[Chimera-users] Docking box

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 18 10:10:37 PST 2011

> (2) If you are using DOCK, you could use the small accessory program that comes with it, "showbox," to draw a box centered on and/or enclosing your docking spheres.  
> <http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Showbox>
> I haven't forgotten that you are looking at a Castp pocket and might not have any spheres, but now Chimera can be used to create the pheres.  A very new feature in Chimera (daily builds from last couple of days) is that it can read/write the Sphgen sphere format used by DOCK.  You could use the castp dialog option to select the pocket atoms, then save those atoms as DOCK spheres making sure to use the "Save selected atoms only" option.

also make sure to save "relative to" your original structure.

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