[phenixbb] Real space refine of long side chains

[Leonid Sazanov]

Hi,

We have addressed exactly this problem by writing a script, in which 
B-factors are refined first and only then real-space refinement happens.

This allows disordered side-chains to acquire high B-factors and so they 
are not pulled into backbone anymore.

This cycle is repeated twice to achieve convergence.

Parameters for B-factor refinement (ADP restrains) were optimized to 
account for consistent lack of density for acidic side chains in cryoEM.

It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636

If needed, I can send a script.

Best

Leonid

-- 
Prof. Leonid Sazanov FRS
IST Austria
Am Campus 1
A-3400 Klosterneuburg
Austria

Phone: +43 2243 9000 3026
E-mail: sazanov at ist.ac.at

Date: Mon, 25 Nov 2019 19:11:16 +0000
From: Luca Pellegrini <lp212 at cam.ac.uk>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Subject: [phenixbb] Real space refine of long side chains
Message-ID: <37F0D7B2-3C9E-4FE1-B0BF-6B23F0D8925B at cam.ac.uk>
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I have noticed that real-space refinement in cryoEM maps has a tendency 
to pull long disordered side chains (Lys, Glu etc) back towards main 
chain density, resulting in unrealistic hairpin-like bent conformations. 
Is there a way to counter or moderate this behaviour? It would save me 
from having to manually straighten them all out again afterwards...

Best wishes,
Luca

Luca Pellegrini, PhD
Department of Biochemistry
University of Cambridge
Cambridge CB2 1GA
United Kingdom

lp212 at cam.ac.uk
tel.: 0044 1223 760469
https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group
@PellegriniLab