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 <jason.vertrees@schrodinger.com>
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 <jason.vertrees@schrodinger.com>
>>
>> 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 <speleo3@users.sourceforge.net>
>> >>
>> >> 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) Jason.Vertrees@schrodinger.com
>> (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
> _______________________________________________
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120