[Chimera-users] select

[Elaine Meng]

Hi Maria,
You can't really select part of a map, but you can delete or "erase" parts of it.

With the Volume Eraser tool (under Tools... Volume Data in menu), you can place a sphere on the map and erase everything outside (or inside) that sphere.  However, that requires moving the sphere by hand, which might be hard.
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html>

Another possibility is to create a surface in the shape of a sphere, or icosahedron, or sphere-icosahedron blend with specified center using the "shape" command, and then use the "mask" command to erase outside that surface.  I'm not sure if the masking gets the inside or outside by default, but there is a keyword to invert so you will be able to both.
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

Actually I don't know what shape that virus is.  The above assumes something roundish or icosahedral.  The "shape" command includes other shapes, but if the virus is irregular, it may be necessary to use some other program to create a surface of the shape needed for masking.

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 3, 2011, at 8:16 AM, maznar wrote:

>       Hello,
>       I working about Bam35c virus (emd_1123.map). That virus has a capsid and other things inside. I want used only exterior part (between 315 and 335 amstrons) and discard other parts. How can I select only this external part?
>       Thank you for your help
>       María