[phenixbb] hydrogens in low resolution structure refinement

Lari Lehtio lari.lehtio at ki.se
Fri Nov 16 07:27:47 PST 2007


AFAIK R-factors should go up as they did. But if you look at the clash scores, they are now 
way better because 
hydrogens are taken into account in the anti-bumping restraints. Soo - do you want better 
model or lower 
Rfactors is the key question. 



 Lari Lehtiö
 Structural Genomics Consortium
 Medical Biochemistry & Biophysics Dept.                   
 Karolinska Institute
 Stockholm, Sweden

----- Original Message -----
From: Stefanie Krieg <stefanie.krieg at uni-konstanz.de>
Date: Friday, November 16, 2007 3:30 pm
Subject: [phenixbb] hydrogens in low resolution structure refinement
To: phenixbb at phenix-online.org

> Dear all!
> I am refining two structures at 3.0 and 2.7 A. In some older 
> threads on 
> this board I found that you recommended adding hydrogens to the pdb 
> file 
> even at this resolution. I tried that (adding hydrogens with reduce 
> and 
> refine with riding hydrogens) but inspite of what I read in your 
> postings, my R-Factors went up by 1% (not down as was predicted).
> Are there any other keywords which could be changed or do you have 
> any 
> other ideas why this could be?
> Thanks in advance!
> Stefanie

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