Dear Jeorge, as you add water molecules to a model, the R _and_ Rfree are bound to drop.
It is important to do it the other way round: let coot add waters, then check the added waters in coot if they make chemically sense, then run refmac5. Don't trust automatic procedures more than your chemical education, no matter how fancy. At 3A I would be careful adding any waters at all, you might just fit noise. Best, Tim On 11/19/2014 07:33 AM, jeorgemarley thomas wrote: > Dear All, > > I am sorry to ask this simple question, but I really need suggestions for > this. As the refinement has been done at 3.0 Angstrom after refinement the > water molecules were added by using "find waters" in coot. After adding > water refinement was done using Refmac 05. Now when I look on the added > water molecules some has density around it and some does not (even no red > density around it). Should I remove later water molecules. and again do the > refinement ? Please give some explanation also for this. as the R free and > R meas has reduced to some extent, also the r m s d contour of map level > was kept at 1.09 after refinement. I welcome your suggestions, thanks in > advance. > > > Regards > > Jeorge > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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