Thanks Paul,
I'm not using the latest version. I'll try it and report back if it fixes my problem. The
structures are at 2.8 and 2.5 Å (with anisotropy).
Lowering the wxc_scale improved the clashes but they are still on the worse side in comparison
to the structures at comparable resolution.
As for the rmsds, that is certainly true, but going down from say 1 degree deviation in angles
seems like over restraining to me. If you over restrain the B-factors will increase, right? The
idea of variable restaints proposed by Jaskolski et al. (PMID: 17452786) sounds really nice.
Will it be available in the next release of phenix? :P
~L~
_______________________________________
Lari Lehtiö
Structural Genomics Consortium
Medical Biochemistry & Biophysics Dept.
Karolinska Institute
Stockholm, Sweden
_______________________________________
----- Original Message -----
From: Paul Adams
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
Hi,
I nowadays use phenix.refine almost always in the first stages of
Lari Lehtio wrote: 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~
_______________________________________
Lari Lehtiö Structural Genomics Consortium Medical Biochemistry & Biophysics Dept. Karolinska Institute Stockholm, Sweden _______________________________________
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