Hi Guizhen,

  Here are a few more details.  This is kind of tricky because Chimera focuses on 3d images, not 2d plots.

  Use volume dialog menu Features / Planes to show one plane of your map, switch to surface style, use volume dialog menu Tools / Surface Color and color the plane by "volume data value”.  Now we make the contour lines by making a copy of the map, volume dialog menu File / Duplicate, show the same plane, set style to Mesh, turn off the “Cap high values at box faces” option (Features / Surface and Mesh Options), add more contour levels using ctrl-click on the histogram, increase line thickness (Featues / Surface and Mesh Options), color all levels black (command "color black #1”).  Since the planes are at exactly the same level the contour lines are probably hidden.  To fix this move the contour plane slightly forward with command “move z 1 model #1 coord #1” (move map #1 by 1 Angstrom along the z direction of the coordinate system of map #1).  I did this on a ryanodine receptor map, emdb 5014 (plane 89). Here’s the result.

Tom




On Nov 5, 2014, at 10:36 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Guizhen,
I don’t know of a way to make a figure exactly like yours, with colors between black lines.  However, I know how to show a slice in which the contour lines themselves are colored, as in the attached image.  To make that image, I used the “Planes” feature in Volume Viewer, with multiple contour levels and other specific settings as described in this previous post:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005454.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

<contourlines.png>
On Nov 5, 2014, at 7:41 AM, Fan, Guizhen <Guizhen.Fan@uth.tmc.edu> wrote:

Hi,
How can I get multi contour lines like attached figure?
Thank you.
Guizhen


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