The command surftransparency changes the transparency of a surface to the specified percent, where 0% is completely opaque and 100% is completely transparent. For molecular surfaces, this overrides any transparencies included in the definitions of the surface colors, but they are remembered and can be restored with ~surftransparency. For other surface models, ~surftransparency sets the transparency to 0%.
The transparencies of per-atom patches of molecular surface can be adjusted independently by specifying the corresponding atoms. Other surface models can only be specified as a whole.
A change in surface transparency can be performed abruptly or over a specified number of frames.
Surfaces colored with tcolor will not be affected by surftransparency.
See also: surface, surfrepr, colordef, the Actions menu, movie-related commands