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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hello everyone,<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">I have a question about ligand fitting into density.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">At this point my maps look quite good with decent density for the peptide (ligand)[Rfactprs 26/31].<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">I tried using ligandfit by giving it the pdb and mtz of the ligand free model along with peptide.pdb (peptide stripped from a pdb where it was complexed with
a homologous protein).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">However the output was a ligand.pdb file with a CC of 0.49. I am not sure how to interpret this. Does this mean it could not find the density for the ligand?<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">Is there a better way to fit the peptide into density?<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">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">S<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>
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<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>Sneha Rangarajan<br>
<b>Sent:</b> Wednesday, October 08, 2014 10:30 AM<br>
<b>To:</b> Nathaniel Echols<br>
<b>Cc:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] (no subject)<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">This was a great idea. My Rfactors after a second round of autobuild are now 25/32. I think it might be getting there afterall
</span><span style="font-size:11.0pt;font-family:Wingdings;color:#1F497D">J</span><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"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">S<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""> Nathaniel Echols [<a href="mailto:nechols@lbl.gov">mailto:nechols@lbl.gov</a>]
<br>
<b>Sent:</b> Friday, October 03, 2014 3:08 PM<br>
<b>To:</b> Sneha Rangarajan<br>
<b>Cc:</b> Pavel Afonine; <a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] (no subject)<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Fri, Oct 3, 2014 at 11:58 AM, Sneha Rangarajan <<a href="mailto:rsneha@umd.edu" target="_blank">rsneha@umd.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I did another round of refinement with default settings (XYZ,realsp, IndB and occ) with and without
weight optimization. </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Without weight opt, the Rfactors are 23/36 with RMSbonds-0.0108 and RMSangles-1.750</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">One idea would be to run AutoBuild again. I've seen cases before where it didn't converge using the default settings, and feeding a previous result back into the program for a second run produced significantly better models. It might
help get rid of the overfitting.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-Nat<o:p></o:p></p>
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