Ofcourse, I did both both geometry and shape correction using adding-hydrogen and tls respectively.
Raja
----- Original Message -----
From: [email protected]
Date: Wednesday, April 21, 2010 11:22 am
Subject: Re: [phenixbb] model vs Wilson b-factor
To: [email protected], PHENIX user mailing list
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: [email protected]
******************************************************************************> "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) _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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