[phenixbb] Confused with ANAISOU in PDB

Pavel Afonine PAfonine at lbl.gov
Tue Oct 9 08:52:04 PDT 2007

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:
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.


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