[Chimera-users] how to get multi contour lines?

Tom Goddard goddard at sonic.net
Wed Nov 5 10:56:51 PST 2014


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 at 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 at uth.tmc.edu> wrote:
> 
>> Hi,
>> How can I get multi contour lines like attached figure?
>> Thank you.
>> Guizhen
> 
> 
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20141105/f835f1a2/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: contour_5014.png
Type: image/png
Size: 298352 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20141105/f835f1a2/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: contourlevels.png
Type: image/png
Size: 287398 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20141105/f835f1a2/attachment-0003.png>


More information about the Chimera-users mailing list