[Chimera-users] Dynamic scolor custom cmap?

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Fri Dec 13 12:16:10 PST 2013

Hi Chimera friends,

I have a volumetric potential file loaded that I want to map onto a molecular surface. For my application, I want the color mapping to use a custom palette of at least three colors that spans the full range of surface values.

I know that I can do this by simply specifying the custom colors in the Surface Color panel and then clicking "Set full range of surface values". That works for me.

However, I want to do this via command line. The following line works for me (I've omitted "cmapRange full" because that is the default setting):

scolor #0 volume #1 offset 1.4 cmap cyanmaroon

My problem become if I want to set a custom palette:

scolor #0 volume #1 offset 1.4 cmap -10,yellow:0,white:10,green

This line also works, but for values lower or higher than –10 or +10, the color ramp "plateaus". And this line only works because the extents of this particular mapping happen to go from –29 to +17.

Is it possible to obtain the values for the full range and specify them for a custom palette? Or is it possible to assign a custom palette and call it like the default palettes?

I'm happy to clarify if needed.


Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)

31 Center Drive, Room 3B62B, MSC 2135
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