[Chimera-users] extract parts of a map based on 'volume data gradient norm'

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 15 09:56:48 PDT 2018

Hi Dieter,
If I understand correctly, you have two maps, the original volume (density) and then another with gradient norm that is used to color the first.

In that case, you could show an isosurface of the gradient norm values, then use the “mask” command to mask the original density map by the gradient-norm isosurface (i.e. zero out parts inside or outside the isosurface):


I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 14, 2018, at 10:43 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> Hi,
>       I want to segment a map based on differences in 'volume data gradient norm' which I can adjust as to color the part of the volume I am interested in in blue and the one I want to get rid of in red. Is there a way of doing so? I admit that I never used the segger tool and do not know whether it would be appropriate for this task. The final aim is it to write out the blue volume!
> Thanks for hints, bw, Dieter

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