difference in estimated error between phenix and refmac
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
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). A*58*, 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
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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
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participants (3)
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Ed Pozharski -
Ling Qin -
Pavel Afonine