Advanced Surfaces Panel

Generate a surface for the selected atoms, with controls for the parameters of the surface. Three types of surfaces are available: a molecular (Connolly) surface, a van der Waals surface, and an extended radius surface.

To open this panel, .

  • Features
  • Additional Resources

Advanced Surfaces Panel Features

Type option menu

Choose the type of surface from this option menu. The three types available are described briefly below.

  • Molecular—a smooth surface that maps the closest possible approach of a probe sphere of a given radius to the van der Waals surface of the molecule. This is also called the Connolly surface. See Appendix: Molecular Surface Technical Details for more information.

  • Extended radius—the outer surface of the collection of atomic spheres for each atom in the molecule. The radius of each atomic sphere is the van der Waals radius of the atom plus a probe radius. Portions of atomic sphere surfaces that lie within other spheres are not part of the surface.

  • van der Waals—the outer surface of the collection of atomic spheres for each atom in the molecule.The radius of each atomic sphere is the van der Waals radius of the atom. Portions of atomic sphere surfaces that lie within other spheres are not part of the surface.

Resolution option menu

Specify the resolution of the surface, which is created using interpolation on a cubic grid. Higher resolution means a smoother surface, which is slower to generate and draw. Lower resolution means a rougher surface but faster to generate and draw (and hence rotating will be faster). When you choose Low, Medium, or High, the grid spacing in angstroms is displayed in the text box to the right. The default choice is Automatic, which selects high resolution for less than 1000 atoms, medium for less than 10000 atoms, and low for more atoms. If you want to specify the grid spacing, choose Custom and enter the desired value in the text box.

Probe radius text box

This text box specifies the radius of the probe that is to be rolled over the van der Waals surface for a molecular surface, or added to the van der Waals radius for an extended radius surface. The default probe radius of 1.4 Å corresponds to a water molecule as the probe.

VDW radius scale text box

Specify the scaling factor for the van der Waals radius.

For partial molecule selections options

If the atom selection for which the surface is created contains parts of molecules, these options allow you to choose whether to leave the surface open (Leave open surface edges) or close it (Close the surface). If you choose to close the surface, the surface will cross bonds in the molecule, and part of the molecule will be outside the surface. If you choose to leave it open, the edges may be a bit rough.

Create button

Generate the surface or surfaces. Surfaces are created for each molecule represented in the atom selection. Large-sized surfaces or surfaces with fine grid spacing can take some time to generate, and Maestro is not available until the task finishes.

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