Hi Aaron,
> I am somewhat new to PYMOL and was trying to create a selection of atoms.
> What I need to do is select all atoms of a protein that are within 5
> angstroms of an inhibitor (the protein and inhibitor are separate
> molecules). I cannot figure out how to do this from the examples in the
> manual. I will want to use this selection to make a surface of the
> selection afterward.
>
You might try this. Select a central atom of your ligand (ALT + left mouse
button). Pymol will name this selection (lb).
select bindingsite = (lb around 5) and not HETATM) # PDB-style, this will
select all not HETATM atoms around your selected atom
or
select bindingsite = (lb around 5) and not ligand) # if your small molecule
is named ligand
show surface, bindingsite
Cheers
Daniel
--
Daniel Kuhn
Department of Pharmaceutical Chemistry
Philipps-University of Marburg
Marbacher Weg 6 Phone: (+49)6421 28-25071
35037 Marburg Fax: (+49)6421 28-28994
Germany
