[Dock-fans] sphere_generator

Sudipto Mukherjee sudmukh at yahoo.com
Tue Jul 16 11:15:28 PDT 2013


Hi Mahesh,

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#SphereSelector


sphere_selector retains all spheres within the specified radius from the mol2 file provided. You can use showsphere to convert the .sph file to a PDB file for visualization. Vary the radius to select the set of spheres you want. 

The spheres selected largely serve as a starting point for sampling ligand conformations. As long as the spheres are roughly in the target binding site, you should be fine. 
 
Regards
Sudipto Mukherjee, PhD
Dept. of Chemistry, Temple University
1901 N 13th St, Philadelphia, PA 19122


________________________________
 From: Mahesh Hegde <mahesh at biochem.iisc.ernet.in>
To: dock-fans at docking.org 
Sent: Tuesday, July 16, 2013 12:54 PM
Subject: [Dock-fans] sphere_generator
 

Hi, What is the basis of selection of spheres by sphere_selector? in my
case its showing wrong sphere (i used one positive control which is
already known for its binding pattern), is there any way to check it or to
modify sphere selected or to select whole sphere? thank you for your time.

-- 
Sincerely,
Mahesh Hegde

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