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.ll 60
.pl 5
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GETTING STARTED

    This is very easy.  First it is necessary to make or pick a directory
from which all subsequent calls to the program will be made.  A fixed
working directory is needed because the program automatically creates
directories within the working directory for storing files.  The main
subdirectory it creates is called RNA_2D3D which, subsequently, will
have the subdirectories BPLfiles, PDBfiles and 3DModels.  The subdirectory
BPLfiles will contain what we term Base_Pairing_List (BPL) files, the
subdirectory PDBfiles will contain Protein_Data_Bank (PDB) formatted
files, and the subdirectory 3DModels will contain user-saved 3D models
generated from BPL files. 

    The format of a BPL file is illustrated
by the following example:
.nf

	# This is a fanciful example for
        illustrating what a BPL file
	should look like.
	> tropical_gem
      	GCACUAUGGG CGCAGCGUCA AUGACGCUGA
      	CGGUACAGGC CAGACAAUUA UUGUCUGGUA
      	UAGUGC
	$ list1
	1 66 7
	11 32
	12 31
	13 29
	14 28
	-4 -27
	-6 -31
	$ list2
	2 65
	3 64
	4 63
	5 62
	6 61
	7  60
	11 32
	12 31
	13 29
	14 28
	-4 -27


.fi
    In this format the beginning line character '#' marks the start of
an arbitrarily long description of the file contents; the
beginning line character '>' marks the start of an RNA sequence;
and the beginning line character '$' marks the start of a base pairing list.
The one-word name of the sequence follows the > mark on the same line
and the one-word name of a base pairing list follows the mark $ on
the same line.  The base denoting characters of a sequence can be upper
or lower case.  For a base pairing list, each line consists of two or
three integers.  If there is no third integer, then the first two integers
are the base positions (relative to the primary sequence) of a single basepair;
otherwise the third integer
is the number of contiguous basepairs following the first as defined by the
first two integers.  In list1 of the above example, the first seven base pairs
are contiguous and
are defined by the first line which consists of the integers 1, 66 and 7.
The next four base pairs, though contiguous, are being specified by the
single base pair convention of using just two integers.
 
    Normal base pairing uses positive base position numbers.  These define
the secondary structure.  Negative
base position numbers define tertiary base pairing.  In a BPL file
there is exactly one base sequence, but there is no limit to the
accompanying base pairing lists.

    A new BPL or PDB file is entered into the Model A or Model B array
following an appropriate sequence of
clicks, starting at the bar menu item 'File', by typing in its full path
name.  Following verification that the typed-in path does indeed specify an
accessible file, a link to it is automatically created.  It is thus
added to the files known to the program.  But please note that
there is no mechanism within
the program for deleting a BPL file or PDB file link once it is
created.  One must go outside the program and manually delete it from
the containing directory (BPLfiles or PDBfiles). Also to be noted is
that the link made is not of the 'soft' type which can accommodate
linking across file systems.  To become linked, the parent directory
of the new file must lie within the same file system as the corresponding
subdirectory (BPLfiles or PDBfiles).

    Upon entering a new BPL file (or selecting a previously entered one),
the corresponding base pair lists are
automatically converted into their 2D and 3D graphical forms, ready for
a variety of editing and rendering options.  In the case of a PDB file
the defined 3D structure is shown together with a secondary structure
that is in the form of a circle corresponding to an unspecified
base pairing list.

    When the Model A or Model B array contains more than one model,
as in the case of loading a BPL file having more than one base pairing
list, there is provided a display control for sequencing
through the corresponding structures in either a manual or automatic
manner.  The structures of a multiple list are completely independent
and may so be rendered and edited.

    To assist you in gaining some experience with the program prior to
any data entry, there is provided some sample BPL and PDB files which are
accessible via the bar menu item 'File'.  Viewing the corresponding
pulldown menu you will notice that the files are divide into two types:
user and sample.  Clicking on the sample BPL files, say, will invoke
a scrolled list of those available.  Selecting any one of these
and then clicking  the button 'Model A' or 'Model B' shown on the
dialog box
results in a display of the corresponding secondary structure in 2D
form and of the initial 3D structure. (See OVERVIEW help topic for method
of generating the initial 3D structure). No refinement
has been applied to these 3D structures.  This is reserved for you
to experiment with after reading the REFINEMENT topic. The same applies,
of course, to the variety of available editing and rendering features.

    As a final note, your attention is called to the bar menu item
(2D A:) or (2D B:) which becomes available when, say, a BPL file
is selected into the corresponding array.  This item provides a pulldown
menu with two entries. One is 'Reset' and the other is 'BPL Description'.
The first provides undoing modeling transformations (translation and
rotations) of the 2D model and the second provides a description of the invoked BPL file. This description is what is actually contained in the BPL file following the '#' character. The 'Reset' feature is also used 
when displaying any 2D or 3D models for undoing translations and rotations.
 
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