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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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFGyzvHPK2zrJwS/lYRAq86AJ99AoyG9i7MsSnV6N6q6+Qu4p9UBACfUiVm Bo6aEWCe4Onyrl3orE6jD6Y= =sW15 -----END PGP SIGNATURE-----
