Thanks, Thomas, Jason

both of the methods are useable :)

By the way I've forced with the problem of the representation of the active sites of different enzymes. I need to view all my protein as the cartoons and the ligand as the shpere in the ligand binding pocket. Besides I need to mark residues wich are contact with the ligand ( E.g I want to mark it as the lines and with the individual colour ). Finally I want to represent Hbonds between active site residues and the ligand.

I've done this manually but its very long if I want to study 20-30 different enzymes during evening :)
Also I've found such sollution wich could do all that i want

 but this way also I need to rewrite script for specified enzyme ( e.g mark the active site residues and the distances for Hbonds etc )

Is there any semi-avtomated way to find ligand binding pocket and do all such things ?


2011/11/28 Thomas Holder <>
Hi James,

most trivial manner:

as cartoon
show sticks, resn LEU+ILE+VAL
set cartoon_side_chain_helper

and eventually something like this:

show spheres, resn LEU+ILE+VAL and not name N+O+C
set sphere_transparency, 0.5


On 11/28/2011 02:58 PM, James Starlight wrote:
Another question also linked with the non-covalent interaction.

In particular I wounder to know how i Could represent all hydrophobic (
Ley Ile Val etc) sidechains in my proteins in most trivial manner? I'd
like to represent the hydrophobic core of the proteins made from those



Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen