[Dock-fans] sphere_selector

William Joseph Allen william.joseph.allen at gmail.com
Thu Jul 18 08:16:37 PDT 2013


Hi Mahesh,

In principal, yes you can use all of the spheres that were generated. In
the .sph file, I think there should be a 'cluster 0' at the bottom which
contains a record of all spheres from every cluster. When you make the box,
you can choose '0' as the cluster. Depending on the size of the box and the
resolution you choose, the grid that you generate will have a very large
file size. I'm not sure what the memory limits are of your computer system,
but it is something to consider.

As far as sphere_selector, it is not designed to 'predict' binding sites.
It is a very simple program that requires three inputs: a sphere file, a
molecule file (mol2 format), and a radius. sphere_selector opens up the
mol2 file, and considers the Cartesian coordinates of each atom in the
file. Then, one by one it considers each sphere from the sphere file to see
if it is within <radius> of any one of the mol2 file atoms. If so, it keeps
the sphere. This process is described in the manual:

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

>From your e-mails, it seems that you have a specific binding site in mind,
but there is no ligand bound. Is this true? If that is the case, you could
generate a new mol2 file that contains atoms in or near your binding site
to be used as input for sphere_selector. One simple way to do this would be
to open up your receptor file in chimera, select a residue in the middle of
the binding site, and save it alone as a new mol2 file. Then when you run
sphere_selector, it can keep all of the spheres within <radius> of that
residue. Trent gave essentially this same response three days ago, so that
is why I didn't answer your question right away - I thought you must be
asking something else.

http://mailman.docking.org/pipermail/dock-fans/2013-July/002803.html

Please let me know if this clarifies things,

Joe Allen


On Thu, Jul 18, 2013 at 10:47 AM, Mahesh Hegde <mahesh at biochem.iisc.ernet.in
> wrote:

>
> Dear Joseph Allen,
>
> Thank you for your reply, ya i meant i used 10 Angstrom to select sphere.
> I have simple straight forward question. Can we use whole SPH file which
> is generated after SPHGEN command as selected spheres? when i used sphere
> selector , instead of binding site it predicted some other site , i saw
> this in chimera too. How to specify region for selection in receptor, if
> you wish i will give you PDB as well as ligand structure.
>
> --
> Sincerely,
> Mahesh Hegde
>
> --
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>


-- 
William Joseph Allen, Ph.D.
Postdoctoral Associate
Dept. of Applied Mathematics and Statistics
Stony Brook University
http://ringo.ams.sunysb.edu/~wjallen/
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