[Dock-fans] reply: Generating spheres manually

[Scott Brozell]

Hi,

On Tue, 28 Oct 2008, zjxu wrote:

> 85，244 are  the atom ids of the protein which are in tangency with the
> sphere.

Yes, I added a clarification to
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm

> If you have the sphere’s coordinates, I think you may determine the
> associated atoms by selecting some radius of the sphere until there are
> three left(the sphere, the first atom and the second atom). However, the
> radius of different elements are different, so maybe you should visualize
> more than 3 atoms, and select 2 which can tangent the sphere.
> 
> 
> And I do have a question, does dock use the associated atom(85,244, as in
> Donna’s example) in the next steps? I mean grid and dock. If not, could I
> use any numbers to substitute them? 

dock6 does not use either associated atom.
it seems that grid does not use either associated atom.
showbox does not use either associated atom.
Thus, it seems that any numbers could be used; try it and report back.

> And as the dock4’s manual said, Only the coordinates of the sphere centers
> are used to orient ligands within the active site; Sphere radii are used in
> clustering(dock4’s manual, P12). Could I manually appoint 0 for my own
> sphere’s radius?

That's also in the Dock 6 manual:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#OverviewoftheDOCKSuiteofPrograms
A code browse confirms that sphere centers are used in orienting,
but i didn't see ANY use of the sphere radii.
So try it and please send us a report.

On Mon, 27 Oct 2008, Donna wrote:

> I am attempting to generate my spheres manually, since I know the
> coordinates of the features I want to include.
> I am not sure what is meant by 'the number of the second atom with which the
> surface point is associated' (244 shown in bold below)? Could anyone please
> explain to me where this number comes from.
> 
> e.g. 
> 
> 85  1.09742  22.78395  21.72392  2.000  244  0  0
> 
> And is there a way to label a sphere as both a donor or acceptor?

It seems that you can have a label 'acceptoranddonor' and then set the
interaction matrix appropriately; see
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#chem_matchtbl

Scott