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