Subject: Nucleic Acid MOdeling Tool

From: [email-masked] (Mark Dalton)
Date: Thu, 26 May 1994 16:06:28 -0500 (CDT)

This was released on the RNA email list.  Since there was interest in
Nucleic Acid Modeling here, I thought I would pass it on.

Thanks!

mark

	Announcing the release of Namot.

NAMOT(Nucleic Acid MOdeling Tool) is a tool developed at Los Alamos National
Laboratory for the structural manipulation of single or double stranded, 
RNA or DNA. NAMOT uses a set of reduced co-ordinates 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. 

An article describing namot is currently in press(CABIOS,1994).

Namot features:

Input:			PDB,Amber, or parameters

Output:			Amber, PDB, or parameters, encapsulated postscript.

General:		Can be used to manipulate ss or ds RNA or DNA via
			reduced parameters. Which have intuitive meaning,
			and allow easy manipulation of the base/unit without 
			bond breakage.

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

Monitors distances:	A simple point and click, connects two atoms with
			a dashed line and displays the distances whenever
			the structure is changed.

Generation of structures:
			Generates the parameters for A,B,& Z. RNA/DNA, ss or ds
			Can be used as a starting place.

Label BP:		Displays the unit number on the right side of the
			screen at the same level as the C3'

Online help:		There is an extensive online help system.

Rotations:		Easily accessible rotational controls.

Currently there are three versions of namot.

NAMOT1:

The original, uses the XView toolkit and basic monochrome Xlib graphics.
It does feature a WYSIWYG(What You See Is What You Get) printing
screen that produces encapsulated postscript output.

NAMOT 1.2:

Features color graphics options, both wireframe and CPK representations.
It produces color encapsulated postscript output. A command line lets the
user set foreground/background to white or black. The user can set the mode
to mono or color(color is the default). The command line also allows the user
to query for atom position, angles, and torsional angles. The online help
for "commands" lists the specific syntax.

NAMOT 1.2s:

Same basic features as NAMOT 1.2, but uses the motif toolkit to build the
interface and has been tested on an SGI Iris Indigo.

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

ftp namot.lanl.gov
login: anonymous
Password:(Your email address)
cd pub/namot
get <which ever version you want>

Note: SGI users may need to use "nlist" and not "ls" to list files.

NAMOT 1. and NAMOT 1.2 have been tested on:
	Sun SparcStation 1+ running SunOS 4.1.3
	Sun SparcStation LX running SunOS 2,3
	Sun SparcClassic running SunOS 2,2

NAMOT 1.2s has been tested on
	SGI Iris Indigo

References:

Base/Unit description:
 
Journal of Biomolecular Structure and Dynamics.
             Volume 6, Issue Number 3 (1988), page 397
                Soumpasis, D.M., and Tung, C.-S.
 
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, Tung, C-S,
		Soumpasis, D. M. & Jovin, T. M., eds, Springer-Verlag, NY

Feedback on NAMOT is greatly appreciated, email can be sent to 
[email-masked].

Gene Carter
[email-masked]

Chang-Shung Tung
[email-masked]

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. Separtment 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 this Notice and 
any statement of authorship are reproduced on all copies. Neither the 
Government nor the University makes any warranty, expressly or implied, 
or assumes any liability or responsibility for the use of this software.

Los Alamos Computer Code:94-6
---------------------------------------------------------------------------
-   email:[email-masked]		|Gene Carter			  |
-   talk: [email-masked]		|MS k710			  |
-   Work Phone: 505 662 2591		|Los Alamos National Laboratory   |
-   Group t-10 LANL			|Los Alamos, NM 87545		  |
===========================================================================

-- 
Mark Dalton                   AUG-GCU-AGA-AAG                  H      
Cray Research, Inc.           M   A   R   K                    |     
Eagan, MN 55121                                  CH3-S-CH2-CH2-C-COOH
Internet: [email-masked]                                         |   
(612)683-3035                                                  NH2

<A HREF="http://lenti.med.umn.edu/~mwd/mwd.html"><B>Marks Info/Resume</B></A>

Thoughts to ponder:
Life is Paradox: one = many, many = one.