[phenixbb] problems with clashes

Lari Lehtio lari.lehtio at ki.se
Sun Jul 29 15:57:26 PDT 2007


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 <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
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
> -- 
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> 




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