ANNOUNCEMENT: Release of namot2

NAMOT-WWW user namot at TRANSPOSON.LANL.GOV
Tue Nov 1 04:14:42 EST 1994


	Announcing the release of Namot2.

NAMOT(Nucleic Acid MOdeling Tool) is a tool developed at Los Alamos National
Laboratory for the structural manipulation of nucleic acid molecules.
NAMOT2 uses the extended set of reduced parameters to describe base/unit,
sugar and phosphate geometry. Detailed description of these parameters can be 
found in the references listed at the bottom of this announcement.

Namot features an X11 graphics interface for display of the molecule while
modifications are being carried out. Both Motif and XView toolkit versions 
exist, which should allow namot to be easily ported to most unix machines.

Namot features:

Input:			PDB,Amber4, or parameters

Output:			Amber4, PDB, or parameters; PPM or encapsulated 
			postscript.

General:		Can be used to manipulate standard or unusual nucleic 
			acid structures(i.e. poly-stranded molecules) using 
			reduced parameters that have intuitive meaning and 
			also allow easy manipulation of the base/unit without 
			bond breakage.

Auto-adjusts:		C5'-O5`-P and O3'-P-O5' to allow the phosphate to cross 
                        varying gaps.

Generation of structures:
			Generates the molecules in A,B,& Z forms.

Online help:		There is an extensive online help system.

Manual:			The manual is availible at URL http://namot.lanl.gov.

Libraries:		A set of external libraries allow users to
				customize their own bases,phosphates, sugars, 
				units, and forms.

Graphics:           Color and monochrome
                    CPK and wireframe

				


Namot is available over the internet via anonymous ftp.
To get namot:

ftp namot.lanl.gov
login: anonymous
Password:(Your email address)
cd pub/namot
get namot2.tar.Z


NAMOT 2 has been tested on:
	SunOS     5.2,4.1.3
	OSF1
	AIX       3
	IRIX      4.0.5F,5.2

References:

Base/Unit description:
 
Journal of Biomolecular Structure and Dynamics.
             Volume 11, Issue Number 6 (1994), page 1327
                Tung, C.-S.,Soumpasis, D.M., and Hummer, G.
 
Sugar description:

Journal of Biomolecular Structure and Dynamics,
                Volume 5, Issue 3(1987), page 513
                Garcia A.E., and Krumhansl, J.A.
 
 
Phosphate description:
 
Computation of Biomolecular Structures: Achievements, Problems,
                and Perspectives(1993), Tung, C-S,
		Soumpasis, D. M. & Jovin, T. M., eds, Springer-Verlag, NY

Feedback on NAMOT is greatly appreciated. Please send email to 
namot at transposon.lanl.gov.

Gene Carter
esc at transposon.lanl.gov

Chang-Shung Tung
cst at transposon.lanl.gov


  Copyright, 1994, The Regents of the University of California. 
  This software was produced under U.S. Government contract(W-7405-ENG-36) 
  by Los Alamos National Laboratory, which is operated by the University 
  of California for the U.S. Department of Energy. The U.S Government 
  is licensed to use, reproduce, and distribute this software. Permission 
  is granted to the public to copy and use this software without charge, 
  provided that this Notice and any statement of authorship are reproduced 
  on all copies. Neither the Government nor the University makes any 
  warranty, express or implied, or assumes any liability or responsibility 
  for the use of this software.


Los Alamos Computer Code 94-11





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