[Chimera-users] Dynamic scolor custom cmap?

Tom Goddard goddard at sonic.net
Fri Dec 13 13:10:21 PST 2013

Hi Darrell,

  There is a tricky undocumented feature that solves your problem.  If you specify the scolor option "cmapRange full" and you also specify the cmap option like "cmap 0,red:0.6,yellow:1,blue" or "cmap 0.2,green:0.8,yellow" then values from 0 to 1 in the cmap spec will be mapped linearly to the minimum to maximum full range values.  The documentation says the "full" is the default for the cmapRange option but that is not true.  Not using cmapRange simply does no range mapping on your specified cmap.

  I wrote this code and didn't adequately explain it to Elaine who wrote the documentation.  We will fix the documentation.


On Dec 13, 2013, at 12:16 PM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh at niaid.nih.gov> wrote:

> 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
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