I have a partially cleaved RNA, so I would like to try refining with
two different dinucleotide segments embedded in the model, one of
which has a broken backbone and 2',3'-cyclic phosphate, and the other
with a standard phosphodiester backbone. This should be analogous to
having two conformations but the covalency would be different.
I'd like to do this in refmac but if it can be done in phenix or CNS
that would be ok I guess too.
Any suggestions? The only thing I have come up with is two have the
end nucleotides at the cleavage site each in two conformations, and
then impose a link on one of these to "fake" the phosphodiester, but
this seems like an ugly hack (and I can't seem to get it to work
anyway).
