[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

> 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.


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