[Dock-fans] End graphical representation from Dock tutorials

[Scott Brozell]

Hi,

See
http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-October/001889.html

An updated DOCK tutorial mentioning viewdock will be posted soon:
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/ligand_sampling_dock/ligand_sampling_dock.html

Scott

On Mon, 8 Oct 2007, Francesco Pietra wrote:

> I carried out all Dock6.1 tutorials with the aid of Chimera 1.2422 and DMS. The
> relevant files used for, and got from, the flexible-ligand docking tutorial are
> attached. I believe I used defaults. The out file attached is the one of the
> four out files (from mpirun -np 4 ....) that seems to me to be relevant.
>
> How to view graphically the best scored ligand from flex_scored.mole2 in the
> protein? Just combine flex_scored.mole2 with the ligand-deprived receptor?
>
> This in view of my project of looking for docking between a family of
> lypophilic natural products (conformationally studied in vacuum with Amber9
> simulated annealing) and a complex, large protein. I.e., by carrying out a
> process of the type illustrated by the docking tutorial for each pocket of the
> protein. I know there is interaction between the two (though a mere
> disassembling of the lipid bilayer can't be rigorously ruled out yet) but no
> idea where.