[Chimera-users] Gradient map

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 21 07:54:19 PST 2007

Hi Huy,
If I understand correctly, you want (1) a isosurface of the density map  
(2) colored by the gradient in that same map.

(1) If you open the density map in Chimera, it will automatically start  
Volume Viewer, in which you can adjust the isosurface display (contour  
level(s), smoothing, etc.).  More details on Volume Viewer:

(2) Then you can use Surface Color (listed under Tools... Volume Data  
in the main menu, or in the Volume Viewer Tools menu) to color that  
isosurface by the data gradient.  You do not have to make a separate  
map with the gradient.  In Surface
Color, choose the option to use the "gradient norm" of the density map  
you already opened.  Then you can adjust how colors should map to the  
gradient norm values.
More details on Surface Color:

I hope this is what you had in mind.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 21, 2007, at 12:49 AM, Bui Khanh Huy wrote:
> Hi,
> I'm pretty newbie for Chimera. Anyone knows there is a function to
> display a density map as a gradient map?
> My purpose is:
> - Having one density map displayed as a surface rendering map
> - Having another different density map displayed as a gradient map only
> on the surface of the surface rendering map above.
> Thanks a lot,
> Huy

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