[phenixbb] phenix.refine v.1.3 vs 1.24

Leo Sazanov sazanov at mrc-dunn.cam.ac.uk
Fri Oct 3 09:18:22 PDT 2008

When refining the same (large) molecule in several different crystal 
forms at about 3.1 A resolution, I noticed that in two cases when 
experimental phase information is available, in phenix.refine-1.3 I get 
worse Ramachandran compared to phenix.refine-1.24 - about 2% less 
residues in most favored regions. In one case when there is no 
experimental phase information, there is no difference between two 
phenix versions.
What could be the reason for that?
These comparisons where done for cases when final RMSDs and R-factors 
are similar (and all RMSDs calculated in v.1.3), so automatic weights 
adjustment in v.1.3 should not have played much role. Adding to other 
people's comments, it would be useful to be able to switch this 
adjustment off, as sometimes one wants full control over final RMSDs, etc.

Dr. Leonid A. Sazanov
Research group leader
Medical Research Council
Dunn Human Nutrition Unit
Wellcome Trust / MRC Building
Hills Road
WEB: www.mrc-dunn.cam.ac.uk
Tel: +44-1223-252910
Fax: +44-1223-252915

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