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