Hi Xplor Users, I am trying to refine an rna molecule using a python script that I have written based on the basic protG python script and force constants from the rna_refi classic xplor script. I want to refine against the orient base pair potential database. The setup files in the databases/rna_rna_pairs are different from the setup file in the rna_refi example. My molecule consists of two helices separated by a three base bulge. Should I include the setup of each base pair, or only the setup of the two segids? I would also like to know whether the quartic or gaussian shape is preferred. Any help would be greatly appreciated.
Thanks, Gokul
