Re: [PyMOL] H-bonds representation

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

Dear all :)

I want to find Hbonds beetween different helices in the membrane receptor (
H bonds beetween sidechains only)

I know possible way to do it wihin selection if I defined different helixes
but is there any way to find almost all Hbonds between polar sidecains
groups ?

Could I use

 find-> polar contact-> sidechain only
for this purpose ?

James

2011/11/30 Jason Vertrees <jas...@sc...>

> James,
>
> > 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 ?
>
> Please ask the pymol-users about this.
>
>
> > By the way, on what assumptions helix elements of my proteins were
> colored
> > after representation of the ligand binding with the cartoons ?
>
> It's colored rainbow from start to end.
>
>
> > 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 :(
>
> Please ask the pymol-users about this.
>
> I'm gearing up for the PyMOL v1.5.0 release, so I won't have time
> right now to personally answer your questions. Please keep relying on
> the pymol-users list--they're very knowledgeable about PyMOL.
>
> Cheers,
>
> -- Jason
>
>
>
>
> > 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
> >>
> >> (e) Jas...@sc...
> >> (o) +1 (603) 374-7120
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > All the data continuously generated in your IT infrastructure
> > contains a definitive record of customers, application performance,
> > security threats, fraudulent activity, and more. Splunk takes this
> > data and makes sense of it. IT sense. And common sense.
> > http://p.sf.net/sfu/splunk-novd2d
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>