Hi Elaine, I meant what is defined by default for use in render by attribute (kdHydrophobicity), but yes it is the same as what is used in the preset. Completely understand the need to accommodate a diverse set of users - just suggesting that for use as a hydrophobicity scale (which is predominantly used, I think, by membrane protein structure people, though perhaps I am biased on that point), there might be better choices to use as a default these days. I know one can use attribute definition files on a case by case basis, but for frequently used "global" attributes like this (that are not dependent on the protein under consideration) it might be nice to be able to have such custom attributes defined by default at startup, in the same way the kdHydrophobicity attribute is. Cheers, Oli. On Thu, Jul 21, 2016 at 1:07 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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:
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defin...
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
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. Best, Elaine ---------- 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@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