[Chimera-users] clipping and capping

I’m a real novice in this kind of operation so I shall try in some detail what I’m trying to achieve. I’m dealing with a long serendipitous ligand that spans through a homodimer (2erb) (see screenshot1). I would like to generate something like the B-factor colouring feature (http://www.cgl.ucsf.edu/chimera/features.html <http://www.cgl.ucsf.edu/chimera/features.html>). I’ve opened the Depiction tool and tried surface clipping and capping to no avail. Reading the manual, I figured out that first I have to generate a volume and then use the sop clip command. If this is the routine, I’m seeking advice on how to generate the volume data and then pass it to the sop clip command. As always grateful for your kind help Regards George