Date: Sat, 19 Apr 2008 15:59:45 -0500
To: "Yang Zhang"
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.