I've created a surface for my entry in the Workspace and only want to clip the surface, and leave the atoms (e.g., the ligand in my protein) intact (i.e., visible). Is that possible?

Yes. Ensure that the Clipping Planes window is visible (the small square view in bottom right hand corner of the Workspace) - you can do this from the Maestro menu (Suite 2010 on) or the View menu (earlier releases) and the Window menu (Suite 2011 on). Right click in this window and select Surface. By default it is set to All. Now when you move the clipping plans, only the surface will be clipped, not the atoms.

Keywords: Maestro, surface, clip

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