Alphafold 3 pLDDT coloring scheme in chimerax?

Question

[mbrav005]

Does anyone know how to get the pLDDT coloring in ChimeraX just like in the alphaphold3 server when you look at the job? Alphaphold modeled a Dimer for me and I want to see the pLDDT score at the inferface in chimerax to see how these residues are modeled and their confidence. Also my ipTM=.13 and pTM=.42 for the model, how should I interpret these scores ? Thanks!

Answer 1

[Mensur Dlakic]

pLDDT scores are stored in the so-called B-factor column in PDB files. Below the File ribbon select Molecule Display and click on b-factor to get the molecule colored by confidence.

Your pTM scores are not good. For an explanation:

https://www.ebi.ac.uk/training/online/courses/alphafold/inputs-and-outputs/evaluating-alphafolds-predicted-structures-using-confidence-scores/confidence-scores-in-alphafold-multimer/

[mbrav005]

Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by b-factor but its only red and blue and white. Not blue and orange like in the alphaphold server google page. I want the alphaphold color scheme so I can hover over the residues and see what they are.

Thanks MB