[phenixbb] model vs Wilson b-factor

Raja Dey rdey at usc.edu
Wed Apr 21 11:27:48 PDT 2010


Ofcourse, I did both both geometry and shape correction using adding-hydrogen and tls respectively.

Raja 

----- Original Message -----
From: sbiswas2 at ncsu.edu
Date: Wednesday, April 21, 2010 11:22 am
Subject: Re: [phenixbb] model vs Wilson b-factor
To: Gino.Cingolani at jefferson.edu, PHENIX user mailing list <phenixbb at phenix-online.org>

> Hi,
> Although your resolution is low, I was wondering if you have tried 
> addinghydrogen during refinement, this sometimes makes a difference 
> althoughwith high resolution data mainly.
> Shya
> 
> 
> 
> 
> 
> > Hi all,
> >
> > we've solved a large structure (~20,000 residues/asymm unit), 
> with 4-fold
> > ncs and diffraction data to 3.3A.
> >
> > The Rfree/Rfac is ~28%-24% with OK geometry with no major 
> outliers in the
> > Ramachandran plot.
> > I would think I'm done (.. after 6 years!).
> >
> > However, my refined model b-factor (~130A2) is >> Wilson b-factor 
> (~80A2).> Obviously I'm not too happy with it.
> >
> > Here is what I tried to resolve this discrepancy:
> > --> play with wxu_scale
> > --> play with B-factor weight in ncs restraint (4-fold ncs)
> > --> play with number of macrocycles
> > --> Redefine tls groups
> >
> > So far nothing really works, except switching from
> > individual_adp to group_adp. However, this increases
> > my Rfree by almost 3%.
> >
> > Any ideas?
> >
> > Thanks in advance,
> >
> > Gino
> > 
> ******************************************************************************> Gino Cingolani, Ph.D.
> > Associate Professor
> > Thomas Jefferson University
> > Dept. of Biochemistry & Molecular Biology
> > 233 South 10th Street - Room 826
> > Philadelphia PA 19107
> > Office (215) 503 4573
> > Lab    (215) 503 4595
> > Fax    (215) 923 2117
> > E-mail:   gino.cingolani at jefferson.edu
> > 
> ******************************************************************************> "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
> > ("You were not born to live like brutes, but to follow virtue and
> > knowledge")
> > Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120)
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> 
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