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

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 21 10:07:25 PDT 2016

Hi Oliver,
I guess by default you mean what is used by the hydrophobicity surface preset? In the absence of a user interface to choose amongst different scales, maybe one of the programmers can describe how to modify the code to use the scale that you want.

It is hard to accommodate a diverse set of users with a single default, so we went with a “classic” scheme that most people have heard of.  I do see your point, of course.

We tried to make it relatively easy to use whatever scale you want by putting the values in a attribute definition file.  As examples we provide files for the Wimley-White and Hessa scales (also included in that review of recent scales you mentioned), so you could simply use one of those, or all you’d have to do to make a file for Moon is swap in the 20 values and choose a reasonable name for the attribute:

Personally I somewhat regret that the hydrophobicity coloring is in the surface preset, because it often appears in figures that would look better with a single-colored surface, or is mischaracterized in the legend as showing electrostatics.
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 21, 2016, at 9:34 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 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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