Boltz structures distorted

[dominik.oberthuer@…]

The following bug report has been submitted:
Platform:        macOS-14.7.6-arm64-arm-64bit
ChimeraX Version: 1.10rc202506032143 (2025-06-03 21:43:02 UTC)
Description
I'm playing around with boltz in chimera and all the resulting molecules look strangely squeezed together. I tried with various proteins and it always looks completely messed up. If I do the same sequence in the boltz colab I do not have this issue.

OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: 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: Mac14,9
      Model Number: Z17G0012PD/A
      Chip: Apple M2 Pro
      Total Number of Cores: 10 (6 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.6 (23H626)
      Kernel Version: Darwin 23.6.0
      Time since boot: 17 days, 23 hours, 22 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U3223QE:
          Resolution: 6720 x 3780
          UI Looks like: 3360 x 1890 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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[Tom Goddard]

Can you attach a Boltz predicted structure that appears distorted? I have not seen that in dozens of predictions. And could you tell me the sequences and ligands so I can run it myself to see if I also get a distorted structure?

We don't develop Boltz so it may be something that needs to be reported to the Boltz developers.

[dominik.oberthuer@…]

Hi Tom,

thanks for looking into it!

Attached are the Boltz-Colab structure and the chimera-boltz-Structure
and the sequence. The Colab-structure looks as expected (can be used for
molecular replacement).

I could also send you other examples, because it is happening for almost
all proteins so far.

Cheers, Dominik

protein1_colab.cif​

protein1_chimera.cif​

protein1.fasta​

[dominik.oberthuer@…]

Added by email2trac

[dominik.oberthuer@…]

Added by email2trac

[dominik.oberthuer@…]

Added by email2trac

[dominik.oberthuer@…]

Hi Tom,

this for example is lysozyme.

Cheers, Dominik

lysozyme_model_0.cif​

[dominik.oberthuer@…]

Added by email2trac

[Tom Goddard]

Hi Dominik,

Thanks for the files. My Mac M2 machine predicts your protein1.fasta sequence producing a very reasonable looking protein with ChimeraX Boltz. Your protein1_chimera.cif has all the residues within a few Angstroms of the origin. I'll attach the correct prediction.

So something is probably broken with your Boltz installation. Maybe the Boltz network parameters (in ~/.boltz) are corrupted. I suggest you reinstall Boltz. Delete directories ~/boltz and ~/.boltz that ChimeraX created, then start the ChimeraX Boltz tool (menu Tools / Structure Prediction / Boltz) and press the "Install Boltz" button that should appear at the bottom of the Boltz panel. After it has installed Boltz try your protein1.fasta prediction again.

Let me know if that fixes the problem.

Tom

[dominik.oberthuer@…]

Hi Tom,

thanks!

Will try that!

Dominik

[dominik.oberthuer@…]

Hi Tom,

I re-installed twice. Problem persists. Here is the install log:

Successfully created Boltz Python virtual environment /Users/dobertr/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/dobertr/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/7r/r953prcj6dv89f_b28f_4jyw0000gp/T/pip-req-build-3ab1m_29

Running command git clone --filter=blob:none --quiet ​https://github.com/RBVI/boltz /private/var/folders/7r/r953prcj6dv89f_b28f_4jyw0000gp/T/pip-req-build-3ab1m_29

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)

Using cached torch-2.7.1-cp311-none-macosx_11_0_arm64.whl (68.6 MB)

Requirement already satisfied: numpy<2.0,>=1.26 in /Applications/ChimeraX-1.10-rc2025.06.04.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)

Using cached hydra_core-1.3.2-py3-none-any.whl (154 kB)

Collecting pytorch-lightning==2.4.0 (from boltz==1.0.0)

Using cached pytorch_lightning-2.4.0-py3-none-any.whl (815 kB)

Collecting rdkit>=2024.3.2 (from boltz==1.0.0)

Using cached rdkit-2025.3.2-cp311-cp311-macosx_11_0_arm64.whl (28.0 MB)

Collecting dm-tree==0.1.8 (from boltz==1.0.0)

Using cached dm_tree-0.1.8-cp311-cp311-macosx_11_0_arm64.whl (110 kB)

Requirement already satisfied: requests==2.32.3 in /Applications/ChimeraX-1.10-rc2025.06.04.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)

Using cached pandas-2.3.0-cp311-cp311-macosx_11_0_arm64.whl (10.8 MB)

Collecting types-requests (from boltz==1.0.0)

Using cached types_requests-2.32.0.20250602-py3-none-any.whl (20 kB)

Collecting einops==0.8.0 (from boltz==1.0.0)

Using cached einops-0.8.0-py3-none-any.whl (43 kB)

Collecting einx==0.3.0 (from boltz==1.0.0)

Using cached einx-0.3.0-py3-none-any.whl (102 kB)

Collecting fairscale==0.4.13 (from boltz==1.0.0)

