[phenixbb] Confused with ANAISOU in PDB

[Partha Chakrabarti]

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 at 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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