[phenixbb] model vs Wilson b-factor

Engin Ozkan eozkan at stanford.edu
Wed Apr 21 11:32:51 PDT 2010

  Dear Gino,

*Sometimes* ignoring the strict B-factor police is a valid option. Much 
of the time, it comes to building in weaker density vs not building, and 
it is a subjective call. I bet if you removed all weaker-density loops, 
your average B-factor would decrease, but you probably would have gained 
nothing, and not improved your model at all (you would probably make it 
worse, actually).

And as Pavel pointed out, at >3 Angstroms, Wilson values are not so 

I would also look at phenix.polygon results.

By the way, I have a related question for Pavel. When you guys were 
culling the PDB for structures, was there any attention paid to correct 
the ones that have residual B-factors in the PDB file? (Urzhumtseva, 
2009 is not clear on this) I have found that a structure which was 
refined by refmac and deposited in 2005, where the residual B-factors 
are in the B column. This used to be a fairly common practice, before it 
was (thankfully!) settled by PDB that the B column should contain the 
full B factor (the way Phenix outputs by default). I still sometimes 
read articles where people report an average B-factor of 8 for a 2.2 
Angstrom structure, and I know what is going on!

I am asking this, because a few structures I solved recently to ~2 
Angstrom resolution were all closer to the upper range of observed 
structures according to POLYGON, so I thought this could possibly be one 


On 4/21/10 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
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> ("You were not born to live like brutes, but to follow virtue and knowledge")
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Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111

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