[phenixbb] problems with clashes

[Lari Lehtio]

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 <PDAdams at lbl.gov>
Date: Sunday, July 29, 2007 7:27 pm
Subject: Re: [phenixbb] problems with clashes
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> 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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