[Xplor-nih] orie potential for rna molecule

[gokulr at umich.edu]

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