[Chimera-users] Contour mapping

Tom Goddard goddard at sonic.net
Mon Apr 30 11:47:34 PDT 2012

Hi Nikolay,

   I guess you mean that the viewing angle of the clip plane surface 
effects the colors on that surface.  That happens because light 
reflections are used to improve the 3-dimensional appearance -- the 
sense of depth.  You can get rid of those light reflections using menu 
Tools / Lighting and switching the lighting mode from the default 
two-point lights to "ambient".  Another way to do this is with the 
Chimera command

     lighting mode ambient

Another problem you will notice is that the coloring on the clip surface 
may have jagged boundaries.  To improve this use menu Tools / Depiction 
/ Surface Capping and increase the cap "mesh subdivision factor" from 1 
to 10.  The coloring is only applied to the vertices of the mesh that 
defines the "cap" (ie flat surface) that covers the  hole made by 
clipping.  This step makes a much denser array of vertices and less 
jagged coloring.


> Hi all,
> I was wondering if anyone could help me create an accurate contour map 
> based on surface charge. I've tried rendering my molecule by charge, 
> then using the surface clipping, capping, and the color zone tools. 
> However, the coloring varies based on how I orient the plane. Does 
> anyone know a better and more accurate way to creating a contour map?
> Nikolay Rodionov

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