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STAND-ALONE MODE

    The stand-alone mode is for running the program rna_2d3d without graphics.
This usage is designed for getting 3D structures from a specified basepair list
without having to graphically draw the structures as is done in the
normal interactive mode.The 3D structures generated are output as PDB files in the user's working directory. The default structures genenerated are of the initial model type involving no improvent. Optionally, three types of improvement can be included. One is that of compacting; another is refinement of all the single strands in the local context mode; and the third is global
refinement of the entire molecule.  In both refinement cases it consists of
energy minimization carried out to an rms gradient of 1.0.

	There is the caveat that the 3D initial models obtained in the stand-alone
mode may contain atom overlaps which are not resolvable by energy minization
or even dynamics.  Such cases are easily corrected in the interactive mode using the editing tools provided. But lacking these, it is therefore wise to proceed as in example (1) below in order to spot bothersome overlaps before attempting to use the stand-alone refinement options.

    The stand-alone mode is invoked by simply typing the command 'rna_2d3d'
with some arguments according to the following usage conventions.

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    USAGE: rna_2d3d [-u] [-h]
	[BPL_File 
	    [-compact] 
	    [-sstrand]
		[-global] 
	    [-o] 
	]

    (With no arguments the interactive mode is invoked.)

    The flag '-u' invokes the help file explaining usage.
    Any other arguments are ignored.

	The flag '-h' provides access to the  help topics
	'overview', 'compacting' and 'refinement'. The topic
	'overview' provides a general description of the
	rna_2d3d program and its use.  It is highly recommended
	reading for the first time user.'compacting' describes
	how and why a molecule is made more by compact by extending
	the helicity of stems at the expense of single strands
	connecting them. 'refinement' describes the energy based
	refinement tools for improving the initial 3D models
	produced by the rna_2d3d program. Only energy minimization
	is used in the stand-alone mode.  Any other arguments
	are ignored.
  
    'BPL_File' means the user-specified base pair list file.
    No Default. Without any other arguments, PDB files of
	unimproved initial 3D models are produced.
	
    The flag '-compact' means do compacting of the initial
	model. Default is no compacting. 

	The flag '-sstrand' means do refinement of all the single
	strands in the  local context mode. That is, each of the
	single strands (those comprising haipin, bifurcation and
	inner loops) is refined subject to the constraint that its
	interaction with the rest of the molecule is only with the
	supporting nucleotides. Thus, if the single strand consists
	of the nucleotides in the position range of b1 to b2, the
	supporting	nucleotides are those at positions b1-1 and
	b2+1. These are held fixed during the refinement.

	The flag '-global' means do energy minimization of the 
	entire molecule.

    The flag '-o' means to use the specified PDB_Format
	for the output file. The choices are 'tinker',
	'msi'(biosym) and 'std' (standard). Default is 'tinker'.


    SOME EXAMPLES:

	(1) rna_2d3d simple.bpl

	    This command will produce a 3D structure 
	    (in tinker PDB format) for each of the basepair
	    lists in the file 'simple.bpl'.  No compacting
	    or refinement will be done.  Assuming that there
	    are two base pair lists, list0 and list1, in the
		file simple.bpl, there will be two output files:
		'simple_list0.tinker.pdb'and 'simple_list1.tinker.pdb'.

	(2) rna_2d3d simple.bpl -compact

	    Same as (1) but structures will be compacted.

	(3) rna_2d3d simple_bpl -sstrand 

	    Same as (1) but single strand will be refined in
	    local mode. No compacting will be done.

	(4) rna_2d3d simple_bpl -compact -sstrand -o std

	    Same as (3) but structures will be compacted and
	    the output files will be: 'simple_list0.std.pdb'
	    and 'simple_listl.std.pdb'.

	(5) rna_2d3d simple_bpl -compact -sstrand -global -o std

		Same as (4) with the added feature that the 3D models
		will be globally energy minimized.

	(6) rna_2d3d -h overview

		The help topic 'overview' is presented to the user.

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