[Chimera-users] Gradient map
meng at cgl.ucsf.edu
Fri Dec 21 07:54:19 PST 2007
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:
> 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,
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