Hi Partha,
I am bit confused with two things. First I did specify individual isotopic, as following, still see ANAISOU in PDB. Is it from TLS strategy? I have used TLS in refmac, don't see it there.
Any atom participating in a TLS group will have ANISOU record. This is explained in the Manual: http://phenix-online.org/documentation/refinement.htm paragraph "Refinement of atomic displacement parameters (commonly named as ADP or B-factors)". You don't see this in Refmac because Refmac does not output this right (= as efficient as it should be).
Second thing is, I want to tighten the water picking. How can I do that?
1) http://phenix-online.org/documentation/refinement.htm paragraph "Water picking". 2) Below is the extract with default water picking parameters related to your question: refinement { ordered_solvent { b_iso_min = 1 b_iso_max = 50 primary_map_cutoff = 3 secondary_map_cutoff = 1 min_solv_macromol_dist = 1.8 max_solv_macromol_dist = 6 min_solv_solv_dist = 1.8 } } To tighten the water picking I would change it like this (for example; depending on model quality, resolution): refinement { ordered_solvent { b_iso_min = 10 b_iso_max = 50 primary_map_cutoff = 3.5 secondary_map_cutoff = 1.5 min_solv_macromol_dist = 1.8 max_solv_macromol_dist = 4 min_solv_solv_dist = 1.8 } } Try several values and see the effect -- you will get less waters and more confidence that they are all real waters. I can explain some more about each parameter, if necessary. As usual, let us know if you have any questions. Pavel.