[chimera-dev] Using Chimera to display family shuffling information.

[Matthew Tiffany]

To Whom It May Concern:

I am interested in displaying results from DNA shuffling experiments on a crystal structure. Here is a graphical tool that I have found to do this: http://qpmf.rx.umaryland.edu/XoverDemo.html

What I would like to do is input an alignment of parental sequences and separately a chimeric protein that is derived from the parental sequences by domain shuffling. Then color code a related structure based upon which domain of a parent the chimeric protein came from. The Xover program does this in a graph, but I would like to be able to do this in 3D space. It is similar to color coding by conservation in MultiAlign, but not exactly. Is there any existing plugin that you may be aware of that does this already or a potential backbone plugin that I can use as a starting point to try and code it myself.

Regards,

Matthew Tiffany
Postdoctoral Fellow
Mark A. Kay Laboratory
Stanford University
269 Campus Drive
CCSR 2110
Stanford, CA 94305