Creating and Displaying Surfaces

Surfaces are a useful way of displaying spatially distributed properties of structures. The molecular surface gives an indication of the van der Waals radius of the molecule, for example.

Surfaces are constructed from a set of elements (pieces) that are joined together to create the desired geometric shape. If the shape is predefined, like a van der Waals surface or a Connolly surface (molecular surface), this can be done directly. Other surfaces are derived from data for a function (such as the electron density) that is available on a three-dimensional grid. This data is called a volume. The surface is created by selecting a value for the function and displaying the surface that corresponds to that value, by interpolation of the data. The value is called an isovalue, and the surface is called an isosurface.

Surfaces can be colored according to the value of some volume property at the surface, using a color scheme or a color ramp to indicate the values of that property. In this way, for example, you could show the value of the electrostatic potential on a molecular surface, and so visually determine the locations where positive or negative charges would be stabilized.

Surfaces (without volumes) can be created in a number of ways:

  • Molecular surface—select the atoms to surface (or none to surface everything), and choose Workspace → Surface → Selected Atoms, or click the Surface button in the Changing Structure Styles.

  • Binding site surfaces—choose Workspace → Surface → Binding Site to create a surface for the ligand and the binding site region of a receptor-ligand complex.

  • Other molecular and related surfaces—choose Workspace → Surface → Advanced to generate surfaces related to the van der Waals radii of the atoms, with control over various parameters of the surface. See Advanced Surfaces Panel for more details.

When surfaces are created, a button labeled S is added to each entry that is surfaced. This button allows you to quickly show or hide the surfaces associated with an entry, or open the Surface Manager Panel to manage all the surfaces in the project. To show or hide all surfaces in the Workspace, you can use the Surface button on the Workspace Configuration toolbar.

Volumes can be generated with a number of applications:

You can also import surfaces or volumes in a number of formats, and associate them with an entry (which should, of course, be related to the volume). In the Maestro main window, choose Workspace → Surface → Import or in the Project Table panel, choose Data → Import → Surface, and open the file using the Import Surface/Volume File Dialog Box, then choose the entry to associate the surface or volume with in the Choose Entry dialog box. An S button is added to the entry for access to the surfaces or volumes. Surfaces are imported automatically by default when the structure file with which they are associated is imported into Maestro. See Import Dialog Box for more information.

If you want to make any changes to the display of the surfaces, or do other management tasks for surfaces, you can use the Surface Manager Panel. You can change the isovalue, color, transparency, and style, and truncate the surface display; import or export surface or volume data; split double surfaces (ones that have a positive and a negative isovalue) into two separate surfaces; duplicate and delete surfaces. Volumes can also be rendered directly as a function of the data value in the Workspace by defining a map of the data values to the opacity and to color ramps. Default values for surface display can be set in the Surfaces Preferences of the Preferences Panel.

You can also make changes to a surface by right-clicking on it and choosing from the shortcut menu. The pointer icon changes to a mesh patch to indicate when you are picking the surface, rather than the atoms. This menu allows you to set display options (in the Surface Display Options Dialog Box), hide or delete the surface, and open the Surface Manager Panel.