<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Francis,<div><br></div><div>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 (<a href="http://robetta.bakerlab.org/fragmentsubmit.jsp">http://robetta.bakerlab.org/fragmentsubmit.jsp</a>) from David Baker's lab.</div><div><br></div><div>These files are used in mr_rosetta for filling in gaps. If your molecule has no gaps, then it doesn't need fragment files.</div><div><br></div><div>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.</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><br><div><div>On Aug 26, 2011, at 6:22 AM, Francis E Reyes wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>What exactly is the nature of the fragment files used for MR/rebuilding? <br><br>I'm an RNA guy and may have to generate them myself for certain projects. <br><br>F<br><br><br>---------------------------------------------<br>Francis E. Reyes M.Sc.<br>215 UCB<br>University of Colorado at Boulder<br><br><br><br><br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br>Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br>PHENIX web site: http:www.phenix-online.org<br>ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></div><div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div></span><br class="Apple-interchange-newline">
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