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.
Thanks,
Teemu
Quoting Pavel Afonine
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! Pavel.
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 eye-pleasing rmsd values always result in worse Rfree.
Is there any reason to worry about the low rmsd values and should I always use 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