                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.

                          THE END



