ViewBoltz

Hello boltz'ers,

Have you run boltz-2 on many small molecules?

Are you tired of trying to load, align, and flip through each output cif file?

Do you wish Chimera had a ViewDock utility for easily scrolling through many boltz-2 predictions?

If you answered yes to any of the above then this new utility may be right for you. Claude code has been gracious enough to help me make a ViewDock utility for boltz predictions called ViewBoltz.

Getting Chimera with ViewBoltz

Download and extract the version of Chimera with ViewBoltz from gimel/epyc. It is at /mnt/nfs/soft/chimera/Chimera_w_ViewBoltz.tar.gz. Once extracted, you can run it from the chimera folder with ./bin/chimera.

ViewBoltz can be found under Tools -> Surface/Binding Analysis (just like ViewDock)

Input to ViewBoltz

Just provide the parent directory which contains all of the subdirectories containing the boltz-2 output cif files. For example,

parent_folder/
├── mol0/
│   ├── msa/
│   ├── processed/
│   └── predictions/
│       └── 0/
│           ├── 0_model_0.cif
│           └── affinity_0.json
├── mol1/
│   ├── msa/
│   ├── processed/
│   └── predictions/
│       └── 1/
│           ├── 1_model_0.cif
│           └── affinity_1.json

In this case you would just provide parent_folder. It doesn't have to be formatted exactly like this, as long as there is some subdirectory that contains the *.cif and affinity_*.json file with the corresponding probability and affinity prediction.

What should happen

Chimera should load each of the predictions into a ViewDock session like you are used to. All of the structures should be aligned. The columns in ViewDock should show the file path for each loaded molecule and the affinity/probability predictions. I think this session should be able to be used like any other ViewDock session.

Some notes

This is super new, was scraped together in an afternoon, and something is bound to break. Please let Brendan know if something isn't working and he can look into it.

H-bonds don't work. Boltz doesn't have a sense of hydrogens so you can't visualize h-bonds like you can in a normal ViewDock session.