[phenixbb] maybe not a phenix issue, but with mr_rosetta:
terwilliger at lanl.gov
Fri Aug 26 07:14:06 PDT 2011
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,
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.
> Francis E. Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
> phenixbb mailing list
> phenixbb at phenix-online.org
Thomas C. Terwilliger
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Los Alamos National Laboratory
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