At 4A, I wouldn't unless I had an exceptionally good reason to. There will always be some blobs, due to random noise and fourier ripples as well as due to an imperfect model. Unless a blob makes nice H-bonds to something else that is nicely ordered, I wouldn't model at water into it. If you can't see nice density for side chains then you probably aren't really seeing density for waters either.
++++++++++++++++++++++++++++++++++++++++++ Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago pr...@uchicago.edu<mailto:pr...@uchicago.edu> ________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sudipta Bhattacharyya [sudiptabhattacharyya.iit...@gmail.com] Sent: Monday, April 13, 2015 1:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Picking water molecules at 4A structure. Dear community, Recently we have been able to solve a crystal structure of a DNA/protein complex at 4A resolution. After almost the final cycles of model building and refinement (with R/Rfree of ~ 22/27) we could see some small water like densities...all throughout the complex. Now my query is, whether one should pick water molecules at this low resolutions or it is totally unscientific to do so? Many thanks in advance...!!! My best regards, Sudipta.
