New executables supporting 5D clustering and Good-Turing-MD

[Nicholas M Glykos]

Dear All,

Athanasios Baltzis wrote a program (cluster5D) which allows
PCA-based clustering using the top five (instead of three)
principal components. We would be grateful if you could
test it and ruthlessly criticise it.


Using it :
----------

Two ways. The first is via the 'grcarma' GUI which has been
updated to support cluster5D. The second way is running
cluster5D stand-alone. For both scenarios proceed as
follows.

___________________________________________________________

Get the file

http://utopia.duth.gr/~glykos/progs/carma_testing.tar.gz

and extract it. In the bin/ subdirectory you can find the
updated executable images and an installer for windoze.
On unix machines, copy 'grcarma', 'cluster5D' and 'carma'
(no significant changes there) somewhere in the path
and rehash if needed. On windows, click on. Then :



GUI-based : in the PCA subwindows a button has been added
to perform 5D clustering _in_addition_ to 3D so that you
can compare the results. This will automatically give you
PDB files of the clusters to play with. The naming
conventions for the 5D-derived clusters are obvious.


Stand alone : go to a directory containing the PCA-derived
fluctuations file. Run cluster5D by saying something like

cluster5D -v carma.dPCA.fluctuations.dat

A file named carma.5-D.clusters.dat will be produced in
the current directory containing the 5D-derived clusters.
___________________________________________________________

As a bonus -and if you have R installed on your machine-
you can run the Good-Turing-based sufficient sampling
calculation from within grcarma (in the RMSD matrix
subwindow).



All the best,
Nicholas



--


Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/