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

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 15 15:06:08 PDT 2018

Dear Dieter,
An isosurface is just the surface of a density map showing a certain level, i.e. the “surface” display in Volume Viewer.

Do you have one map or two maps?  I tried to ask that by saying “if I understand correctly” in my previous message.  I thought you were just coloring the isosurface of one density map by the values in a second map, where the second map is gradient norm map.  

It might help if you attached a picture of the display and Volume Viewer dialog.  “blue part” and “red part” are ambiguous.
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 15, 2018, at 2:51 PM, Dieter Blaas <dieter.blaas at meduniwien.ac.at> wrote:
> Dear Elaine,
>    thank you! I am sorry, but I do not understand: how do I get the isosurface? What is the command? Carefully adjusting the boundaries of the gradient norm, I got a blue and a red part. How can I make an isosurface of one of them? Is this a function in the GUI or do I have to use the command line? Can you please give an example of how to proceed!
> Thank you very much, bw Dieter

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