[Dock-fans] problem selecting spheres

Carlo Zambonelli zambonel at gmail.com
Sun Apr 27 07:28:42 PDT 2008


Dear Dock-fans,
after successfully completing all the tutorials using L-arabinose 
binding protein I started working on my first real docking. Everything 
went smoothly until I reached the point where I have to select spheres. 
Following the instruction in the Generating Spheres tutorial I start 
having problems in "STEP 3: Select a subset of spheres to represent the 
binding site(s) - Option 1". How do I create a selected_spheres.sph 
file? This is clear with option 2 using sphere_selector (which is what I 
did in the tutorial), but what should I do if I have no idea where is 
the binding site on my protein? Since I do not know where is the binding 
site on my molecule, or if there is only one binding site, can I create 
a selected_spheres.sph file containing all spheres in rec.sph?
Thanks,
Carlo


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