[Chimera-users] PipesAndPlanks coloring not accurate

Andrew Hagen arhagen at lbl.gov
Fri Nov 17 18:04:02 PST 2017


Hello,

I have a protein model that I colored according to region:

N-terminal domain (green),
a domain that I inserted (gray),
and the flanking (GGS)2 linkers (tan).

When I apply PipesAndPlanks, the tan regions are changed to either green or
gray, which is not desired (and apparently, the PipesAndPlanks' color
cannot be changed once rendered). Is this a bug or am I doing something
wrong?

To add a little more detail, I manually Frankensteined this model together.
At the genetic level, it's just a domain insertion, flanked by linkers, but
in Chimera I did this by:
Opening my wt protein model (green), splitting the chain into two models at
an internal site, generating GGSGGS linkers de novo in Chimera and joining
these to the new models, and then finally joining those two fragments
through a "bridge" of another model. There was lots of manual torsioning
and minimizing using FoldIt in this process.

I can imagine a work around is just to overlay two PipesAndPlanks renders
and masking different regions, but this seems inelegant.

Any assistance/advice is appreciated!

--Andrew
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