[Dock-fans] reply: reply: Generating spheres manually

zjxu zjxu at mail.shcnc.ac.cn
Mon Nov 3 02:55:16 PST 2008


Yes, I have done a test for dock4(SGI,IRIX64).The original sphere file was
like this:
  133 -42.89248  28.54200  -2.92289   2.217 1079 0  0
  168 -41.83802  30.89100   0.22209   1.708  120 0  0
  169 -40.14960  25.35247  -0.79977   2.365  514 0  0
  170 -41.25857  30.29124  -1.41077   2.405 1078 0  0
  250 -41.21507  22.58200   0.86687   1.666  630 0  0
  251 -41.74216  21.88000   1.53374   1.489  612 0  0
  252 -37.67489  27.09433  -0.02991   2.390 1078 0  0
  255 -41.03080  24.57371   1.82191   1.401  252 0  0
  264 -41.55431  23.68900  -0.68502   2.391  514 0  0
  266 -42.16452  23.86300  -1.93140   2.537  514 0  0
  409 -43.01282  20.53600  -3.07001   1.776  435 0  0
  435 -42.60943  20.61176  -2.80630   1.961  630 0  0
  509 -40.06703  18.72623  -3.68394   1.452  435 0  0
  511 -40.43344  19.69706  -4.32734   1.485  435 0  0
  513 -36.58878  25.08497  -0.67519   1.828  252 0  0
  514 -41.71731  24.24883  -1.26918   2.488  170 0  0
  612 -42.39545  21.24406   0.83724   1.401  630 0  0
  615 -42.95685  21.80597  -0.83201   1.963  264 0  0

I changed the associated atoms and the spheres' radius to zero, so it seemed
like this:
  000 -42.89248  28.54200  -2.92289   0.000 0000 0  0
  000 -41.83802  30.89100   0.22209   0.000  000 0  0
  000 -40.14960  25.35247  -0.79977   0.000  000 0  0
  000 -41.25857  30.29124  -1.41077   0.000 0000 0  0
  000 -41.21507  22.58200   0.86687   0.000  000 0  0
  000 -41.74216  21.88000   1.53374   0.000  000 0  0
  000 -37.67489  27.09433  -0.02991   0.000 0000 0  0
  000 -41.03080  24.57371   1.82191   0.000  000 0  0
  000 -41.55431  23.68900  -0.68502   0.000  000 0  0
  000 -42.16452  23.86300  -1.93140   0.000  000 0  0
  000 -43.01282  20.53600  -3.07001   0.000  000 0  0
  000 -42.60943  20.61176  -2.80630   0.000  000 0  0
  000 -40.06703  18.72623  -3.68394   0.000  000 0  0
  000 -40.43344  19.69706  -4.32734   0.000  000 0  0
  000 -36.58878  25.08497  -0.67519   0.000  000 0  0
  000 -41.71731  24.24883  -1.26918   0.000  000 0  0
  000 -42.39545  21.24406   0.83724   0.000  000 0  0
  000 -42.95685  21.80597  -0.83201   0.000  000 0  0
  
And I got the same results for both, so maybe it was easier to add spheres
manually.
zjxu
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_s
pheres.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#OverviewoftheDOCKSuiteo
fPrograms
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
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