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Analyzing normal modes.
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The normal mode file format must be the "CERFACS" one,
as produced by the programs diagstd, diagrtb or Blzpack.
(diagstd is provided with pdbmat, for computing modes
using Tirion's model)

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A few references:
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M.M. Tirion (1996):
"Large amplitude elastic motions in proteins from
a single-parameter, atomic analysis",
Phys. Rev. letters vol.77(9), p1905-1908.

I. Bahar, A.R., Atilgan, B. Erman, B (1997):
"Direct evaluation of thermal fluctuations in proteins
using a single-parameter harmonic potential",
Folding & Design vol.2, p173-181.

K. Hinsen (1998):
"Analysis of domain motions by approximate normal mode calculations",
Proteins vol.33, p417-429.

F. Tama, Y.H. Sanejouand (2001):
"Conformational change of proteins arising 
from normal modes calculations"
Protein Engineering vol.14, p1-6.

M. Delarue , Y.H. Sanejouand (2002): 
"Simplified normal mode analysis of conformational transitions in
DNA-dependant polymerases: the Elastic Network Model", 
J. Mol. Biol. vol.320, p1011-1024. 
 
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PROGRAMS: 
*********

To compile them:
----------------
Under Linux, just type:
COMPILE
Otherwise, you have to modify the Makefile:
Get rid of the "#" corresponding to your computer, and add some
to the lines corresponding to the Linux case.

What they do:
-------------

bfactors:
       Harmonic B-factors from modes.
       Output: "bfactors.pred".

rms_mode:
       Pick a normal mode.
       Outputs: "rmsmod.res" and "eigvec.res".

proj_modes: 
       Project a "reference structure->other conformer vector" on modes.
       Can displace a structure along a given normal mode.
       Outputs: "dr.res" and "projmod.res".

       Remember that if the reference structure is the one for which 
       modes have been calculated -with the same associated atomic masses !-
       and if there is not net global translation or rotation
       between the "other conformer" and the "reference structure",
       that is, if the "other conformer" has been fitted on the
       "reference structure", using the Profit program for instance,
       which is available on the Web, then, projections on the six 
       rotation-tranlation modes should be numerically null)

check_modes:
       Check eigenvector norms (has to be one).
       Yields the degree of collectivity for each eigenvector. 
       Output: "Chkmod.res".

traj_modes:
       Yields trajectories corresponding to normal mode motions,
       in "CHARMM" format (.DCD).
      (this is an old program, presently in a bad shape)

trans_modes:
       Translates a "CHARMM" normal mode file into a "CERFACS" one.

