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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>What Pavel describes is how to get a “difference map”. But it is not an “omit map” per the original definition.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>The omitted part should never have been part of the model during any refinement step before the omit map is calculated. The purpose is to prevent bias.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>If the model has already been refined with a ligand, then the technique of simulated annealing refinement can be used to remove the bias after removing the ligand. This approximates an “omit map” (still one may argue not a real “omit map”, but close enough).<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thierry<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> phenixbb-bounces@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] <b>On Behalf Of </b>Manoj saxena<br><b>Sent:</b> Sunday, November 15, 2015 11:20 PM<br><b>To:</b> Pavel Afonine<br><b>Cc:</b> phenixbb@phenix-online.org<br><b>Subject:</b> Re: [phenixbb] Omit map output map files<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>Thanks Dr. Pavel,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>This looks simple. <o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>regards<o:p></o:p></p></div><div><p class=MsoNormal>Manoj<o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On Sun, Nov 15, 2015 at 11:49 PM, Pavel Afonine <<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>> wrote:<o:p></o:p></p><p class=MsoNormal>Hi Manoj,<br><br>you can do it this way:<br><br>1) remove ligand from PDB file;<br>2) compute mFo-DFc map. This is your ligand-omit map.<br><br>Some would advise to do a round of refinement between steps 1-2 above in order to remove "memory from the ligand". I'm not convinced this is critical though.<span style='color:#888888'><br><br><span class=hoenzb>Pavel</span></span><o:p></o:p></p><div><div><p class=MsoNormal><br><br>On 11/15/15 12:18, Manoj saxena wrote:<o:p></o:p></p><p class=MsoNormal style='margin-bottom:12.0pt'>Greetings,<br><br>I would be very grateful if someone can help<br>me to explain in I can get F0-Fc omit maps of a particular<br>ligands using Phenix.<br>I am trying to generate an omit map<br>for the ligands in my protein model using the<br>composite omit map GUI feature of phenix version 1.10.1-2155.<br>I selected my ligands by using atom selection feature under the<br>map options(and in the omit map method I put refine). What map type I should give in the map types<br>input to get the F0-Fc maps. Currently I may getting a map<br>that look like my 2F0-Fc map that I got after my refinement.<br>Also, I have no waters in my model.<br>Can we define areas (boxes) around the ligand to generate<br>omit map of that particular region to get output maps with densities<br>like Fo-Fc maps.<br><br>So many thanks in advance.<br><br>Regards<br>Manoj<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div><P>Notice: This e-mail message, together with any attachments, contains<br>information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, <br>New Jersey, USA 07033), and/or its affiliates Direct contact information<br>for affiliates is available at <br>http://www.merck.com/contact/contacts.html) that may be confidential,<br>proprietary copyrighted and/or legally privileged. It is intended solely<br>for the use of the individual or entity named on this message. If you are<br>not the intended recipient, and have received this message in error,<br>please notify us immediately by reply e-mail and then delete it from <br>your system.</P></body></html>