I'm still waiting for accademical license on lig prot. By the way it's very strange that PoseView have not been accompanied with 'internal water detector' ;) i've sent  the letter to developers with this question and hope they can help
 
James

2012/6/26 Thomas Holder <speleo3@users.sourceforge.net>
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 <speleo3@users.sourceforge.net
<mailto:speleo3@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.roth@bbz.uni-leipzig.de
   <mailto:christian.roth@bbz.uni-leipzig.de>
    > <mailto:christian.roth@bbz.uni-leipzig.de

   <mailto:christian.roth@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