[Chimera-users] radial clipping

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 15 19:09:50 PDT 2011

Hi Kelly,
As far as I know there is no spherical clipping capability in Chimera other than using Volume Eraser to erase outside the sphere.  However, you could do almost the same thing by creating spherical or icosahedral surfaces of progressively larger (or smaller) radii and coloring them by the density values in the map.  See for example the movie at the very bottom of our animation gallery:

See the "shape" command for creating spherical or icosahedral surfaces,
also Icosahedron Surface tool

and "scolor" for coloring the surface by density values,
also Surface Color tool

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 Mar 15, 2011, at 1:29 PM, Kelly Dryden wrote:

> Hi,
> I would like to radially clip a density map.  There are nice ways to do radial coloring, but I haven't found anything that allows a similar cropping (preferably with capping).  Is there an easy way to do this?  I do not want to erase the density, but rather be able to see the surface at varying radii, just as you can do with planes.  (At the moment, I can only run v1.4).
> Thank you,
> Kelly

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