[Xplor-nih] orie potential for rna molecule

[Charles at Schwieters.org]

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Hello Gokul--

> 
> 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.

I would follow the example in the rna_refi example. That example uses
the preferred quartic shape. I would keep store4 empty (don't designate
watson-crick pairs), as it hasn't been verified to help things...

definitive answers to you questions await John's return from vacation.

best regards--
Charles
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