[Chimera-users] coloring by property

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 15 12:48:27 PST 2008

Hi everybody,
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  
line too.

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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