<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br><div>You can supply the model from the first run to phenix.autobuild and it will start from there. You want to say "rebuild_in_place=False" so that autobuild knows you want to add more residues, not to just adjust the ones you have supplied. You will also want to supply the same freeR set that was used in the first run. If you provided freeR flags in your input datafile, use that again. If phenix.autobuild generated them, then you want to use "data= AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz":</div><div><br></div><div>phenix.autobuild data=data_with_freeR_set.mtz \</div><div> model=model_from_run_1.pdb \</div><div> seq_file=seq.dat \</div><div> rebuild_in_place=False</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><div><div>On Sep 3, 2009, at 10:30 AM, crystallogrphy wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi,<br>I have used phenix.automr followed by phenix.autobuild to build a 264 residue model against my 2.1A resolution data set. The first run of autobuild gives me about 180 residues built. I have adjusted the model according to the denity. The N-terminal of the model has OK density to add more residues to the model. Can phenix.autobuild has some command to just put more residues to the N-terminal of my current model according to the density, so that the cost of CPU time will be much less than rerun the job completely?<br> <br>Thanks!<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></blockquote></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></body></html>