[Chimera-users] Gradient map

Bui Khanh Huy huy.bui at mol.biol.ethz.ch
Mon Dec 24 15:29:07 PST 2007

Hi Elaine,
I tried what you told me, and it seems to work like what I expected. But I just want to confirm what I did is right as I don't fully understand the guide on the webpage you gave me.
My question: I have volume A & B. I want to color the surface of volume A by the gradient of volume B.
What I did:
- I chose iso surface display of volume A using Volume Viewer.
- Go to Tools/Volume Data/Surface Color, choose Color Surface A, using B gradient norm, then Color.
Best regards,


Von: Elaine Meng [mailto:meng at cgl.ucsf.edu]
Gesendet: Fr 12/21/2007 4:54
An: Bui Khanh Huy
Cc: chimera-users at cgl.ucsf.edu
Betreff: Re: [Chimera-users] Gradient map

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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