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.
2012/6/26 Thomas Holder <>
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:

A LigPlot wrapper may follow...


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 <
> <>>
>     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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