Re: [PyMOL] H-bonds representation

[James S. <jms...@gm...>]

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 <sp...@us...>

> 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
>