<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Susan,<div><br></div><div>Your SA omit map should have a mean of 0, yes. Note that the SA omit</div><div>map only has meaning inside the boundaries of the omit region (as illustrated</div><div>by the map you get from the file AutoBuild_run_xx_/OMIT/omit_region.mtz).</div><div><br></div><div>Some things to try:</div><div><br></div><div>1. delete the Mg-water cluster from your structure and just refine it with phenix.refine</div><div>and look at the maps.</div><div><br></div><div>2. same as above, but include simulated annealing. This is another way to get an SA-omit map </div><div>around your Mg-water cluster.</div><div><br></div><div>If #2 gives a very different result than the phenix.autobuild SA-omit map, then let me know and </div><div>I will try to figure out why.</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><div><div>On Sep 3, 2009, at 12:28 PM, Susan Tsutakawa wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>I am trying to generate a simulated annealing omit map of a Mg-water <br>cluster in the active site of my protein but when I run the SA omit <br>map, I can only see the Mg when I use the Mgwater cluster as the <br>target pdb.<br><br>When I was building the model which did not have the metal present <br>(phases solved by MR), I observed this Mg-water cluster in the Fo-Fc <br>maps. Geometry and distance were ideal, etc. Now that I'm at the <br>final stages of refinement, I would like to do a SA omit map as a <br>figure for the paper. However, if I goto the lowest sigma, I only <br>see the Mg. I'm using coot with the weights included to view the SA <br>omit maps. I noticed that there is very little noise at the lowest <br>sigma and so I'm wondering if the 0 sigma is truly 0 sigma and any <br>suggestions on what to do.<br><br>Thank you in advance.<br><br>Sincerely,<br>Susan<br><br><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 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>