[Xplor-nih] how to generate an RNA stem-loop?

[Brendan Duggan]

Greetings

I am new to Xplor and have been having difficulties trying to generate
an RNA stem-loop as a starting structure for further refinement.  I have
been using the Python interface and have been able to generate a random
extended structure using

   seqToPSF('rna.seq',seqType='rna',startResid=135)
   protocol.genExtendedStructure("rna_extended.pdb",verbose=1)

However, when I apply distance restraints for the hydrogen bonds that
define the base pairing, I get a globular structure rather than a stem-
loop.  Does anyone have any tips or tricks on how to get the bases to
pair up nicely?

Brendan
-- 
Brendan Duggan <bmduggan at musc.edu>
Medical University of South Carolina
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