<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Gino,<div><br></div><div>I think that we should be able to modify the AutoMR wizard to take density maps instead of models. I'll work with Randy and Airlie and Nat to do this.</div><div><br></div><div>-Tom T<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 May 11, 2009, at 2:24 AM, Randy Read wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi,<br><br>As it happens, we've been working very hard over the last few months <br>first to make all commands in Phaser available from Python (done) and <br>second to make all options available from the new Phenix GUI (getting <br>close). ("We" in this context mostly means Airlie at our end and Nat <br>at the Berkeley end.) So it should become easy to switch to using <br>density instead of coordinates for your models without switching to <br>the command-line mode of running Phaser. We're also very interested <br>in optimizing the way that we use density from EM, which is something <br>we haven't spent enough time playing with yet. It's not yet possible <br>to use density for a model in the MR-SAD mode--that's been on the wish <br>list and shouldn't be too hard. Do you need that feature right now?<br><br>I really like your other ideas, so we'll have to talk to Tom about <br>adapting the AutoMR wizard so that it doesn't require a coordinate <br>file. As you say, this will be a real growth area!<br><br>All the best,<br><br>Randy<br><br><br>On 8 May 2009, at 15:39, Gino Cingolani wrote:<br><br><blockquote type="cite">Hi Randy,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">what about implementing the use of EM-models (e.g. structure factors<br></blockquote><blockquote type="cite">from EM model) in Phenix to carry out MR and/or MR-SAD?<br></blockquote><blockquote type="cite">There's a growing number of macromolecular complexes that have been <br></blockquote><blockquote type="cite">imaged<br></blockquote><blockquote type="cite">at medium/low res by EM, which could be of great help to<br></blockquote><blockquote type="cite">phase at low res or located anomalous scatterers in phased maps.<br></blockquote><blockquote type="cite">And the EM database keeps growing!<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">At this moment, it is certainly possible to use EM models in Phaser,<br></blockquote><blockquote type="cite">but the Phenix pipeline could add much more to that. For instance,<br></blockquote><blockquote type="cite">Phenix would allow for better phase extension of low res EM phases <br></blockquote><blockquote type="cite">to higher<br></blockquote><blockquote type="cite">res by ncs-averaging or multi-crystal averaging (in Resolve).<br></blockquote><blockquote type="cite">Or Phenix could help combining low res EM phases with other phase<br></blockquote><blockquote type="cite">sources such as SeMet sites, poorly occupied heavy atom sites, etc <br></blockquote><blockquote type="cite">(MR-SAD).<br></blockquote><blockquote type="cite">Or Phenix could rigid body refine (at low resolution) pseudo-atomic <br></blockquote><blockquote type="cite">models<br></blockquote><blockquote type="cite">obtained by filling in EM-models with dummy atoms.<br></blockquote><blockquote type="cite">This would help defining averaging masks and so on.<br></blockquote><blockquote type="cite">What do you think?<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Thanks in advance,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Gino<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">***********************************************************<br></blockquote><blockquote type="cite">Gino Cingolani, Ph.D.<br></blockquote><blockquote type="cite">Assistant Professor<br></blockquote><blockquote type="cite">Dept. of Biochemistry and Molecular Biology<br></blockquote><blockquote type="cite">SUNY Upstate Medical University<br></blockquote><blockquote type="cite">750 E. Adams Street, Syracuse, NY, 13210<br></blockquote><blockquote type="cite">Tel. (315) 464 8744<br></blockquote><blockquote type="cite">Fax. (315) 464 8750<br></blockquote><blockquote type="cite">Email: <a href="mailto:cingolag@upstate.edu">cingolag@upstate.edu</a><br></blockquote><blockquote type="cite">***********************************************************<br></blockquote><blockquote type="cite">"Nati non foste per viver come bruti, ma per seguir virtute e <br></blockquote><blockquote type="cite">conoscenza"<br></blockquote><blockquote type="cite">("You were not born to live like brutes, but to follow virtue and<br></blockquote><blockquote type="cite">knowledge")<br></blockquote><blockquote type="cite">Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)<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><br>------<br>Randy J. Read<br>Department of Haematology, University of Cambridge<br>Cambridge Institute for Medical Research Tel: + 44 1223 336500<br>Wellcome Trust/MRC Building Fax: + 44 1223 336827<br>Hills Road E-mail: <a href="mailto:rjr27@cam.ac.uk">rjr27@cam.ac.uk</a><br>Cambridge CB2 0XY, U.K. www- <br>structmed.cimr.cam.ac.uk<br><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></body></html>