Re: [PyMOL] Visualisation of protein-ligand interactions in pymol

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

Thomas,

Its really great )

Could you tell me if you find a possible way to take into account burried
water from the protein interiour in the Pose View protein-ligand
interaction 2D plots ?
Most of my proteins consist of such internal water ( like a het atoms in
the protein.pdb ) but pose view didnt take this mollecules into account so
the final plot lack of many crussial h_bonds between ligand and protein
itself.


James
2012/6/26 Thomas Holder <sp...@us...>

> Hi all,
>
> I thought it would be nice to run such tools directly from PyMOL. So
> there is a PoseView wrapper on the PyMOLWiki now:
>
> http://pymolwiki.org/index.php/PoseView
>
> A LigPlot wrapper may follow...
>
> Cheers,
>   Thomas
>
> On 06/26/2012 10:13 AM, James Starlight wrote:
> > Christian,
> > Also I've found the same software- pose view (in that article I've also
> > found link on it). Its very friendly but I've noticed some erorrs during
> > representation of the non-covalent contacts partly in case of the vdw
> > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but some
> > crussial interactions could not be visualized)
> > And the main disadvantage of that software is that it does not take into
> > account burrial water and it's h-bond networks within protein.
> > I've ordered free license on the lig prot and hope that this software
> > will be better ;)
> > James
> > 2012/6/26 Christian Roth <chr...@bb...
> > <mailto:chr...@bb...>>
> >
> >     Hi James,
> >
> >     LigPlot is free for academic users. You just have to verify that you
> >     are a
> >     academic user. MOE does a simimlar representiation but is definitely
> >     not free.
> >
> >     Christian
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>