[phenixbb] Low rmsd values
thaikara at btk.fi
thaikara at btk.fi
Wed Mar 23 05:50:00 PDT 2011
I have actually played with the weights quite a bit. For example, by using the
default weights without optimization, I get the conventional rmsd values
(0.015 for bonds and 1.4 for angles) with R/Rfree of 0.123/0.189.
I guess the manual method of weight picking is not as objective as the Rfree
minimization... That is one of the reasons I would like to know if there is any
reason not to use weight optimization during refinement, whatever rmsds it
might result to.
Quoting Pavel Afonine <pafonine at lbl.gov>:
> Hi Teemu,
> the statistics you quoted looks good to me. Weight optimization tries an
> array of different weights and chooses the one that brings lower Rfree
> and not yet distorted geometry (so it has upper limit on geometry
> deviations but doesn't have a lower limit).
> What pleases your eye does not necessarily please the Rfree -:)
> What are the Rwork/Rfree if you choose such a weight that will bring you
> the rmsds you like? What are the values if you do not optimize the weights?
> All the best!
> On 3/23/11 3:01 AM, Teemu Haikarainen wrote:
> > Hi all,
> > I am getting quite low rmsd values for my structure. I am finishing the
> > refinement and I have rmsd of 0.003 Å for bonds and 0.67 for angles, with
> > R/Rfree of 0.148/0.176. The resolution is 2.0 Å. I am refining with riding
> > hydrogens and using the automatic weight optimization.
> > I have also tried to change the weights manually, but the more
> > rmsd values always result in worse Rfree.
> > Is there any reason to worry about the low rmsd values and should I always
> > the optimized weights in refinement?
> > I am using the latest version of Phenix.
> > Regards,
> > Teemu
> > --
> > Teemu Haikarainen (M.Sc.)
> > Turku Centre for Biotechnology
> > Tykistokatu 6
> > BioCity, Turku
> > FIN-20521, Finland
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