PCM Solvation Cavity


The PCM Solvation Display Dialog

The PCM Solvation Display displays the solvation cavity computed via the SCRF=Read facility’s PDens additional keyword.

When the Show Surface button is checked, the overall surface of the molecule is activated. Its format can be specified via three checkboxes below.

When the Show Solid button is checked, it displays the surface as a solid, hiding the molecule. When the Show Mesh button is checked, it displays the surface as a mesh, allowing you to still see the atoms and the bonds beneath the surface. When the Show Points button is checked, it displays the surface as a series of points, offering a better view of the atoms and bonds than the Show Mesh display does. More than one display type can be used at the same time.

The Color menu allows you to choose which color the surface is displayed as. This functionality is not available if the Color by Atom button is checked, which will color different portions of the surface using the color of the atoms that generated it.

The Cull Backside button removes the portion of the surface “behind” the molecule. This can sometimes result in an improved display.

The dropdown menu below the Cull Backside button is only available for the Show Mesh and Show Points buttons. The options for this are Small, Medium, and Large. They control the size of the mesh lines or the points that surround the molecule.

The Solid Opacity slider is only available when Show Solid or Show Mesh are selected. This slider controls how opaque/transparent the surface is. The left end of the slider corresponds to a completely transparent surface (invisible), and the right end corresponds to a completely opaque surface.