Re: [PyMOL] H-bonds representation

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,


James

2011/11/29 Jason Vertrees <jas...@sc...>

> James,
>
> > 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.
>
> Cheers,
>
> -- Jason
>
>
> > 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
> >
> >
> >
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>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
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