Hi Michael, The carve command displays the radial density of a selected atom. As per the example, a carve=1.6 would mean that density around a selected atom will be shown with a 1.6 Angstrom radius. The carve command can prove useful in figures in which density obscures relevant information. It is important that if implemented the audience is made aware so as to avoid confusion. The carve command is not set by default within PyMOL therefore the density will not be manipulated without user input. Alternatives to PyMOL that maybe of interest are UCSF Chimera and Discovery Studio Visualize.
Take Care, Sean http://store.p212121.com/
