[Chimera-users] Chimera & dock grids

[chimera-users at cgl.ucsf.edu]

  Dear Dr. Tyndall,
Thanks for your interest - DOCKgrid is indeed undocumented, partly
because we have a much more advanced extension for viewing 3D data
sets, Volume Viewer.  This would let you have multiple contour surfaces
or transparent solids in colors of your choosing, with interactively
adjustable thresholds.

The current hitch is that the DOCK grid formats have not yet been added
to the Volume Viewer extension.  We are actively looking into this and
hope to incorporate it soon (we will let you know when this happens).

I believe the values are directly those stored in the grid files, which
(for dock 4 at least) are described in
    http://dock.compbio.ucsf.edu/dock4/html/Manual.1c.html#pgfId=850
The VDW repulsion, VDW attraction, and electrostatic grid values
are described in equation 9 (all three are in the *.nrg grid).
These are not in energy units until multiplied by ligand atom parameters.

I believe the color choices in DOCKGrid are red and red.  Display with
Volume Viewer should be a vast improvement.

To close molecules and also these contour surfaces, one way is to
open the Model Panel (Tools... Inspectors... Model Panel in version 1.1700).
In the Model Panel, choose the model(s) you want to close on the left side,
then click "close" on the right side (not the Model Panel Close button).
Unfortunately the contour surfaces created by DOCKgrid are each VRML
files without an informative title, so it may be hard to tell which is
which.  If you only have one, of course, it will be obvious.
I hope this helps!
  Best regards,
    Elaine
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Elaine C. Meng, Ph.D.
Computer Graphics Lab and Babbitt Lab
meng at cgl.ucsf.edu
http://www.cgl.ucsf.edu/home/meng/index.html
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