[phenixbb] model vs Wilson b-factor

Paul Adams pdadams at lbl.gov
Wed Apr 21 11:30:49 PDT 2010


A couple of questions:

- How did you calculate the Wilson B-factor?
- What does the Wilson plot look like (can be seen in the Phenix GUI  
using xtriage)

On Apr 21, 2010, at 10:42 AM, Gino Cingolani wrote:

> 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
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> E-mail:   gino.cingolani at jefferson.edu
> ******************************************************************************
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> 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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-- 
Paul Adams
Acting Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

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