[Dock-fans] reply: Generating spheres manually

[zjxu]

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

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? 

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?

 

Thanks in advance

 

zjxu

  _____  

发件人: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org]
代表 Donna
发送时间: 2008年10月27日 星期一 21:13
收件人: Dock-fans at docking.org
主题: [Dock-fans] Generating spheres manually

 


Hello,

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?

I hope someone can help.

Donna

 

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