Re: [AMBER] Principal COORDINATES analysis

From: Antje Wolf <antje.wolf.scai.fraunhofer.de>
Date: Thu, 24 Feb 2011 13:19:49 +0100 (CET)

Dear Massimiliano,

I have used R to read in the PairwiseDistance matrix. Here is a code snippet (num is the number of snapshots contained in the distance matrix):

# get command line arguments
args <- commandArgs()
num <- as.integer(args[4]) # number of snapshots

# read in binary data
data = file("PairwiseDistances", "rb")
vals = readBin(data, numeric(),size=4, n=num*num) # float has 4 bytes in C

# to matrix
m <- matrix(vals,ncol=num)

Hope this is useful,
Antje

----- Urspr√ľngliche Mail -----
| Dear all,
|
| I would like to perform a principal coordinates (not components)
| analysis,
| using as similarity matrix the RMSD pairwise distances.
|
| Is there any procedure I could use within Amber software?
|
| I know that the clusters analysis produces the above RMSD distances
| matrix in a file called PairwiseDistances, but it is not in ascii
| format.
|
| If there is no procedure to accomplish the principal coordinates
| analysis
| I might diagonalize this matrix to find eigenvectors/eigenvalues and
| then
| project the configurations onto the space of the first two
| eigenvectors.
|
| But, in this case, I need to know the format of this PairwiseDistances
| file in order
| to use it as a input.
|
| Any hint would be truly appreciated.
|
| Best regards,
| MP
|
| --
| Dr Massimiliano Porrini
| P. E. Barran Research Group
| Institute for Condensed Matter and Complex Systems
| School of Physics & Astronomy
| The University of Edinburgh
| James Clerk Maxwell Building
| The King's Buildings
| Mayfield Road
| Edinburgh EH9 3JZ
|
| Tel +44-(0)131-650-5229
|
| E-mails : M.Porrini.ed.ac.uk
| mozz76.gmail.com
| maxp.iesl.forth.gr
|
| _______________________________________________
| AMBER mailing list
| AMBER.ambermd.org
| http://lists.ambermd.org/mailman/listinfo/amber

-- 
Antje Wolf
Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI)
Department Bioinformatics
Schloss Birlinghoven
D-53754 Sankt Augustin
Tel.: +49 2241 14 2552
E-mail: antje.wolf.scai.fraunhofer.de
Internet: http://www.scai.fraunhofer.de
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Received on Thu Feb 24 2011 - 04:30:12 PST
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