[phenixbb] metal refinement: adps and restraints

Nigel Moriarty nwmoriarty at lbl.gov
Thu Jul 2 09:22:36 PDT 2015


Alexandra

The restraints refining to a too short a distance is a real problem. The
first thing to do is check in the .geo file to ensure that the restraints
are being set correctly. It is a simple text file so it should be easy to
read.

Feel free to send it to me driectly (with the .pdb file) if you want me to
take a look.

Cheers

Nigel

---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Thu, Jul 2, 2015 at 9:14 AM, Alexandra Marques <at.marques at fct.unl.pt>
wrote:

> Hi,
>
>
>
> 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. 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
>
>
>
> 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…
>
>
>
> 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 MO   and chain A and resname 4MO and resseq 1
>
>     atom_selection_2 = name  O   and 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?
>
>
>
> Thank you very much,
>
> Alexandra
>
>
>
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