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@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