[Chimera-users] End graphical representation from Dock tutorials

[Elaine Meng]

Hi Francesco,
Yes, now that you have DOCK results, you would open and display the  
"empty" receptor in Chimera and with the ViewDock tool, open and  
display the docked ligands (your mol2 file).  You can just open the  
receptor structure (pdb or mol2) the normal way, with File... Open.

See the Chimera tutorial on viewing docked ligands:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html

There is also full documentation on the ViewDock tool (the tutorial  
does not use all of its many features):
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/ 
framevd.html

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Oct 8, 2007, at 2:34 AM, 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.
>
> Thanks
> francesco pietra
>