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

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 21 10:59:25 PDT 2016

> On Jul 21, 2016, at 10:16 AM, Oliver Clarke <olibclarke at gmail.com> wrote:
> 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.

Ah, I get it.  Currently (without coding) the least annoying approach I can think of is to put the attribute files on your system and make a startup command file that aliases reading them.  Unfortunately it doesn’t work for the startup file to simply read the attributes because nothing will happen unless the structure(s) are already open.

For example, I put the Wimley and Hessa scale files (or could be concatenated into a single file, you could define multiple attributes in one file) in directory  ~/Desktop/chimera-keep/ 

Then in ~/.chimera/midasrc I put commands:

alias ^wimleyscale defattr ~/Desktop/chimera-keep/wwHydrophobicity.txt
alias ^hessascale defattr ~/Desktop/chimera-keep/hhHydrophobicity.txt
alias ^bothscales defattr ~/Desktop/chimera-keep/wwHydrophobicity.txt; defattr ~/Desktop/chimera-keep/hhHydrophobicity.txt

Upon startup I then have an Aliases menu with those 3 entries: wimleyscale, hessascale, bothscales.  After opening some protein of interest, choosing what I want from the Aliases menu will assign the corresponding attribute(s).

Admittedly, not conveniently portable for using Chimera on different machines, and requires an extra step after opening a structure (choosing from the Aliases menu or using the alias in the command line).
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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