Thanks Jason.

It works quite well in case of not very compliated ligands ( e.g bonds beetween aa-tRNA and the  aa-tRNA syntase were correct ) but in the sugar-bound enzyme there were some mistakes in representation of the H-bonds netween water/ligand/active center ( some water also partisipate in the ligand binding but in case where water and some residues of the active sites were positioned iclosely the bonds were incorect ). So a I understood I can fix this mistakes only manually ?

By the way, on what assumptions helix elements of my proteins were colored after representation of the ligand binding with the cartoons ?

Finally how I could represent ionic contacts in the ion-binding proteins ?
E.g now I'm studing calmodulin wich has Ef-hand Ca-binding motifs. I've tried to represent bonds beetwen some polar residues of the active site with the ligand but failed :(

Thanks again,


2011/11/29 Jason Vertrees <>

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

For your given object, click A > preset > ligands sites > cartoon. Try
other options under that menu.


-- Jason

> 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
>> 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
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