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Rappsilber-Laboratory / AlphaLink2

AlphaLink2: Integrating crosslinking MS data into Uni-Fold-Multimer
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Can pLDDT coloring be applied to models in ChimeraX? #20

Closed joshwa-s closed 4 months ago

joshwa-s commented 4 months ago

I am not sure how to color the models by pLDDT. I use ChimeraX and normally with AlphaFold models I open the model, then I open the .pkl file to view the PAE. On the PAE plot there is a button to color by pLDDT. Alternatively you can type 'color bfactor palette alphafold' to view the pLDDT coloring. Is there a way to do this with AlphaLink models?

I am interested in per residue confidence. For one model we are interested in I noticed that alphafold produces a lower PAE plot and I want to know if pLDDT corresponds to this.

lhatsk commented 4 months ago

Thanks for pointing this out! The b-factors we produced were between 0 and 1. ChimeraX expects something between 0 and 100. I fixed this issue in the latest commit. Here is a script to fix your old models: https://gist.github.com/lhatsk/f8abc8174f9a96ccb28999e69e5556b3

joshwa-s commented 4 months ago

Many thanks for this.