In this sort of case, I find that often the Rama-bad residues appear unfixable
because small distortions in many bond lengths and angles have made the side
chain appear correctly fit even though the rotamer choice was wrong.
My recipe for fixing that:
* Mutate the offending residue to glycine or alanine in coot
* Optimize the bond lengths & angles of the backbone
* If that doesn’t move the residue into an allowed region, manually fix
it and re-optimize the bond lengths & angles
* Then put the side chain back on and choose the rotamer that best fits the
density. You’ll probably fit it to be different than the original one.
My colleagues wrote a rebuild + refine server based on automating, more
rigorously, that sort of logic:
https://godzilla.uchicago.edu/pages/projects.html
In my own experience at least, you should use the results from their server as
a buffet of (often quite useful) suggestions for how to rebuild your refmac- or
phenix- refined model.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Tereza Skalova
<t.skalova.c...@gmail.com>
Reply-To: Tereza Skalova <t.skalova.c...@gmail.com>
Date: Friday, March 8, 2019 at 3:08 AM
To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] Ramachandran outliers
Dear all,
I have structure at 3.3A resolution and I have ca. 35 Ramachandran outliers.
Do you have any idea how to reduce the number?
I refine in Refmac, using h-bond based Prosmart restraints based on PDB
structures (identical molecules with high resolution) and I use NCS, medium
between AB (protein 1) and loose between CDE (protein 2). I use overall
B-factor and 8 TLS groups.
Is it possible to optimize Ramachandran plot directly in Refmac?
Thank you
Tereza Skalova
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