.layout()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
Error processing trigger "new frame":  
RuntimeError: wrapped C/C++ object of type QFrame has been deleted  
  
File "C:\Program Files\ChimeraX 1.10\bin\Lib\site-
packages\chimerax\boltz\boltz_gui.py", line 792, in _boltz_install_finished  
layout = self._button_row.layout()  
^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 10.18.10.4252
OpenGL renderer: Intel(R) HD Graphics 4000
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: Hewlett-Packard
Model: HP Pavilion g6 Notebook PC
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 8,483,348,480
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-3632QM CPU @ 2.20GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    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: 2025.6.15
    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-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
    comtypes: 1.4.10
    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
    narwhals: 1.48.1
    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: 2.2.6
    numpy: 1.26.4
    nvidia-cuda-cupti-cu12: 12.9.79
    nvidia-cuda-nvcc-cu12: 12.9.86
    nvidia-cuda-nvrtc-cu12: 12.9.86
    nvidia-cuda-runtime-cu12: 12.9.79
    nvidia-cufft-cu12: 11.4.1.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.2.0
    OpenMM-CUDA-12: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    plotly: 6.0.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pyKVFinder: 0.8.1
    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
    pywin32: 310
    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
    tomlkit: 0.13.2
    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
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 8 weeks ago

Component:	Unassigned → Structure Prediction
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Boltz tool: wrapped C/C++ object of type QFrame has been deleted

comment:2 by Tom Goddard, 8 weeks ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

This error while installing Boltz is harmless. It installed correctly. I've fixed the problem that caused the error. It happened because Boltz installation was in progress and you closed the ChimeraX session which removed the Boltz user interface panel. When the Boltz installation finished it notified the Boltz user interface and that caused an error because the interface was gone.

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