[Chimera-users] Color by hydrophobicity - select default scale?

[Oliver Clarke]

Hi,

As explained here (
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html),
Chimera currentlyuses the Kyte-Doolittle scale by default for coloring
proteins by hydrophobicity.

I wonder whether it might be worth updating this to use e.g. the scale
described by Karen Fleming and co here (
http://www.pnas.org/content/108/25/10174.full)?

This scale (and indeed most more recent scales in the literature, see
review here:
http://www.sciencedirect.com/science/article/pii/S0968000411001320) differ
quite dramatically from the Kyte-Doolittle scale, which places trp and tyr
as comparable to serine, which does not seem reasonable based on analysis
of membrane protein structure.

The Moon et al scale has the advantage that it is derived from studies of
the energetics of protein folding and membrane insertion, as opposed to the
energetics of isolated amino acid partitioning between ethanol and water,
which as I understand it is what the K-D scale is mostly based on.
Alternatively, would it be possible to allow users to select the default
scale which it used for this purpose (I know it is possible to define a
custom attribute for this, but this is a little cumbersome for something
which sees frequent use).

Cheers,
Oli
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