Unfortunately once it’s made, it’s made.  Instead you have to get the coloring you want on the original model, and then recreate the pipes (& planks). Each whole pipe would be the same color, though, taken from the ribbon color of the first residue in that helix; it is not divided into independently colorable per-residue segments. The new pipes model should overwrite the existing pipes model, but f you seem to be getting duplicate models, extras can be closed using the Model Panel (under Favorites in the menu). 

You could try to “highlight” a position by also displaying the atomic structure CA atom of that residue as a ball or sphere, but I don’t know how well that would meet your needs, sorry.

In our next-gen program ChimeraX, not yet publicly available but will be soon (as early development, not a finished product), 

<http://www.rbvi.ucsf.edu/chimerax/>

...there are helix “tubes” (like cylinders but curved) that are better integrated with the atomic model and cartoon ribbons, and can be recolored even in per-residue segments after they are shown.  Example image with leucine segments in red attached below.

I hope this helps,

Elaine

On Dec 2, 2016, at 3:40 PM, Kyle Morris <kylelmorris@berkeley.edu> wrote:

Dear Chimera dev,
I am using the pipes representation. In this case is it still possible to color/highlight a segment by residue number? Using the normal commands when displaying pipes doesn’t update the color, only on the original model.
Thanks for your help!
Best wishes,
Kyle
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