Create Binding Site Surfaces Dialog Box

In this dialog box you can set options for the generation of binding site surfaces and create the surfaces. Two types of surfaces can be generated: molecular surfaces and interaction surfaces.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Workspace Operations → Surface (Binding Site)
  • In the Maestro main window, choose Workspace → Surface → Binding Site
  • Features
  • Additional Resources

Create Binding Site Surfaces Dialog Box Features

Surface type options

Select an option for the type of surface to create.

  • Interaction Map—Create a binding site surface. This is the surface map generated by SiteMap—see SiteMap Surface Map for more information.
  • Molecular Surface—Create molecular surfaces for the receptor and ligand. See the Advanced Surfaces Panel topic for more information.
Create surface for options

Select options to control which surfaces are created: ligand surface, receptor surface, or both. These options are only present if the Surface type option selected is Molecular Surface.

Truncate receptor surface at N Å from ligand text box

Specify the distance from the ligand at which the receptor surface is truncated.

Surface transparency text box

Specify the surface transparency as a percentage.

Style options

Select an option for the kind of surface to draw, from Solid, Mesh, or Dot.

Color scheme option menu

Choose a color scheme for coloring the surface. Apart from coloring with a single color, the option menu lists various properties by which the surface can be colored. If a single color is chosen, a color button with the current color for the surface is shown to the right of the menu, or two color buttons if both surfaces are selected for creation. The button for the receptor is the first of these two.

If more than one ligand is detected, find binding site for options

Choose an option for the ligands to find binding sites for. The ligands are detected using the Ligand detection settings in the Preferences Panel.

  • All ligands in Workspace—find binding sites for all ligands in the Workspace.
  • Selected ligands only—find binding sites for the ligands that are selected in the Workspace. Make sure you select the desired ligands before creating the surfaces.
Reset button

Reset the values in the panel to their defaults.

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