Knowledge Base

Article ID: 1515 - Last Modified: August 16, 2012

When I generate a surface, I only want to see the portion that is in the active site. Is there a way of doing this?

Yes. When generating a molecular surface, you can pick the atoms to use for displaying the surface, and you can use the Surface Context option "Selected atoms" to limit the surface to those atoms. When you display the surface, only the parts of the surface for those atoms that were selected in the "Atoms for surface display" section are displayed.

If you have a surface you have already generated, you can click "Limit" in the Manage Surfaces panel, and then choose the atoms that you want to limit the surface display to. To specify the active site, you can use the Proximity dialog box to select residues within a specified distance of the ligand, or use the ASL expression 'within n (res.ptype "LIG ")' where n is the distance from the ligand that defines the active site residues.

Keywords: Maestro

Back to Search Results

Was this information helpful?

What can we do to improve this information?


To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles