<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Rebecca,<div><br><div>I'm sorry this didn't get answered on the phenix_bb! I somehow missed it too.</div><div><br></div><div>When you run an omit map with </div><div><br></div><div>model=mymodel.pdb omit_box_pdb=mymodel.pdb <span class="Apple-style-span" style="font-family: Consolas; ">omit_res_start_list=500 omit_res_end_list=500</span></div><div><br></div><div>the autobuild wizard edits mymodel.pdb, setting the occupancies of all atoms that are within a box enclosing the atoms in residue 500 of mymodel.pdb (plus a 2 A border) to zero. Then it runs the cycles of autobuild you specify (in this case just a SA step), and produces a density-modified map (resolve_composite_map.mtz) using the resulting model to generate phase information (and keeping the occupancies of these atoms at zero). If mydata.mtz contains phase information, that is used as well. </div><div><br></div><div>The output map is in </div><div><br></div><div>resolve_composite_map.mtz</div><div><br></div><div>and a pseudo-map showing where the OMIT region(s) is(are) located is in</div><div><br></div><div>omit_region.mtz</div><div><br></div><div><br></div><div>The file </div><div><span class="Apple-style-span" style="font-family: Consolas; "></span></div><div><font class="Apple-style-span" face="Consolas"><br></font></div><div><span class="Apple-style-span" style="font-family: Consolas; ">overall_best_denmod_map_coeff.mtz</span></div><div><br></div><div>is actually not really relevant or useful when you are doing OMIT maps because it is just one of the intermediate files that are produced. In this particular example it will be identical to resolve_composite_map.mtz but if you do other types of OMIT maps it won't be the same.</div><div><br></div><div>I changed the output of the autobuild wizard recently, so you might want to upgrade to the 1.3-final version. The end of the log file in this case should say:</div><div><br></div><div><div>--------------------------------------------------</div><div>Summary of model-building for run 1 Tue Oct 7 08:17:30 2008</div><div>Files are in the directory: /net/chevy/raid1/terwill/misc/test/AutoBuild_run_1_/</div><div><br></div><div><br></div><div>Starting mtz file: /net/chevy/raid1/terwill/misc/test/perfect.mtz</div><div>Sequence file: /net/chevy/raid1/terwill/misc/test/seq.dat</div><div><br></div><div>Composite omit map is in : /net/chevy/raid1/terwill/misc/test/AutoBuild_run_1_/OMIT/resolve_composite_map.mtz</div><div><br></div><div>Boundaries of omit regions are in : /net/chevy/raid1/terwill/misc/test/AutoBuild_run_1_/OMIT/omit_region.mtz</div><div>--------------------------------------------------</div><div><br></div><div>Which I hope is clearer than earlier output in which the <span class="Apple-style-span" style="font-family: Consolas; ">overall_best_denmod_map_coeff.mtz <span class="Apple-style-span" style="font-family: Helvetica; ">file is mentioned but is irrelevant.</span></span></div></div><div><br></div><div>I hope that helps!</div><div>All the best,</div><div>Tom T</div><div><br></div><div><br><div><div>On Oct 7, 2008, at 7:19 AM, Page, Rebecca wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; 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 lang="EN-US" link="blue" vlink="purple"><div class="Section1"><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Hi Tom,<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I posted the question on the phenix bb and, when I got no response, shot an email over to Frank von Delft, an old friend, to see if he knew answer.<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">He didn�t, but recommended I email you directly and to �ask him to post the answer on the general bb :)�. He also mentioned he hadn�t seen the post on the phenix bb and I would be interested to know if you did not see it either (I received it).<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">At any rate, here it goes:<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> I am newcomer to phenix and have a rookie question about the generated<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> files using the phenix.autobuild command. I generated an sa-omit map<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> of my model, omitting the coordinates for a bound ligand (ligand is<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> residue<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> 500):<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> phenix.autobuild data=mydata.mtz model=mymodel.pdb<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> omit_box_pdb=mymodel.pdb omit_res_start_list=500 omit_res_end_list=500<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> omit_chain_list=A composite_omit_type=sa_omit<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> The output omit map (resolve_composite_map.mtz) looks great.<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> My question is:<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> What, exactly, is the "overall_best_denmod_map_coeff.mtz" in this case<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 10.5pt; font-family: Consolas; ">> and how is it related, if at all, to the "resolve_composite_map.mtz"?<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Thanks for your help,<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Rebecca<o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: Arial, sans-serif; color: black; ">Rebecca Page</span><o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: Arial, sans-serif; ">Brown University</span><o:p></o:p></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div></div></span></blockquote></div><br></div></div></body></html>