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Hi Tom-- > > 1) I noticed that there is an example in the eginputs directory of an > RNA refinement using orient and rama; is there a simplified example that > doesn't use these, analogous to the protG example that uses "dynamics > internal" rather than "dynamics torsion?" Starting from the tutorial > directory I generated an input file using the old "dynamics torsion" > scripting format with "soft" noe wells rather than "square," which works > OK. When I switch to "square" I get the dreaded rotation matrix error as > others have seen with "dynamics torsion." So presumably I'd want to > switch over to "dynamics internal" but I'd prefer a more simplified > example to start off with, preferably with a dynamics schedule > appropriate for nucleic acids. While it's not too simple, a second nucleic acid example using the IVM may be found at http://spin.niddk.nih.gov/clore/Software/Xplor_NIH_example.html I currently do not have a nucleic acid example script which uses the Python interface- but one will be available after the next release of Xplor-NIH. In the long run, you will find it much easier going if you switch over to the Python interface. Dealing with multiple RDCs in the XPLOR interface (particularly when used with the IVM) gets hairy quickly. I've handed off your second question to John Kuszewski- he's be dealing with the dna parameters recently. > > 3) Related to 2, I renumber half of the RNA residues by hand at the psf > stage (Ugh) so that the input template has a numbering analogous to its > postion in the larger wild-type RNA, ie 257-272, 284-299. I know how to > change the starting number when generating the psf file, but I can't > seem to figure out how to restart the numbering sequence halfway allong > the chain. Any assistance would be great. > You can just break the sequence up and specify the start resid of the two (or more) sequences using seq2psf. Right? best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFA/DVRPK2zrJwS/lYRAsmpAJsGojHlsh36p8EqP129L1DljPv/ZgCfX7sF c97TpMI8ld1cTxMmbZ0MpKw= =JXPx -----END PGP SIGNATURE-----
