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PDB-REDO / alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
https://alphafill.eu
BSD 2-Clause "Simplified" License
90 stars 18 forks source link

Coloring by pLDDT #33

Closed prihoda closed 6 months ago

prihoda commented 1 year ago

Hi @mhekkel I just want to let you know that Mol* has a native ability to color AlphaFold cif files by pLDDT score.

The example app demonstrates how to activate this behavior: https://github.com/molstar/molstar/blob/master/src/apps/viewer/app.ts

Relevant lines:

https://github.com/molstar/molstar/blob/master/src/apps/viewer/app.ts#L136-L139

https://github.com/molstar/molstar/blob/master/src/apps/viewer/app.ts#L188

https://github.com/molstar/molstar/blob/master/src/apps/viewer/app.ts#L200-L202

https://github.com/molstar/molstar/blob/master/src/apps/viewer/app.ts#L489-L517C1

I'm no expert, I just recently experimented with implementing this logic into Nightingale, you can check the PR here https://github.com/ebi-webcomponents/nightingale/pull/259/files

prihoda commented 1 year ago

You can try it out by drag-and-dropping your CIF file here: https://molstar.org/viewer/