hm, looks like PoseView ignores all water molecules :(
Have you tried LigPlot? It has a "-w" option to include waters.
On 06/26/2012 05:11 PM, James Starlight wrote:Thomas,<mailto:firstname.lastname@example.org>>
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
2012/6/26 Thomas Holder <email@example.com> <mailto:firstname.lastname@example.org
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:
> Also I've found the same software- pose view (in that article
> found link on it). Its very friendly but I've noticed some erorrs
> 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
> crussial interactions could not be visualized)
> And the main disadvantage of that software is that it does not
> 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 ;)
> 2012/6/26 Christian Roth <email@example.com
> Hi James,
> LigPlot is free for academic users. You just have to verify
> are a
> academic user. MOE does a simimlar representiation but is
> not free.
MPI for Developmental Biology