I'm thinking a good work around is simply this.
Select the binding site of the amino acids and ligand in pymol.
Then copy those selected aa's and atoms to another object:
save -> model -> copied_object as output.pdb
output.pdb will then contain all the x,y,z coordinates of only what was
selected.
Then just get those columns and upload them to swiss dock.
Jordan
On Jul 18, 2012, at 2:23 AM, James Starlight wrote:
> Dear PyMol users!
>
>
> Some of docking servers (e.g swiss dock) which I'm using need in
> explicit definition of the coordinates (in XYZ) of the docking region
> as well as coordinates of its COM. How I could obtain such coordinates
> of intrested pdb file based on the knowing protein-ligand interaction
> sites ( e.g if i visualize ligand binding site by means of Pymol
> itself ).
>
>
> Thx for help
>
>
> James
>
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