I want to calculate the surface area of a protein binding site, defined as any residue 6 Å from the ligand, and also the volume of the binding site. How do I do this?

For the surface area, the best option is to use the Binding Surface Area Analysis panel, which you can open with Scripts → Project Table → Binding Surface Area Analysis.

Another option is to use use Workspace → Surface → Molecular Surface (Suite 2010 on) or Display → Surface → Molecular Surface (earlier releases), with the following ASL:

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

assuming your ligand is molecule #2 in the complex structure. Make sure that "Surface Context" is set to "Molecule"; also if your ligand is covalently bound or has zero-order bonds to the receptor (and thus not considered a separate molecule) you might want to break the bonds first using Delete → Bonds or Delete → Zero-Order Bonds from the Delete toolbar button. The area of the surface (Connolly) is reported in the Manage Surfaces panel in Ų.

Probably the best option for the volume is to use Applications → SiteMap. You can pick the ligand to specify which site to consider and how far from the ligand to extend the buffer region. The SiteMap job reports the site volume in the Project Table and also reports the surface area for the surface map in the "Manage Surfaces" panel.

Keywords: surface area, volume , measurement, Manage surfaces

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