Using cached fairscale-0.4.13-py3-none-any.whl

Collecting mashumaro==3.14 (from boltz==1.0.0)

Using cached mashumaro-3.14-py3-none-any.whl (92 kB)

Collecting modelcif==1.2 (from boltz==1.0.0)

Using cached modelcif-1.2-py3-none-any.whl

Collecting wandb==0.18.7 (from boltz==1.0.0)

Using cached wandb-0.18.7-py3-none-macosx_11_0_arm64.whl (15.2 MB)

Collecting click==8.1.7 (from boltz==1.0.0)

Using cached click-8.1.7-py3-none-any.whl (97 kB)

Collecting pyyaml==6.0.2 (from boltz==1.0.0)

Using cached PyYAML-6.0.2-cp311-cp311-macosx_11_0_arm64.whl (172 kB)

Collecting biopython==1.84 (from boltz==1.0.0)

Using cached biopython-1.84-cp311-cp311-macosx_11_0_arm64.whl (2.7 MB)

Collecting scipy==1.13.1 (from boltz==1.0.0)

Using cached scipy-1.13.1-cp311-cp311-macosx_12_0_arm64.whl (30.3 MB)

Collecting numba==0.61.0 (from boltz==1.0.0)

Using cached numba-0.61.0-cp311-cp311-macosx_11_0_arm64.whl (2.8 MB)

Collecting sympy (from einx==0.3.0->boltz==1.0.0)

Using cached sympy-1.14.0-py3-none-any.whl (6.3 MB)

Collecting frozendict (from einx==0.3.0->boltz==1.0.0)

Using cached 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)

Using cached omegaconf-2.3.0-py3-none-any.whl (79 kB)

Collecting antlr4-python3-runtime==4.9.* (from hydra-core==1.3.2->boltz==1.0.0)

Using cached antlr4_python3_runtime-4.9.3-py3-none-any.whl

Requirement already satisfied: packaging in /Applications/ChimeraX-1.10-rc2025.06.04.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-rc2025.06.04.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-rc2025.06.04.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)

Using cached llvmlite-0.44.0-cp311-cp311-macosx_11_0_arm64.whl (26.2 MB)

Collecting tqdm>=4.57.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)

Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)

Collecting fsspec[http]>=2022.5.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)

Using cached fsspec-2025.5.1-py3-none-any.whl (199 kB)

Collecting torchmetrics>=0.7.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)

Using cached torchmetrics-1.7.2-py3-none-any.whl (962 kB)

Collecting lightning-utilities>=0.10.0 (from pytorch-lightning==2.4.0->boltz==1.0.0)

Using cached lightning_utilities-0.14.3-py3-none-any.whl (28 kB)

Requirement already satisfied: charset-normalizer<4,>=2 in /Applications/ChimeraX-1.10-rc2025.06.04.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-rc2025.06.04.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-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from requests==2.32.3->boltz==1.0.0) (2.4.0)

Requirement already satisfied: certifi>=2017.4.17 in /Applications/ChimeraX-1.10-rc2025.06.04.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)

Using cached 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)

Using cached GitPython-3.1.44-py3-none-any.whl (207 kB)

Requirement already satisfied: platformdirs in /Applications/ChimeraX-1.10-rc2025.06.04.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)

Using cached protobuf-5.29.5-cp38-abi3-macosx_10_9_universal2.whl (418 kB)

Requirement already satisfied: psutil>=5.0.0 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from wandb==0.18.7->boltz==1.0.0) (7.0.0)

Collecting sentry-sdk>=2.0.0 (from wandb==0.18.7->boltz==1.0.0)

Using cached sentry_sdk-2.29.1-py2.py3-none-any.whl (341 kB)

Collecting setproctitle (from wandb==0.18.7->boltz==1.0.0)

Using cached setproctitle-1.3.6-cp311-cp311-macosx_11_0_arm64.whl (11 kB)

Requirement already satisfied: setuptools in /Users/dobertr/boltz/lib/python3.11/site-packages (from wandb==0.18.7->boltz==1.0.0) (65.5.0)

Requirement already satisfied: python-dateutil>=2.8.2 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==1.0.0) (2.9.0.post0)

Requirement already satisfied: pytz>=2020.1 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2)

Requirement already satisfied: tzdata>=2022.7 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from pandas>=2.2.2->boltz==1.0.0) (2025.2)

Requirement already satisfied: Pillow in /Applications/ChimeraX-1.10-rc2025.06.04.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-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from torch>=2.2->boltz==1.0.0) (3.18.0)

Requirement already satisfied: networkx in /Applications/ChimeraX-1.10-rc2025.06.04.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-rc2025.06.04.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-rc2025.06.04.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)

Using cached aiohttp-3.12.12-cp311-cp311-macosx_11_0_arm64.whl (469 kB)

