ANNOUNCE: NAOMI Version upgrade

Simon M. Brocklehurst smb at
Thu Jan 4 23:28:58 EST 1996

NAOMI - Version Upgrade Announcement
(Please note, NAOMI is provided at zero charge for academic use)

(e-mail contact smb at

The computer program NAOMI Version 2.3b is available as of now from the
NAOMI Web site at:

or via anonymous ftp  

i.e. at

in directory pub/smb/naomi/

Users of versions older than 2.10 will need new license keys to allow 
the upgrade to work (please contact the author in this case).

Upgrade features :  Side-chain manipulations now include hydrogen
atoms where appropriate.  This makes for more seamless integration with 
X-PLOR (e.g. for molecular dynamics simulations, energy minimization, 
NMR structure calculation etc after manipulation of protein 
structures using NAOMI).


What is NAOMI?

NAOMI is an easy-to-use, state-of-the-art computer program which is 
aimed at both specialist and non-specialist researchers who make use of 
three-dimensional structures of proteins in their work.  It has
hundreds of users Worldwide.

Some facilities offered by the program for working with structure

   automatic 'key' residue identification
   automatic hydrophobic core/packing analysis
   automatic hydrogen bonds main-chain and side-chain 
                   identification (including high quality energy
   automatic secondary structure (helix, strand and turn) classification
                   using fuzzy logic
   automatic supersecondary structure classification (beta-hairpin
   conformational parameters: phi,psi,chi1,chi2,chi3,chi4,chi5 etc
   solvent accessibility (both absolute and percentage) calculations
   automatic identification of disulphide bonds, salt bridges,
   side-chain modelling and manipulation 
   applying symmetry operators
   automatic structure repair (building in missing atoms)
   NMR structure refinement module
   interfaces to graphics programs (MOLSCRIPT (and thus Raster3D), 
        INSIGHT, QUANTA to allow automatic preparation of figures

More details are available on the Web site.

NB NAOMI currently works only on Silicon Graphics workstations running 
IRIX 5.*
|  ,_ o     Simon M. Brocklehurst,
| /  //\,   Oxford Centre for Molecular Sciences, Department of
|   \>> |   University of Oxford, Oxford, UK.
|    \\,    E-mail: smb at | WWW:

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