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PSEUDOKNOT STACKING/EDITING

    Activating the 'Pseudoknot Stacking' item of the 3D 'Edit' pulldown
menu allows one to interactively alter the stacking of the stems
of a pseudoknot by rotating one of the stems (the 3' one) about
any of two axes.
Recalling that the backbone atom is the C1' atom, there is
a well-defined line segment connecting the C1' atoms of a basepair.
One rotation axis (colored cyan) corresponds to the line passing
through the midpoint
of the line segment of each of the top basepairs.  The other axis
(colored blue) corresponds to the line segment of the 5' stem's top basepair.

    The need for this kind of editing became evident following
detailed refinement of several pseudoknots. It was found that the
participating stems are not perfectly stacked but instead have
a joint conformation which roughly corresponds to a 50 degree rotation
about the cyan axis and a 20 degree rotation about the blue axis
as measured from the perfectly stacked conformation. These are
the suggested rotations to initially try.  The actual amount of 
rotation about these two axes will of course depend upon the
particular pseudoknot, especially with regard to how the branching
loop of each of the stems interact with the paired bases of the other
stem.
That is why there is also provided on the control panel two other
rotation axes, one colored white and the other colored red.
The white axis provides rotation of the 3' stem loop and the red
one provides rotation of the 5' stem loop.  Both are initially set to -50
degrees rotation as the starting point for subsequent user modification.
The editing provided by these two additional rotation axes is the same
as could be achieved with the 'Segment Position' 3D editing item, but
the feature is also included in this control panel because of its natural
relevance to pseudoknot stacking.
 
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