[phenixbb] weights optimization, add hydrogens

Ursula Schulze-Gahmen uschulze-gahmen at lbl.gov
Tue Feb 23 10:19:58 PST 2010

I am refining a 2.0 A structure in Phenix using mostly the graphical 
interface. The maps are very good and the R factors are low 
(0.208/0.173). But the geometry is not so great with bond deviations of 
0.208 and Angle deviations of 1.85.  What is the best thing to do to try 
to improve the geometry. Should I try to optimize the weights?

The other question is about adding hydrogens to the model. I did add 
them in a previous refinement cycle. After rebuilding the model in coot, 
most of the model still has the hydrogens in the input file for the next 
refinement cycle, but some residues and waters don't have hydrogens. 
When I tried to add hydrogens again to the model, I got an error message 
about atoms being to close. Does Phenix know where to add hydrogens if 
the input model has already hydroegns on many residues?



Ursula Schulze-Gahmen, PhD.
QB3, Tjian Lab
MCB, 16 Barker Hall #3204
University of California Berkeley
Berkeley, CA 94720-3204
Phone: (510) 642 8258
uschulze-gahmen at lbl.gov

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