Hi Abhishek Im by far not as experienced as others in the bulletin board, but I made the experience that automated water update with Phenix leads to an aggressive placement of solvent molecules, which can be damped a bit by restricting H-bond distances of newly placed waters. As Robbie and Eleanor mentioned, manual inspection is a must. In your situation, I would first check for the optimal refinement strategy (amount of TLS groups for example) and the use FEM maps to rebuild missing residues. If this does not help, start filling waters slowly. At this point, I always run paired refinement of models with manually placed waters and one model where I unleash phenix water update. Usually, Phenix is doing a good job there and produces reasonable water placements. I regularly let PDB_REDO have a look at waters and cross check those desities with a FEM map. It could be that one model reveals density and information that you then can transfer to the other model. Its worth a try, but no guarantee this helps.. Especially the PDB_REDO *_final.scm turned out to be a handy script for coot, allowing for manual inspection of the water molecules removed by PDB_REDO. Please correct me if Im wrong, but if it comes to water placement, a model with reduced Rfree is not neccessarily a better model. Rfree will most probalbly go down while loading more waters, simply as you reduce the degrees of freedom (see Merritt, To B or not to B, ActA D 2012.). best, matthias
>>> Eleanor Dodson <eleanor.dod...@york.ac.uk> 18.04.17 13.34 Uhr >>> 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
