[phenixbb] difference in estimated error between phenix and refmac

[Ed Pozharski]

Well, it's Cruickshank DPI (Acta Cryst D55:583 for review)

On Thu, 2010-08-12 at 11:49 -0700, Pavel Afonine wrote:
> Hi Ling,
> 
> I have no idea what the error estimate based on R means. In
> phenix.refine the ML based coordinate error estimate is done as
> described in formula #19 in
> 
> Acta Cryst. (2002). A58, 270-282
> 
> with the ML parameters determined as described here:
> 
> Acta Cryst. (1995). A51, 880-887.
> and
> J. Appl. Cryst. (1996). 29, 741-744.
> 
> This number is sensitive to many (irrelevant) thins such as
> bulk-solvent model, etc.. So I wouldn't take it too literally. Model
> to map fit, map quality, local and global, geometry stats and Rfactors
> are all much more useful model quality characteristics than this
> number.
> 
> Pavel.
> 
> 
> 
> On 8/12/10 10:04 AM, Ling Qin wrote: 
> > Dear Colleagues,
> > 
> > I am refining a 2.15 A structure that was previously refined with
> > refmac by someone else. Without changing anything in the
> > refmac-refined model and using all the default phenix.refine
> > settings, I am getting pretty much the same R and Rfree (from
> > 19.3%/21.7% to 18.9%/21.8%), with an ML estimated error of 0.22 A.
> > In the refmac-refined pdb file, the estimated error is much lower:
> > 0.16 (based on R), 0.144 (based on Rfree), and 0.096 (based on ML).
> > I am using phenix.refine version 1.6_289, but also tried 1.5_2 with
> > the same result. Is there an underlying reason for this difference?
> > Thank you very much for your insightful opinions in advance.
> > 
> > Cheers,
> > 
> > Ling   
> > 
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> 
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-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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