[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.

Thanks!
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

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