<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Gino,<div><br></div><div>I should have added that the use of a model mask in autobuild is most appropriate for calculating maps (maps_only=true) . If you use it in a full cycle of autobuild you may get into trouble because autobuild also uses the keyword "model=..." and so the model building may not work correctly. </div><div><br></div><div>So the best thing to do is try it in a single cycle, with maps_only=true, and have a look at the map.</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><br></div><div><div><div>On Oct 14, 2009, at 8:35 AM, Gino Cingolani wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Thanks Tom!<br><br>Gino<br>******************************************************************************<br>Gino Cingolani, Ph.D.<br>Associate Professor<br>Thomas Jefferson University<br>Dept. of Biochemistry & Molecular Biology<br>233 South 10th Street - Room 826<br>Philadelphia PA 19107<br>Office (215) 503 4573<br>Lab (215) 503 4595<br>Fax (215) 923 2117<br>E-mail: <a href="mailto:gino.cingolani@jefferson.edu">gino.cingolani@jefferson.edu</a><br>******************************************************************************<br>"Nati non foste per viver come bruti, ma per seguir virtute e conoscenza"<br>("You were not born to live like brutes, but to follow virtue and knowledge")<br>Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120) <br><br><br>---- Original message ----<br><blockquote type="cite">Date: Wed, 14 Oct 2009 08:28:09 -0600<br></blockquote><blockquote type="cite">From: Tom Terwilliger <<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>> <br></blockquote><blockquote type="cite">Subject: Re: [phenixbb] Autobuild for very elongated models <br></blockquote><blockquote type="cite">To: <a href="mailto:Gino.Cingolani@jefferson.edu">Gino.Cingolani@jefferson.edu</a>,PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Hi Gino,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Here is how to specify a mask in phenix.autobuild (see <a href="https://www.phenix-online.org/documentation/faqs.htm">https://www.phenix-online.org/documentation/faqs.htm</a> <br></blockquote><blockquote type="cite">#anch68):<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">-----------------<br></blockquote><blockquote type="cite">How can I specify a mask for density modification in AutoSol/AutoBuild?<br></blockquote><blockquote type="cite">If you want to specify a mask, add this command:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">resolve_command_list=" 'model ../../coords.pdb' 'use_model_mask' "<br></blockquote><blockquote type="cite">where there are " and ' quotes and coords.pdb is the model to use for <br></blockquote><blockquote type="cite">a mask. Note the "../../" because coords.pdb is in your working <br></blockquote><blockquote type="cite">directory but when resolve runs the run directory is 2 directories <br></blockquote><blockquote type="cite">lower, so relative to that directory your coords.pdb is at "../../ <br></blockquote><blockquote type="cite">coords.pdb". You will know it is working if your resolve_xx.log says:<br></blockquote><blockquote type="cite">"Using model mask calculated from coordinates"<br></blockquote><blockquote type="cite">-----------------<br></blockquote><blockquote type="cite">I am not so sure this is the problem, however. I would suggest that <br></blockquote><blockquote type="cite">you do a quick composite omit map before refinement on your mr model:<br></blockquote><blockquote type="cite">phenix.autobuild data=data.mtz model=MR.1.pdb <br></blockquote><blockquote type="cite">composite_omit_type=simple_omit<br></blockquote><blockquote type="cite">It is important that this start with you MR unrefined model so that <br></blockquote><blockquote type="cite">you have no worries about model bias. This procedure will omit a <br></blockquote><blockquote type="cite">region, refine, calculate a 2Fo-Fc map for the omitted region, then <br></blockquote><blockquote type="cite">repeat for all other parts of your model and paste them all together <br></blockquote><blockquote type="cite">and put it in<br></blockquote><blockquote type="cite">AutoBuild_run_1_/OMIT/resolve_composite_map.mtz<br></blockquote><blockquote type="cite">which you can use to calculate a map with LABIN="FP=FP PHIB=PHIM <br></blockquote><blockquote type="cite">FOM=FOMM" (you need to include the FOM).<br></blockquote><blockquote type="cite">If this map shows density for your whole model...you are in great <br></blockquote><blockquote type="cite">shape and the problem may indeed be the mask. If it does not...then <br></blockquote><blockquote type="cite">the model may not be very close and it may be difficult to proceed.<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 Oct 14, 2009, at 7:57 AM, Gino Cingolani wrote:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hi Everyone,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I am trying to solve a very elongated structure (~180A-long) formed <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">by two long a-helices. I have a good MR solution (Log-Likelihood <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Gain ~168.537 to 3.0A resolution), which refines OK immediately <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">after MR (Rfactor/Rfree 46/50%). The electron density has clear side <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">chain features and high res data is available to ~2.1A resolution.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Logically, I should be able to plug everything into Autobuild and <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">get a good final model (or at least something better than my input <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">MR solution). I have tried a million time using different parameters <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">and datasets, but Autobuild always breaks up my long helical model <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">into short helical bundles, that refine to random Rfree. In other <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">words, if my starting MR model is a continuous<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">80aa-long helix, Autobuild fragments it into three helices of ~30aa <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">each packed laterally (I see back my initial model if I visualize <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">symmetry-related atoms in Coot).<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">In parallel, I have made the following observation.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">If I use DM to improve my phases, prior to Autobuild, I noticed that <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">something similar happens. DM gives great density for less than half <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">of my long helix while the rest is flattened.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">If I look at the solvent mask generated by DM, it basically flattens <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">half of my elongated model. It seems that at least DM fails to <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">generate a solvent mask that makes sense with such an elongated <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">structure (by the way, the unit cell is a=25, b=37, c=220 in <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">P212121). This problem can be circumvented in DM where<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">an outside solvent mask can be inputted, but what about in phenix?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Is it possible that Autobuild is failing because Resolve also makes <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">a poor solvent mask? Is there a way to see and/or edit the solvent <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">mask generated by Resolve? Or even better, can I input a new solvent <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">mask in Autobuild?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks in advance for the feedback!<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Gino<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">Gino Cingolani, Ph.D.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Associate Professor<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thomas Jefferson University<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dept. of Biochemistry & Molecular Biology<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">233 South 10th Street - Room 826<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Philadelphia PA 19107<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Office (215) 503 4573<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Lab (215) 503 4595<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Fax (215) 923 2117<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">E-mail: <a href="mailto:gino.cingolani@jefferson.edu">gino.cingolani@jefferson.edu</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">******************************************************************************<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">"Nati non foste per viver come bruti, ma per seguir virtute e <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">conoscenza"<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">("You were not born to live like brutes, but to follow virtue and <br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">knowledge")<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)<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><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">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><br></blockquote><blockquote type="cite">ISFI Integrated Center for Structure and Function Innovation 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">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>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>