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.ll 60
.pl 5

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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. Although the  very convenient features of 
interactive 2D and 3D editing are necessarily lost, the corresponding
effects may sometimes be obtained by the imposition of suitable constraints.
The 3D structures generated are output as PDB files in the user's
working directory.

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

.nf
    USAGE: rna_2d3d [-u]
	[BPL_File 
	    [-s SSR_Type]
	    [-l LR_Type]
	    [-g GR_Type] [-b BellyGroupFile] 
	    [-c GR_ControlFile] [-r SA_RestraintFile] 
	    [-n Runs_Limit] [-h GR_Host]
	    [-o PDB_Format]
	]

    (With no arguments the interactive mode is invoked.)

    The flag '-u' invokes the help file explaining usage.
        Any other arguments are subsequently ignored.
    
    'BPL_File' means the  user-specified Base Pair List file.
        No Default. Without any other arguments, PDB files
	of the 3D structures are produced without any
	refinement.

    The flag '-s' invokes single-strand refinement of the
	specified SS_Type (Single-Strand Refinement Type).
	The choices are:
            lc (for Local Context mode only),
            gc (for Global Context mode only),
            lc_gc (for Local and Global Context modes).
 
    The flag '-l' invokes refinement of all the inner,
	bulge, hairpin and branching loops. The refinement
	type choices are:
	    min_md_min (for minimization & dynamics),
	    siman (for simulated annealing).

    The flag '-g' invokes global refinemnt of the specified
        'GR_Type'.  The choices are:
            min (for energy minimization alone),
            md (for molecular dynamics alone),
            min_md_min (for minimization & dynamics),
            siman (for simulated annealing).

    The flag '-b' means to use the specified BellyGroupFile.
	Default is the whole sequence as the belly group 
	(everything is allowed to move).

    The flag '-c' means to use the specified GR_ControlFile
	(Global Refinement Control File).
         Default is the interactive mode control file.

    The flag '-r' means to use the specified SA_RestraintFile
	(Simulated Annealing Restraint File). 
        Default is the interactive mode restraint file.

    The flag '-n' means to use the specified Runs_Limit
	(number of runs of given Refinement Type.
         Default is 1.

    The flag '-h' means to use the specified GR_Host
	(Global Refinement Host) for doing the global
	refinement.
	Default is the local machine.

    The flag '-o' means to use the specified PDB_Format
	for the output file. The choices are:
	amber41,msi(biosym) and std.
	Default is amber41.


    SOME EXAMPLES:

	(1) rna_2d3d simple_bpl

	    This command will produce a 3D structure 
	    (in PDB format) for each of the basepair lists
	    in the file 'simple_bpl'.  None of the optional
	    refinements will have been done.  Assuming that
	    there are two base pair lists in the file
	    'simple_bpl', there will be two output files,

		simple_bpl_0.amber41.pdb
	    and
		simple_bpl_1.amber41.pdb.

	(2) rna_2d3d simple_bpl -s lc

	    Same as example (1) but with LC single-strand
	    refinement.

	(3) rna_2d3d simple_bpl -s gc -g min

	    Same as example (1) but with GC single-strand
	    refinement followed by global refinement of
	    minimization alone.  The parameters for the
	    global refinement are as in the default file
	    used in the interactive mode.  Also, since
	    no BellyGroupFile is specified it is assumed
	    that the entire sequence is allowed movement.

	(4) rna_2d3d simple_bpl -s gc -g min -b my_bg_file

	    Same as example (3) but using the belly groups
	    specified in the file 'my_bg_file'.  Assuming
	    that this file consists of the two lines

		6	14
		21	25

	    their interpretation will be:
		the first belly group is residues 6 through
		14 and the second belly group is residues
		21 through 25.  All other residues are to
		be held fixed.

	(5) rna_2d3d simple_bpl -s gc -g siman -b my_bg_file
						-h nciymp

	    Same as example (4) except that the global
	    refinement consists of simulated annealing
	    using the default interactive mode GR_ControlFile
	    and SA_RestraintFile.  The latter will contain
	    restraints for the hydrogen bonding implied by
	    the BPL_File 'simple_bpl'. In addition, the
	    global refinement is to be done on the remote
	    host computer 'nciymp'.

	(6) rna_2d3d simple_bpl -l -g minmd -n 10 
					
	    This example calls for an initial loop refinement
	    followed by 10 runs of global refinement, each of
	    which consists of minimization and dynamics.

	NOTE: When using control or restraint files it is a
	  good idea to first try these out in the interactive
	  mode.  These files can conveniently be generated
	  by interactively editing the default ones and then
	  copying the edited files. (Lower the 'rna_2d3'
	  graphics window and use a separate window for the
	  copying.)
	
 
	

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THE END
