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 <spel...@users.sourceforge.net>
> 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 <christian.r...@bbz.uni-leipzig.de
> > <mailto:christian.r...@bbz.uni-leipzig.de>>
> >
> > 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
>
>
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