                      GETTING STARTED

    This  is  very  easy.   First it is necessary to make or
pick a directory from which all subsequent calls to the pro-
gram  will be made.  A fixed working directory is needed be-
cause the program automatically creates  directories  within
the working directory for storing files.  The main subdirec-
tory 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:

        # 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


    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 po-
sitions (relative to the primary sequence) of a single base-
pair;  otherwise the third integer is the number of contigu-
ous basepairs following the first as defined  by  the  first
two integers.  In list1 of the above example, the first sev-
en 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 posi-
tion 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  au-
tomatically 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 correspond-
ing subdirectory (BPLfiles or PDBfiles).

    Upon entering a new BPL file (or selecting a  previously
entered one), the corresponding base pair lists are automat-
ically 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 ei-
ther a manual or automatic manner.  The structures of a mul-
tiple list are completely independent and may so be rendered
and edited.

    To assist you in gaining some experience with  the  pro-
gram  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  corre-
sponding  secondary  structure in 2D form and of the initial
3D structure. (See OVERVIEW help topic for method of  gener-
ating  the initial 3D structure). No refinement has been ap-
plied 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 pro-
vides undoing modeling transformations (translation and  ro-
tations)  of the 2D model and the second provides a descrip-
tion of the invoked BPL file. This description  is  what  is
actually contained in the BPL file following the ’#’ charac-
ter. The ’Reset’ feature is also used when displaying any 2D
or 3D models for undoing translations and rotations.

                          THE END





