[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:
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.
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