[Chimera-users] help on virus visualization

[Elaine Meng]

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.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html>

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.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

There is also the "vop" command with which you could chop out an octant:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html>

I hope this helps,
Elaine
----------
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.