From: James S. <jms...@gm...> - 2011-11-29 14:44:37
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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 > |