[Chimera-users] cutting the surface

Elaine Meng meng at cgl.ucsf.edu
Mon Jul 15 09:45:45 PDT 2013

Hi Victor!

Per-Model Clipping (in menu under Tools… Depiction) or its command version "mclip" allow you to do exactly this.  You just need to display the surface and then specify the surface model as the one to clip.


In your wikipedia image example, I see that there is no "cap" so the surface looks open.  You can also do that in Chimera.  Here are a few example commands:

open pubchem:12123
setattr s density 10
mclip "#0 & ~ @"
sop cap off
back solid gray

To change the angle/position of the clipping, it is probably easiest to use the mouse with the option in the Per-Model Clipping dialog.

The "B-factor coloring" image tutorial includes another, fancier example where the surface is capped.

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

On Jul 15, 2013, at 9:26 AM, Victor Muñoz <chewaka.87 at gmail.com> wrote:

> Dear all,
> I want to make an image using the Surface Cliping option in Chimera. The problem is that I just want to cut the surface and not the molecule when using the Viewer to do that. As an example, I want to so something like this image from the wikipedia (http://en.wikipedia.org/wiki/File:MM_PEF.png).
> Thanks for everything in advance.
> Kind Regards,
> Victor Muñoz

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