I have read the manual about shape sphere. What I would like to do is retaining all proteic, nucleosidic, organic ligands, ions and water molecules that exist within a sphere of, say, 25A centered at a certain atom of a ligand, while discarding everything outside the sphere.

Because of the content, are there special flags to be used?

thanks

francesco pietra

(actually I am already trying with general commands but python is already working from 1 and 1/2 hr without any outcome)