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SEGMENT POSITIONING

    Activating the 'Segment Position' item of the 3D 'Edit' pulldown
menu allows one to interactively define a collection of segments, each of
which may then be repositioned and reoriented as a rigid body relative
to predefined sets of axes.  Recalling that a segment is a contiguous
set of bases, the axes sets for each segment are defined as follows.
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    axis set O:  The line connecting the backbone (C1')
		 atoms of the 3' and 5' ends. It is
		 denoted as (S:3'-5').
    axis set 1:  The line connecting the midpoint (MP)
		 of the line (S:3'-5') and the center of
		 mass (COM) of the segment. It is denoted
		 as (S:MP-COM).
    axis set 2:  The normal cartesian X,Y,Z axes
		 positioned at the backbone (C1') atom of
		 the 3' end.  It is denoted as (X,Y,Z:3').
    axis set 3:  The normal cartesian X,Y,Z axes positioned
		 at the backbond (C1') atom of the 5' end.
		 It is denoted as (X,Y,Z:5').
    axis set 4:  The normal cartesian X,Y,Z axes positioned
		 at MP.  It is denoted as (X,Y,Z:MP).
    axis set 5:  The normal cartesian X,Y,Z axes positioned
		 at COM.  It is denoted as (X,Y,Z:COM).

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Translation along and rotation about any of these axes can be performed
to provide a wide variety of positioning and orientation possibilities.
These possibilities are compounded by the feature that for any of the
axis sets a segment can
be designated as being closed (includes both of its ends),
open (does not include either end) or semi-open (includes only one end).

   The purpose of segment location and orientation editing
is for conveniently eliminating any overlapping of bases that might
have occurred during the 2D_to_3D conversion process used to obtain the initial
3D model from its 2D counterpart.  It is also used for maniplating
the 3D model in a manner that will enhance the refinement of specified
tertiary interactions.

   An example of the first use is with regard to the sample "pk_mcpheeters"
BPL. This is a pseudoknot structure whose initial 3D structure shows some
potentially conflicting overlap of the single strand (21-25) with the
stem shown in red.  Defining a segment as the bases from
20 through 26 and then rotating it as an open segment by 36 degrees or so
nicely eliminates
the potential conflict and provides a favorable starting point for
refinement, - such as single-strand refinement in the gobal context mode.

   An example of the second kind of use is with regard to the sample "6tna" BPL,
which corresponds to phenylalanine transfer RNA.  After doing
stem stacking (the first with the fourth and the second with the third),
there remains the task of single-strand and tertiary bond refinement.
The tertiary bonds are colored in red and it is evident that they need
to be considerably shortened in order to achieve the classic 3D form.
The shortening will be accomplished with global refinement techniques, but
these need to be aided by a preliminary relative movement of the two
helices in order to get around some potential relative minima that will
inhibit reaching the correct 3D form.  A number of rotation axes can
be used to achieve the relative movement, among which is the one connecting
the base numbers 9 and 49.  A positive rotation of 80 degrees about this
axis gives a favorable starting point for further refinements.

   The kind of segment movement that is employed is somewhat unreal because
of the local distortions that it introduces depending on whether the segment
is being regarded as closed, open or semi-open. These distortions are
partially eliminated by a prerefinement process that is automatically
invoked during any of these movements that eliminates large scale
distortions.  Small scale distortions  are easily corrected
in subsequent refinements (single-strand and/or global), and hence a small
price to pay for the facility of convenient large scale manipulations. 

   Finally, it should be noted that there is no limit on segment size,
large or small.  At the large level, whole branches of bases can be 
accommodated, while at the small level an individual nucleotide can
be manipulated as the 2nd base of a three-base sequence designated
as open or as the single base of a one-base sequence designated as closed.   

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THE END
