<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Francis,<div><br></div><div>I think multi-crystal averaging is going to be useful only if the crystals are completely different or the amplitudes are nearly uncorrelated. In cases where there are only small changes the averaging procedure has almost nothing different in the two structures to work with and it won't do much. Another way to say this is that multi-crystal averaging works because two or more very different ways of sampling the Fourier transform of the molecule are occurring, and each must be consistent with the corresponding measured data. If the molecules are nearly the same and the measured data are nearly the same in all cases, then there are few constraints on the phases.</div><div><br></div><div>Yes, experimental phases can be included in multi-crystal averaging, just as for NCS averaging. And yes, experimental phases are most helpful.</div><div><br></div><div>If some regions are different in the different crystals, then the masking procedure needs to be adjusted to exclude the variable regions from the averaging process.</div><div><br></div><div>Perhaps someone else can suggest a good paper to read on this. Kevin Cowtan's paper on dmmulti is listed on his program documentation as: K. Cowtan (1998) Joint CCP4 and ESF-ECBM Newsletter on Protein Crystallography, 31, p34-38. </div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><br></div><div><br><div><div>On Jun 26, 2009, at 8:37 AM, Francis E Reyes 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; ">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><a href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><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></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 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>