From - Sat Apr 19 16:47:11 2008
From: Yang Zhang
Subject: Re: side chain center of mass
Hi,
>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.
Correct.
>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?
Both are right, i.e. the vectors are defined relative to their Ca
positions and the orientations are decided in a local Cartesian
system. Suppose A and B are two unit vectors from Ca(i-1) to Ca(i)
and from Ca(i) to Ca(i+1) respectively, the unit vectors (ex,ey,ez)
of the local Cartesian system are defined as following:
ex=(A+B)/|A+B|
ey=(A(x)B)/|A(x)B|
ez=ex(x)ey
Here "(x)" denotes a cross pruduct.
>By the way, do you also provide the position of Cbeta atoms
>on your website?
I have put the file on the website. The format and usage are the
same as "sidechain.comm".
Yang