Molecular surfaces

EasyHybrid draws molecular surfaces for any object, protein or small molecule. They are independent of the QC surfaces (orbitals, electron density and electrostatic potential), which are described in Orbitals and Surfaces.

Surface types

• Van der Waals (VWS): the union of the atomic van der Waals spheres.

• Solvent-Accessible (SAS): the surface traced by the center of a probe sphere rolling over the molecule, that is, the van der Waals spheres grown by the probe radius.

• Solvent-Excluded / Connolly (SES): the surface traced by the probe itself: the region the solvent cannot reach. It is the usual "molecular surface".

Creating a surface

• Right-click the object in the tree of the main window and choose Representation > New Surface...

• In the Surface Setup dialog (Figure 1), choose the Surface type (VWS, SAS or SES; default SES), the Probe radius (SAS/SES only; 1.4 Å for water), the Grid spacing (default 0.8 Å; smaller values give a finer surface but are slower), the coloring (Atom colors, Chain or Carbon color (system)) and, optionally, Taubin smoothing with its number of iterations.

• Click Generate.

How surfaces behave

• Each surface is a new object, nested under its molecule in the tree. Several surfaces can exist at the same time, even of the same type (for example SAS and SES, or different probe radii), and each can be shown or hidden independently.

• For a trajectory, a surface is generated for every frame (in parallel) and follows the frame shown by the Trajectory Handler.

• The surface area (Å2) is printed in the terminal when the surface is generated.

Changing a surface afterwards

Right-click the surface object and choose Setup. The options are Wireframe, Opacity, Smooth shading, Decimate (merges vertices closer than a given distance, in Å, to make the mesh lighter) and Taubin smoothing. The default values for new surfaces are set in Edit > Preferences > Viewer > Representations > Surfaces.