[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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