[Chimera-users] delete volume densities

Tom Goddard goddard at sonic.net
Wed Aug 17 17:48:22 PDT 2011

Hi Hernando,

   In tonight's Chimera daily builds there will be a new "vop zone" 
command, for example,

     vop zone #0 #1:.B 5

will mask map #0 within 5 Angstroms of chain B of molecular model #1, 
creating a new masked volume.  Also I added a Mask button to the volume 
dialog Zone panel to make the masked volume.  The Zone button in that 
dialog only hides part of the surface far from the selected atoms.

   These two improvements should make it a bit easier to mask volumes 
within a radius of some set of atoms.


Tom Goddard wrote:
> 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.
>       Tom
>> This is what I was looking for.
>> Thanks!
>> -----Original Message-----
>> From: Elaine Meng [mailto:meng]
>> 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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