[phenixbb] problems with clashes
Paul Adams
PDAdams at lbl.gov
Sun Jul 29 10:18:00 PDT 2007
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~
>
> _______________________________________
>
> Lari Lehtiö
> Structural Genomics Consortium
> Medical Biochemistry & Biophysics Dept.
> Karolinska Institute
> Stockholm, Sweden
> _______________________________________
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
--
Paul Adams
Senior Staff Scientist, Physical Biosciences Division
Head, Berkeley Center for Structural Biology
Deputy Principal Investigator, Berkeley Structural Genomics Center
Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909
http://cci.lbl.gov/
Lawrence Berkeley Laboratory
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