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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks everyone for your suggestions.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I have managed to fit my peptide into the density.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">My Rfactors are now 25/30 and geometry looks good too.<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">One more question- When does one use “add hydrogens” in refinement? Does it help in the final stages of refinement?<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 a lot,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Sneha<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 [mailto:nechols@lbl.gov]
<br>
<b>Sent:</b> Thursday, October 09, 2014 5:21 PM<br>
<b>To:</b> Sneha Rangarajan<br>
<b>Cc:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] ligand fitting<o:p></o:p></span></p>
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<p class="MsoNormal">On Thu, Oct 9, 2014 at 1:16 PM, 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">@Nat: If I want to run autobuild to fit the ligand into the density, should I give it my “apo” model
as ‘starting model’ and peptide.pdb as ‘ligands’ alongwith the mtz?</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">No, in AutoBuild terminology, "ligands" means "atoms I want AutoBuild to leave alone (but include in refinement)", which would mean your apo model. You wouldn't supply peptide.pdb at all, because AutoBuild isn't going to move it into the
correct place; ideally you want it to just build new residues into the appropriate density.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">To be honest I think I would be tempted to simply build the peptide by hand, which shouldn't be too difficult at this resolution. I'm normally a big fan of letting the program do all of the heavy lifting, but this is one of those corner
cases where the manual approach might be more efficient. (This is a point for future improvement in Phenix, of course.) Your own opinion of how easy it will be may be different than mine, however.<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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