Hi Dialing,
Most water picking tools are rather overenthusiastic and end up placing some waters at places where they should not be. This causes some overfitting and an increase of R-free. I'm hideously old-fashioned and recommend conservatively building waters by hand. There are some good validation tools that help get rid of excess water: centrifuge in PDB_REDO does the basic work; "check/delete waters" in Coot highlights other suspicious waters; WHAT_CHECK checks hydrogen bonding thoroughly, finds nonsense clusters of water and also finds possible ions. It must be noted that all these tools break down at very high resolution where you may get alternate waters. Fortunately, this problem doesn't occur very often. Cheers, Robbie From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Dialing Pretty Sent: Tuesday, February 07, 2012 09:31 To: [email protected] Subject: [ccp4bb] on Rwork and Rfree Dear All, After we refine the structure of the protein to satisfactory with satisfactory Rwork and Rfree, we pick water by phenix refine, and I find Rfree always increases slightly after the water picking refinment. Do you have nay idea to solve this problem or any comment? Cheers, Dialing
