
                      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 in-
teractive mode.The 3D structures generated are output as PDB
files in the user’s working directory.  The  default  struc-
tures genenerated are of the initial model type involving no
improvent. Optionally, three types of improvement can be in-
cluded.  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 ob-
tained in the stand-alone mode  may  contain  atom  overlaps
which are not resolvable by energy minization or even dynam-
ics.  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  or-
der 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 fol-
lowing usage conventions.

    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.

                          THE END


