What tools are most widely used for generating a mesh surface of a protein from an x-ray crystallographic structure (from the PDB)? Pros and cons would be appreciated.
I'd prefer the output to be a watertight triangle mesh of the protein surface. Also, I'd like the tool to be scriptable (i.e. no need to open a GUI).
So far, I've been playing with MSMS and EDTSurf. But I was wondering what was standard in research, as well as if there was anything in the standard bioinformatics libraries.