Hi Francis, These fragment files are 3- and 9-residue pieces of proteins from the PDB, chosen on the basis of sequence similarity to 3- and 9-residue segments in the target protein. They are normally generated by the Robetta server (http://robetta.bakerlab.org/fragmentsubmit.jsp) from David Baker's lab. These files are used in mr_rosetta for filling in gaps. If your molecule has no gaps, then it doesn't need fragment files. Now...as to RNA...I have not tried mr_rosetta on RNA and I think that there may be some or even many things that might need adaptation for this. You could give it a try, but as soon as you run into trouble email me and I'll see if there is something I can do. All the best, Tom T On Aug 26, 2011, at 6:22 AM, Francis E Reyes wrote:

What exactly is the nature of the fragment files used for MR/rebuilding?

I'm an RNA guy and may have to generate them myself for certain projects.

F

--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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