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STEM-GROUP POSITIONING

    Activating the 'Stem-group Position' item of the 3D 'Edit' pulldown
menu allows one to interactively define a group of stems 
which may then be translated and rotated as a rigid body.
Rotation is about any of the three axes
of a Cartesian frame located at the group's center of mass, and 
translation is along these same axes. 

   The purpose of this type of editing originated from a pseudoknot-related
problem.  By default, our 2D model of an RNA molecule assumes
that a pseudoknot has its participating stems coaxially stacked.  As
became evident for a particular case, this may not be appropriate for all
proposed pseudoknots.  Hence the need to undo the stacking. But this
unstacking is not easy to accomplish by editing the 2D model, -as when
unstacking or stacking non-pseudoknot stems.  Moreover, it appears to
introduce stereochemically incorrect distortions that argue for conformations
intermediate to those of the fully unstacked case. These 
intermediates are better achieved by doing editing at the 3D level.  Hence
the  requirement of  moving one of the two stems of the pseudoknot relative
to the
other as a rigid body.  And because in this particular case the loop
of one of the stems also contained two other stems, 
it proved necessay to also consider moving these as a group of rigid
bodies in concert with and independent of the unstacking. These
motions could not be achieved in terms of segment repositioning (see the
help topic SEGMENT POSITIONING), and so the new editing feature.

   A member of a stem_group can only be a hairpin (a non-branching
stem and its hairpin loop) or a stem of a pseudoknot. This restriction
is necessary for the editing to be applicable to pseudoknots.

   An example of usage is with regard to the sample BPL "hcvirus".
It has a total of four stems.  The yellow and red colored stems constitute
a proposed pseudoknot, and the two that are cyan colored belong to the
branching loop of the red colored stem.  Invoking the STEM_GROUP POSITION
feature and picking the yellow stem as the one to be repositioned (it
becomes green upon picking), it is readily evident that unstacking
can be accmplished by combining translation along the white and blue
axes.  Some of these translations will suggest that the two cyan colored
stems should be moved in concert with the yellow stem.  Picking these
will add them to the "stem_group".  It is also of interest to observe
that the cyan colored stems can be stacked to each other.  This can
only be done at the 2D level and must precede generation of the 3D model.
So invoke the 2D editing option "Stem Stacking" and stack these two stems.
The 3D model will automatically be regenerated and one can then continue
with the 3D editing,- although the stem_group must first be redefined.
During all these motions it will be noticed that the single strands 
connecting the stem_group to the rest of the molecule tend to be adjusting
their conformation to the new positions of the stem_group.  This is because
at the end of each translation or rotation step there is automatically invoked
a refinement of these strands at the same level that is used at the end
of the 2D to 3D conversion process (Help topic PRE-REFINEMENT).

   Needless to say, the "stem-group position" editing feature is only
for achieving alternate starting conformations.  As in the unedited case,
these conformations should be regarded as first-order approximations
to stable ones, and hence the need for subsequent refinement.

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