Hi again, I upgraded my phenix to the prerelease and I didn't see major improvement with the clashes (ranking 13%). If I take the phenix refined coordinates, keep the aniso records from TLS and run some refmac cycles, my structure is better than average with regards to the clash scores (69 %). I do not know how valid refinement strategy this is. (Rfree-R = 5.4 %) Only way I have found so far to fix it in phenix is:
phenix.reduce -build -flips mymodel.pdb > hydrogens.pdb phenix.refine remove_hydrogens=False hydrogens.pdb mydata.mtz params_july29.txt ncs=true hydrogens.mode=riding
This results in higher Rfree (Rfree-R = 6.4 %) but the clashscores are ok (66%)
I still feel that I'm missing some keyword to prevent the clashes.
~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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