[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
accurate.
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
reason.
Engin
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
> 233 South 10th Street - Room 826
> Philadelphia PA 19107
> Office (215) 503 4573
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> 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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--
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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