[R] Cluster analysis of protein time series

[Leonardo Sepulveda Durán]

Hello!!!

I have a question about clustering. I'll present my problem first.

I have a simulation of a protein trayectory (a file with a time series
of protein 3D-coordinates), from it I can calculate the Root Mean
Square desviation (RMSD) beetween any pair of  structures in the
trayectory, which is a rough idea of 3D similarity beetween them. If
for every conformation (trayectory frame) I calculate the RMSD with
all other frames in the trayectory, I get a RMSD matrix, which is the
data i  have now.

In some published works a conformational analysis is performed with
this. They represent every frame of the trayectory as a point in the
space (or plane); and having N(N-1)/2 independent distances (RMSD
matrix, D[i, j]) they arrange them in space in a way that the real
distance d[i, j] in the plot would be very close to the Matrix
distance, so the residual 'e'
is minimized 
                              N
                      e = SUM( | D[i, j] - d[i, j] |  )
                            i, j; i<j

I have attached a .jpg  file with an example taken from a paper. It
would be also usefull for me to link points beetwen them acording with
time, to have an idea of the temporal changue in conformation.

I read the class and cluster package, and i did not find any function
able to do this, and I cannot imagine how to use existent funtions to
obtain results i want. I would like to ask, according to what i expose
above, whether is posible to obtain a graph like that in R. I Know
from manuals that in R is not posible to interact with graphs, So if
it would be posible to obtain that graph, there would be difficult to
zoom on it, or to know  the identity of a particular point by
clicking. Nevertheless i read that there is other programs that can be
used to obtain movies of R data, or interact with graphs ¿Someone
knows their(s) name(s)?

Any help or comment would be very useful

Leonardo