I tried the hydrophobic/hydrophilic surface view, but I noticed that changing the isovalue changes the view dramatically. What exactly is this?

When the hydrophobic/hydrophilic surface view is first selected, a volume potential is computed. The displayed surface is an isosurface representing points of a particular potential value (i.e., the isovalue) within the volume. The online help for the hydrophobic/hydrophilic surfaces panel describes how these potentials are computed.

The -0.5 default isovalue for hydrophobic surfaces shows the region of relatively strong hydrophobicity. If you move the slider to the left (more negative values) the surface will shrink (showing the region of even stronger hydrophobicity), and if you move the slider to the right the surface will grow (showing the larger region that includes weaker hydrophobicity).

If you want to set a hydrophobic constraint in Glide, but the boxes don't cover quite the region you want, you can increase the isovalue (i.e., the "threshold phobic potential") to add more boxes. Keep in mind, though, that our software considers these additional boxes to be regions of weaker hydrophobicity.

Keywords: Glide, Maestro, hydrophobic, constraint, isovalue

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