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

Yao Cong cong at bcm.edu
Mon Aug 16 16:18:17 PDT 2010

Dear Elaine,

You are so helpful, and I was really amazed by how powerful Chimera  
can be.

Many thanks,

On Aug 16, 2010, at 5:54 PM, Elaine Meng wrote:

> 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
> ----------
> 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
> <contour.png>

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