How do I calculate the surface area of the active site's Connolly surface?

You can use the Molecular Surface panel with the following ASL, assuming the ligand is molecule #2 in the complex structure:

not (mol.entry 2) and fillres within 6 (mol.entry 2)

Make sure that "Surface Context" is set to "Molecule". If the ligand is covalently bound or has zero-order bonds to the receptor (and thus not considered a separate molecule) you should first break the bonds using Bonds or Zero-Order Bonds on the Delete toolbar button. The area of the Connolly surface will be reported in the "Manage Surfaces" panel in Ų.

Keywords: active site, binding site, surface area, Connolly surface, Maestro

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