<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Yu Seon,<div><br></div><div>A couple things to trh:</div><div><br></div><div><br></div><div>1. You might try SAD with the autosol option</div><div><br></div><div>part_pdb_file=my_mr_model.pdb</div><div><br></div><div>which will use your SAD data in phaser along with the MR model to try to identify the anomalously-scattering atom locations and to phase including the MR model and the SAD data.</div><div><br></div><div>2. You might check whether the Se sites you have previously found are near your SD atoms of Met using phenix.emma if you have not already. This routine will take care of origin offsets and inversions for you so it is more comprehensive than simply superimposing the ha sites on your model. I'm thinking of something like this:</div><div><br></div><div>cat mr.pdb |grep 'ATOM'|grep ' MET '| grep ' SD ' > sites_from_mr.pdb</div><div>phenix.emma sites_from_mr.pdb ha.pdb</div><div><br></div><div>All the best,</div><div>Tom T </div><div><div><div>On Aug 27, 2009, at 8:58 AM, YS. Chung wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear all,<br><br>I have a 3 angstrom structure which I am trying to solve with MAD or<br>SAD. The structure was previously solved with molecular replacement but<br>refinement could not continue due to poor phasing at the N-terminal<br>domain of the protein. I have run solve and autosol which are able to<br>find the Se sites. However, Se sites are not anywhere near the<br>methionines when I superimpose the ha.pdb and the pdb file that I<br>obtain from a new run of molecular replacement. The<br>exptl_fobs_phases_freeR_flags.mtz and the overall_best.pdb do not show<br>any connected densities. I have also tried autobuild with the solutions<br>from AutoSol, but the model that it builds in is incorrect. Any<br>suggestions would be appreciated. <br><br>Thank you,<br>Yu Seon Chung<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 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></body></html>