Bwhall61 at 22:29, 19 November 2025

2025-11-19T22:29:34Z

← Older revision		Revision as of 22:29, 19 November 2025
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	== Getting Chimera with ViewBoltz ==		== Getting Chimera with ViewBoltz ==

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

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

Bwhall61: Created page with "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 ViewBol..."

2025-11-19T22:27:56Z

Created page with "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 ViewBol..."

New page

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 <code>/mnt/nfs/soft/chimera/Chimera_w_ViewBoltz.tar.gz</code>. 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,

<syntaxhighlight lang="text">
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
</syntaxhighlight>

In this case you would just provide <code>parent_folder</code>. 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.

ViewBoltz - Revision history

Bwhall61 at 22:29, 19 November 2025