[phenixbb] problems with clashes

Lari Lehtio lari.lehtio at ki.se
Sun Jul 29 09:50:12 PDT 2007


I nowadays use phenix.refine almost always in the first stages of the
refinement and later usually move to refmac. Now I have two modest
resolution structures which behave much better in phenix than in refmac. 

In addition to the more tedious deposition (I guess), I have a problem
with clashes. When I analyse the structures with molprobity, I get much
better clashscores with refmac refined files. Is there a way to increase
the restraint for these contacts or should I just keep decreasing the
wxc_scale (from the default)? Rmsds reported by refmac (0 cycles) for
bonds and angles are already lower than what I'm used to. B-factors on
the other hand seem to be less restrained in phenix.



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

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