[phenixbb] metal refinement: adps and restraints
Pavel Afonine
pafonine at lbl.gov
Thu Jul 2 10:02:36 PDT 2015
Hi Alexandra,
> I am refining a protein with a Mo in the active site and which is
> bound to a cofactor and to a water molecule. After each refinement
> step there is always a lot of positive and negative density around the
> Mo and the cofactor molecules, although their occupancy refined to 1.
the map artifacts may be Fourier truncation ripples: see pages 8-14 here
https://www.phenix-online.org/presentations/faq.pdf
> I read this message
> http://www.phenix-online.org/pipermail/phenixbb/2015-May/022031.html,
> but I still have doubts about how to choose the refinement parameters.
> I know I have to select the Mo atoms to be refined anisotropically.
> And the other atoms, do I have to specifically select them to be
> refined isotropically?. For instance:
>
> Isotropic atoms: not element Mo
>
> Anisotropic atoms: element Mo
>
This is not a bad idea.
> I am asking that because I have been using TLS for the protein atoms
> during refinement, so I am not sure if it is correct to select the
> other atoms as isotropic or if I leave it in blank…
>
This should be fine. Selections above are for individual ADPs.
> My other problem is with the metal restraints. I am not sure about the
> ideal distance between the Mo and O atom but based on homologous
> protein structures I choose the following:
>
> refinement.geometry_restraints.edits {
>
> bond {
>
> action = *add
>
> atom_selection_1 = name MOand chain A and resname 4MO and resseq 1
>
> atom_selection_2 = nameOand chain A and resname O and resseq 2
>
> distance_ideal = 1.900000
>
> sigma = 0.050
>
> }
>
> }
>
> However after the refinement this ideal distance interval (1.95-1.85)
> is not respected; I have 4 active sites and in some of them the Mo-O
> distance refines to 0.83 A although there is a lot of density for the
> water molecule to be at 1.9 A. How to make the restrainst work? Am I
> missing something?
>
Hm.. this sounds like a problem. Could you please send me input files so
that I can reproduce this problem and either fix it at our end or
explain what's done wrong.
Pavel
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