[Chimera-users] delete volume densities

Tom Goddard goddard at sonic.net
Tue Aug 16 15:47:45 PDT 2011

Hi Hernando,

   I'm going to put in a Chimera request to allow the "vop" command to 
do the zone masking so you don't have to do the silly business of saving 
the zoned map and reloading it.  Not sure when I'll get to that but it 
should be quite simple to add.


> This is what I was looking for.
> Thanks!
> -----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.
> <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
> <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#organization>
> 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 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
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