[Chimera-users] help on virus visualization

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 25 09:33:43 PDT 2010

Hi C.J.,
I assume you are looking at a density map.  In that case...

There is a Volume Eraser tool (under Tools... Volume Data) that allows you to position a sphere interactively and then erase the density inside or outside the sphere.

However, it might be hard to position the sphere interactively.   A similar approach would be to use the "shape" command to place a sphere, and in that case you can enter the center coordinates, and then the "mask" command to erase the density outside that sphere.

There is also the "vop" command with which you could chop out an octant:

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 Oct 24, 2010, at 9:50 AM, jh wrote:

> Dear all,
> I want to mask area outside certain surface and to visualize the inner
> capsid of a virus by Chimera.
> Anyone would be kind to help me with that?
> C.J.

More information about the Chimera-users mailing list