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
http://www.pymolwiki.org/index.php/PLoS#Case_2:_Ligand-binding_sites_.28.E2.89.A5_novice.2Fintermediate.29

 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 ?

James



2011/11/28 Thomas Holder <speleo3@users.sourceforge.net>
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


Cheers,
 Thomas


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
residues.

Thanks,

James

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