[Chimera-users] delete volume densities

Hernando J Sosa hernando.sosa at einstein.yu.edu
Tue Aug 16 15:34:56 PDT 2011

This is what I was looking for.


-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Tuesday, August 16, 2011 5:56 PM
To: Hernando J Sosa
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] delete volume densities

Hi Hernando,
You can hide density that is farther than a cutoff from selected atoms, and then if you actually want to delete the hidden part, you can save a new density map with values in the hidden area set to zero.

Hiding the zone:  In Volume Viewer, go to the Features menu, choose Zone to show the zone controls in  the dialog.  Select the atoms of interest, then click the Zone button.  The cutoff radius can be edited directly or controlled with a slider.

Saving a new density map with values outside the zone set to zero: After applying the zone, use "File... Save map as" in the Volume Viewer menu.


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 Aug 16, 2011, at 2:44 PM, Hernando J Sosa wrote:

>   A while ago I remember using a Chimera function to delete map densities that were outside a  given distance from selected atoms in a structure.  I can't seem to find this utility anymore.   Can somebody please remind me where to find it. Is this utility still there in the new chimera versions?
> Thanks 
> Hernando

More information about the Chimera-users mailing list