Hi Pavel,

Thanks a lot as usual. I learnt that one can also make Refmac output like that, but it is not the default. So, that confusion is clear.

At your leasure, if you could explain a bit about the water picking parameters, that would be great. In my case, for 132 residues and 55% solvent content, the default setting was picking 330 waters, which is bit too much I felt. Did change the b_iso_min = 10 and b_iso_max = 40, just to see what happens.. (because I thought for ordered water the later should not be too high..) but I was not sure what the other parameters mean. Like pick water above 3 sigma, remove below 0.9 sigma as we are used to from Arp..

No comparison between the different programs and what their keywords are.. just a feeling that if some of these key words are explained at the last section instead of True/False in Red / Blue, it could help the users, just as b_iso_min/max is explained..

Best, Partha




On 10/9/07, Pavel Afonine <PAfonine@lbl.gov> wrote:
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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