<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi James,<div><br><div>I'm sorry for the slow reply, I missed your email when you sent it and just saw it today.</div><div><br></div><div>There are several ways you can try and get autobuild to build just a little more. One is just to put in the last model from the previous run in as model=mybestmodel.pdb and specify "rebuild_in_place=false" and run it again.</div><div><br></div><div>In your case it sounds like you really want to fit a loop. Here is a good way to do that:</div><div><br></div><div>phenix.autobuild data=mydata.mtz model=model_missing_loop.pdb \</div><div>input_map_file=map.mtz seq_file=sequence.dat rebuild_in_place=false \</div><div>include_input_model=true number_of_models=0 fit_loops=true \</div><div>connect=true build_outside=false insert_helices=False \</div><div>helices_strands_start=False n_cycle_rebuild_max=1 \</div><div>thorough_loop_fit=true number_of_parallel_models=1 </div><div><br></div><div><br></div><div>Here the key parameters are fit_loops=true and skipping build_outside_model and insert_helices. The connect=true will help if you do not have sequence assigned at the ends of your loop. The thorough_loop_fit=true tell it to try hard for the loop. The number_of_models=0 says don't bother to rebuild the model from scratch.</div><div><br></div><div>This should run relatively quickly. It is possible that it will "lose" some good parts of your model, so it may be necessary to do some splicing if that happens. </div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><br></div><div> </div><div> </div><div> <br><div apple-content-edited="true"> <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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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:<a href="http://www.phenix-online.org">www.phenix-online.org</a><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></div></span><br class="Apple-interchange-newline"> </div><br><div><div>On Mar 3, 2009, at 6:37 AM, James Whittle wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear all,<br><br>AutoBuild has successfully built almost my entire model - I copied <br>loops built better in one NCS copy to the other, and now only one 16 <br>residue loop connecting two helices is missing. It initially built a <br>chain through the density for this loop, but could not join it to the <br>rest of the structure or place the sequence there, so I deleted it.<br><br>When I re-run autobuild on my modified model, rebuild_in_place=True is <br>automatically set and this loop is not completed. The density is <br>there, so it should be possible.<br><br>How does one instruct AutoBuild to finish an almost complete model (in <br>particular this loop), without much change to the existing model?<br><br>--James<br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://www.phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br></div></div></body></html>