[Chimera-users] 2D image contour plot using Chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 16 15:54:34 PDT 2010

Dear Yao,
If you mean to show contour lines in a plane of a density  map, you can do that with Volume Viewer.
Open the density map, and then in Volume Viewer:

- show Planes options by choosing "Features... Planes" from the Volume Viewer menu

- In the Planes options, choose which axis the plane should be perpendicular to
and click "One."  This will automatically change style to "solid," but just change it 
back to "surface" or "mesh."   Use the slider or entry area to specify which plane is shown.

- Ctrl-click on the histogram to add more contour levels, can assign them different colors

- now there are planar "blobs" instead of outlines.  To show just the outlines, choose
"Features... Surface and Mesh options" from the Volume Viewer menu, and in those
options, turn off the bottom one, "Cap high values at box faces." 

- you may want to change the background color, for example with command:
set bg_color white

- you can make the contour lines thicker  by entering a larger "Mesh line thickness" in the
Volume Viewer Surface and Mesh options

I attached an example image.  I hope this is what you had in mind.  Best,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 12, 2010, at 8:51 AM, Yao Cong wrote:

> Dear Chimera developer,
> I was wondering that is there any way that I can use Chimera to do a  
> 2D image contour plot? Do I need some extra plug in or tools?
> Thanks a lot,
> Yao

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