This may be a useful paper to read, although it is a bit dated:
Acta Cryst. (1999). D55, 479-483 How many water molecules can be detected by protein crystallography? In general, 3 A resolution is beyond where you can reliably add waters (I start adding them only at 2.7-2.8 A resolution or better). If you do want to add waters, make sure they make sense (H-bonding/distance) and do not have positive Fo-Fc density after refinement, in which case they could be metal ions. If after refinement the (2Fo-Fc) density disappears then whatever you thought was there isn't. best, bert ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of jeorgemarley thomas [kirtswab...@gmail.com] Sent: Wednesday, November 19, 2014 6:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Water molecules after refinement 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
