[Chimera-users] clipping and capping

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 7 11:04:06 PDT 2015

Hi George,
You do NOT need to generate a volume or use sop clip.  It’s just a clipped molecular surface.

You can just follow all the steps in the B-factor coloring image tutorial.  If you don’t want to do the coloring part you could skip just that part.  The feature highlight you mention has an “image how-to” link that goes to that tutorial.


Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 7, 2015, at 10:40 AM, George Tzotzos <gtzotzos at me.com> wrote:

> 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).
> 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

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