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

Hi James,

hm, looks like PoseView ignores all water molecules :(

Have you tried LigPlot? It has a "-w" option to include waters.

Cheers,
   Thomas

On 06/26/2012 05:11 PM, James Starlight wrote:
> 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...
> <mailto: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...>
>      > <mailto: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