[phenixbb] maybe not a phenix issue, but with mr_rosetta:

Tom Terwilliger terwilliger at lanl.gov
Fri Aug 26 07:14:06 PDT 2011

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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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

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