On 14/04/2025 11:49, 张馨丹 wrote:
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Dear Coot Subscribers Forum
I hope this message finds you well.
I am currently working on refining a protein structure using
Coot and aim to achieve 100% residues in the "In Favoured Regions" of
the Ramachandran Plot. While there is no outlier, some residues still
fall outside these regions.I can't find a way to increase the
percentage of "favoured" any further. I hope to get your help.
You didn't say what you have already tried. That would have been helpful.
Whether one should want to do this I will not discuss (in this message).
Here is how I would do it:
turn on torsion restraints
turn on Ramachandran restraints
turn up the Ramachandran plot restraints weight to 10
try turning off planar peptide restraints - maybe that will help - maybe
not.
residue by residue in the set of residues that are not in the favoured
regions:
Centre on that residue
Use long residues to RSR refine to refine a 5 residue stretch.
Alternatively, if this is a cryo-em structure refined with phenix
refine, I image that you could increase the ramachandran plot restraints
there.
Regards,
Paul
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