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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