Date: Sat, 19 Apr 2008 15:59:45 -0500
To: "Yang Zhang" <yzhang@ku.edu>
Subject: side chain center of mass

Hi Yang,

In your file sidechain.comm, there are two vectors for each 
amino acid type. According to my understanding, one vector 
is for extended local structure and the other for compact
local structure. The local structure is determined using
the angle formed by three consecutive Ca atoms.

However, I don't quite understand the meanings of these two 
vectors. Are these two vectors calculated as the positions of 
the side chain center relative to its Ca position? Or are 
these two vectors calculated as the positions of the side chain
center relative to the local coordinate system defined by three
consecutive Ca positions? If so, how do you define the local 
coordinate system?

By the way, do you also provide the position of Cbeta atoms 
on your website?

thanks a lot for your help.