Dear Lisa,
you can specify custom bond and angle restraints by using the option
refinement.geometry_restraints.edits. Best is to save them to a file (e.g.
"restraints_edits.params") and use this as input for your next
phenix.refine run. Assuming the ideal distance for your Mg is 2.1A and the
amino acid is asp113 of chain A, the according file entry could look like
this:
refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = name MG01 and chain G and resname MG and resseq 1
atom_selection_2 = name OD2 and chain A and resname ASP and resseq 113
distance_ideal = 2.1000
sigma = 0.01
}
You can check the phenix hompage for detailed documentation:
http://phenix-online.org/documentation/refinement.htm
Yours,
Joern
******************************************
Address:
Joern Krausze
University of Leipzig
Centre for Biotechnology and Biomedicine
Deutscher Platz 5
04103 Leipzig
Germany
eMail: [email protected]
Phone: +49 (0)341 9731312
Fax: +49 (0)341 9731319
******************************************
On Mon, 16 Feb 2009, Lisa Wang wrote:
> Hi all,
> The resolution of my structure is 3.1A. There are three Mg binds in this
> structure. I try to refine it with phenix. There are cleare extrea density
> before I add Mg atoms. But when I put Mg in the central of density with good
> coordination and try to refine it by phenix, those Mg move away.Does phenix
> need addiational paramters file to refine Mg and keedp it 2.1A 2.1A from
> it coordinated atom?
> Thanks.
> Lisa
>
