[Chimera-users] coloring by property
meng at cgl.ucsf.edu
Tue Jan 15 12:48:27 PST 2008
There is another set of possibilities I neglected to mention. These
simply categorize residues into discrete sets which could be colored
differently, as opposed to coloring continuously over a numerical range.
There are amino acid categories that can be specified with "Select...
Residue... amino acid category... [category-name]" where category-
name is hydrophobic, positive, negative, etc. These names could
also be used in the command line, e.g.:
color blue positive
color red negative
We took the default categorizations from a paper,
but you can change which residues are in which category as well as
create entirely new categories with the ResProp tool. The new
categories will show up in the menu and can be used in the command
A similar approach is to use the "alias" command, for example:
alias myres :phe,tyr,leu
col hot pink myres
alias thezone ligand z<4
rep stick thezone
Aliasing can use any type of specification and is not limited to
amino acids like ResProp.
To color by some continuous numerical property, however, attributes
would definitely be the way to go.
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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