[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.


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
> _______________________________________
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> phenixbb at phenix-online.org
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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

Lawrence Berkeley Laboratory
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