I routinely use coot " difference map peaks" to inspect maps to see errors - fit residues - find alternate conformations- etc. it is often obvious then that you have found a solvent molecule; good hydrogen bonds, clear density, and then I add it. i know this is old fashioned, but honestly I think no slower than invoked automated searches then having to correct the errors they introduce..
Eleanor On 18 April 2017 at 10:35, Robbie Joosten <robbie_joos...@hotmail.com> wrote: > Assuming you do this by hand (which I highly recommend), you can add > waters as soon as it becomes obvious that they are not something else > (particularly missing parts of the protein). It is best to be conservative > at start. > > > > Cheers, > > Robbie > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Dr > A.A. Jalan > *Sent:* Monday, April 17, 2017 23:46 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] When should one add solvents > > > > Dear All, > > I have a very elementary question. At what stage of refinement is it > appropriate to start adding solvent (water). For example, during refinement > of a structure, I was able to build ~ 90% of residues. The density of the > remaining residues is not complete. If I take a guess and add residues > based on my knowledge of the sequence, the r-free increases. Since I see no > further way to improve the maps (any suggestions?), should I start adding > water in the hope of improving the overall density and revealing the > missing bits. I would really appreciate any inputs. > > thank you > > Abhishek > > >