Collecting gitdb<5,>=4.0.1 (from gitpython!=3.1.29,>=1.0.0->wandb==0.18.7->boltz==1.0.0)

Using cached gitdb-4.0.12-py3-none-any.whl (62 kB)

Requirement already satisfied: msgpack in /Applications/ChimeraX-1.10-rc2025.06.04.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)

Using cached mpmath-1.3.0-py3-none-any.whl (536 kB)

Requirement already satisfied: MarkupSafe>=2.0 in /Applications/ChimeraX-1.10-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages (from jinja2->torch>=2.2->boltz==1.0.0) (3.0.2)

Collecting aiohappyeyeballs>=2.5.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)

Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)

Collecting aiosignal>=1.1.2 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)

Using cached aiosignal-1.3.2-py2.py3-none-any.whl (7.6 kB)

Collecting attrs>=17.3.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)

Using cached attrs-25.3.0-py3-none-any.whl (63 kB)

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)

Using cached frozenlist-1.7.0-cp311-cp311-macosx_11_0_arm64.whl (47 kB)

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)

Using cached multidict-6.4.4-cp311-cp311-macosx_11_0_arm64.whl (37 kB)

Collecting propcache>=0.2.0 (from aiohttp!=4.0.0a0,!=4.0.0a1->fsspec[http]>=2022.5.0->pytorch-lightning==2.4.0->boltz==1.0.0)

Using cached propcache-0.3.2-cp311-cp311-macosx_11_0_arm64.whl (43 kB)

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)

Using cached yarl-1.20.1-cp311-cp311-macosx_11_0_arm64.whl (89 kB)

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)

Using cached smmap-5.0.2-py3-none-any.whl (24 kB)

Building wheels for collected packages: boltz

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=4bff148c95022886ca643c7269c3efbd835ed0d5920a108075583370fbdd8bb5

Stored in directory: /private/var/folders/7r/r953prcj6dv89f_b28f_4jyw0000gp/T/pip-ephem-wheel-cache-npc7eg89/wheels/cf/72/1c/bb985c095c0d1f3b385f30452dcb2ac8f404a8439c7b383eef

Successfully built boltz

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-rc2025.06.04.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages, outside environment /Users/dobertr/boltz

Can't uninstall 'scipy'. No files were found to uninstall.

Successfully installed aiohappyeyeballs-2.6.1 aiohttp-3.12.12 aiosignal-1.3.2 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-2025.5.1 gitdb-4.0.12 gitpython-3.1.44 hydra-core-1.3.2 lightning-utilities-0.14.3 llvmlite-0.44.0 mashumaro-3.14 modelcif-1.2 mpmath-1.3.0 multidict-6.4.4 numba-0.61.0 omegaconf-2.3.0 pandas-2.3.0 propcache-0.3.2 protobuf-5.29.5 pytorch-lightning-2.4.0 pyyaml-6.0.2 rdkit-2025.3.2 scipy-1.13.1 sentry-sdk-2.29.1 setproctitle-1.3.6 smmap-5.0.2 sympy-1.14.0 torch-2.7.1 torchmetrics-1.7.2 tqdm-4.67.1 types-requests-2.32.0.20250602 wandb-0.18.7 yarl-1.20.1

[notice] A new release of pip is available: 23.1.2 -> 25.1.1

[notice] To update, run: /Users/dobertr/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/dobertr/boltz/bin/python /Applications/ChimeraX-1.10-rc2025.06.04.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/dobertr/.boltz/ccd.pkl. You may change the cache directory with the --cache flag.

Downloading the model weights to /Users/dobertr/.boltz/boltz1_conf.ckpt. You may change the cache directory with the --cache flag.

Boltz model parameters and CCD database are installed in ~/.boltz
Successfully installed Boltz.

Dominik

[Tom Goddard]

Ok, so reinstalling boltz did not help. There is likely something installed on your computer that is effecting Boltz and messing up the predictions. No one else has reported this problem and there are probably at least 100 Mac ChimeraX Boltz users. Because the possiblities are so numerous it will be hard to figure out.

The next step would be to zip the entire directory of a ChimeraX Boltz run and send that. You also can look at the files stdout and stderr in that directory to see if you spot anything unusual, although there is lots of junk output so it will probably be hard for you to tell if something is unusual.

Other ideas for why it is broken for you include: You have some ChimeraX extension installed that installed a Python package that boltz uses but is a different version and breaks boltz. You have environment variables set for example for PyTorch by other machine learning packages and those break boltz.

[dominik.oberthuer@…]

Dear Tom,

I upgraded my Mac to macOs 15.5 and installed an empty version of 
ChimeraX (latest built, no plug-ins) and it works.

Cheers, Dominik

On 10.06.25 19:51, ChimeraX wrote:
>
>
>

[Tom Goddard]

Glad you got it to work. Maybe there was a conflict between a ChimeraX extension you installed and Boltz. I think it is very unlikely that updating to macOS 15.5 fixed it.