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
