<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">On a side note, for those who have successfully applied multi-xtal averaging,<div><br><div><br></div><div>Under what criteria would one embark on using multi-xtal averaging? </div><div><br></div><div>-Same unit cell / s.g. (isomorphism) </div><div>-Data was collected from xtals from different conditions? </div><div>-MR model shows different/unrecognizable features in 2Fo-Fc maps for each xtal individually? </div><div>-What if some residues are dynamic (different orientations in each xtal) or disordered? Would these show up garbage or not at all in the averaged map?</div><div><br></div><div>Any *good* (i.e. well detailed) papers discussing the details of multi-xtal averaging would be great. </div><div><br></div><div><br></div><div>Tom: Are only model phases used? In other words, are/can experimental phases used? Would having experimental phases from any of the xtals help in cases where the current model is incomplete (say 60%/70% built or Rfree in the 30's) ?</div><div><br></div><div><br></div><div><br></div><div><div><div>On Jun 26, 2009, at 7:39 AM, Tom Terwilliger wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Frank,<div>I have not done this with twinned data....but I would say yes, detwin everything for this step if you can (but of course refine against the twinned data with a twin target). It is probably good to detwin because the density modification procedure does not know about twinning...</div><div>All the best,</div><div>Tom T</div><div><br><div><div>On Jun 26, 2009, at 1:18 AM, Frank von Delft wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Tom,<br><br>Yep, that I figured out, but do I need to detwin the native F's first? <br><br>Cheers<br>phx<br><br><br><br><br>Tom Terwilliger wrote:<br><blockquote type="cite">Hi Frank,<br></blockquote><blockquote type="cite">To use phenix.multi_crystal_average you need one more step: take the <br></blockquote><blockquote type="cite">model from your SeMet dataset and do MR on it in the native cell with <br></blockquote><blockquote type="cite">native F. Now you have the correspondence between the two cells, and <br></blockquote><blockquote type="cite">you can plug the 2 models and the one phase set and the native F's <br></blockquote><blockquote type="cite">straight into phenix.multi_crystal_average to transfer the phase <br></blockquote><blockquote type="cite">information to the native (and cross-crystal average).<br></blockquote><blockquote type="cite">All the best,<br></blockquote><blockquote type="cite">Tom T<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On Jun 23, 2009, at 1:44 AM, Frank von Delft wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi, I'm trying to to figure out how to transfer phases from a twinned<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">SeMet dataset to the native one for refinement.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">1) SeMet dataset (2.9A) is solved (despite twinning), structure built,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">refines 29/35 (ish)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">2) SeMet crystals are hemihedrally twinned (confirmed by refining with<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">twin law), native probably too.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">3) Native dataset (2.7A) has 5A difference in the long cell edge (478 vs<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">483A).<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">So I could (and will try to) simply copy the SeMet phases into the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">native dataset, even though CC Fnat and Fsme is rather low (80-20%). <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">But would phenix.multi_crystal_average know what to do with this? It<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">has no explicit options, so I expected not.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Or how *would* one approach this?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Cheers<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Frank<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">phenixbb mailing list<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a> <<a href="mailto:phenixbb@phenix-online.org">mailto:phenixbb@phenix-online.org</a>><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thomas C. Terwilliger<br></blockquote><blockquote type="cite">Mail Stop M888<br></blockquote><blockquote type="cite">Los Alamos National Laboratory<br></blockquote><blockquote type="cite">Los Alamos, NM 87545<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Tel: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a> <br></blockquote><blockquote type="cite"><<a href="mailto:terwilliger@LANL.gov">mailto:terwilliger@LANL.gov</a>><br></blockquote><blockquote type="cite">Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br></blockquote><blockquote type="cite">PHENIX web site: http:<a href="http://www.phenix-online.org">www.phenix-online.org</a> <<a href="http://www.phenix-online.org">http://www.phenix-online.org</a>><br></blockquote><blockquote type="cite">ISFI Integrated Center for Structure and Function Innovation <br></blockquote><blockquote type="cite">web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br></blockquote><blockquote type="cite">TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a><br></blockquote><blockquote type="cite">CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">------------------------------------------------------------------------<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br></blockquote><blockquote type="cite"><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote><blockquote type="cite"><br></blockquote>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><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></div>_______________________________________________<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> <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>---------------------------------------------<br>Francis Reyes M.Sc.<br>215 UCB<br>University of Colorado at Boulder<br><br>gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D<br><br>8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D</div></div></span> </div><br></div></div></body></html>