It should be possible to play around a bit with the PyMOL command line options to come up with better configurations for batch processing several structures. It's a bit funny at the moment - sometimes PyMOL will fail to compute/output the mesh properly. Perhaps there's another way to compute these meshes - blender springs to mind? Having said that, I think the dedicated functionality PyMOL brings is worth the pain.
Added base protein mesh functionality.
It should be possible to play around a bit with the PyMOL command line options to come up with better configurations for batch processing several structures. It's a bit funny at the moment - sometimes PyMOL will fail to compute/output the mesh properly. Perhaps there's another way to compute these meshes - blender springs to mind? Having said that, I think the dedicated functionality PyMOL brings is worth the pain.