Announcing the release of NAMOT2.1
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 model base/unit,
sugar and phosphate structure. Detailed description of these parameters can
be found in the reference section 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 ported to most unix machines.
NAMOT 2.1 is the result of numerous bug fixes and added features.
One of the features that has been added is the "curve" command. Curve creates
a super-helical DNA duplex with a given pitch and radius. Another new feature
is the "align" command with which two molecules can be superimposed
Other new added features can be found in the file "changes" on the web server
http://namot.lanl.gov.
This distribution of NAMOT also contains demonstration scripts to
demonstrate the modeling of a DNA cube, a 6way junction, a curved
DNA fragment, and a drug-DNA complex. These scripts represent work
for a paper in preparation.
NAMOT features:
Input: PDB,Amber4, or parameters
Output: Amber4, PDB, or parameters; PPM,EPS(raster and line), TIFF
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 bridge
varying gaps.
Generation of structures:
Generates molecules in A,B,& Z forms, or user specified
conformations.
Online help: There is an extensive online help system.
Manual: The manual is available at URL http://namot.lanl.gov.
Libraries: A set of external libraries allow users to
customize bases,phosphates, sugars, units, and forms.
Graphics: Color and monochrome
CPK and wire-frame
Specifiers: A set of specifiers that allows users to select/identify
a subset of atoms in the molecule.
NAMOT is available over the internet via anonymous ftp.
ftp namot.lanl.gov
login: anonymous
Password:(Your email address)
cd pub/namot
get namot2.tar.Z
NAMOT 2 has been compiled on:
SunOS 5.4,4.1.3
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.
Chang-Shung Tung
cst at transposon.lanl.gov
Gene Carter
esc 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
