Hi Lari, are you using the latest (d7) prerelease of phenix? We have made some changes to the way the vdw interactions are dealt with that I would expect to improve the clash scores. Note that the rmsds are likely to be smaller for a lower resolution structure (there is less data available to support differences in the model from ideality). However, you can of course try a few different values of wxc_scale to see what happens to r-factors etc. Cheers, Paul Lari Lehtio wrote:
Hi,
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~
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Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden _______________________________________
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