<div dir="ltr">Yes Sneha.., "apo" structure and the tweaked-peptide should be merged (under the calculate pull-down menu in coot) before subsequent refinement cycle(s).<div><br></div><div>Best Wishes,</div><div>Partha</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Oct 9, 2014 at 4:16 PM, Sneha Rangarajan <span dir="ltr"><<a href="mailto:rsneha@umd.edu" target="_blank">rsneha@umd.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">@Partha: My peptide is 13 residues long. I don’t see the density for all of it (just few of them). Pardon me for the naïve question but once I superimpose it
in coot and adjust its position should I merge it with my “apo” structure (make it part of my model) and refine it to make it fit the density better or something like that?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><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?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">And yes, the peptide was never part of any model or sequence file right from the start since I wanted to avoid any bias. While I see positive density, autobuild
has not built any peptide into it.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks a lot,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Sneha<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></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""> Parthasarathy Sampathkumar [mailto:<a href="mailto:spartha2@gmail.com" target="_blank">spartha2@gmail.com</a>]
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<b>Sent:</b> Thursday, October 09, 2014 2:06 PM<br>
<b>To:</b> Sneha Rangarajan<br>
<b>Cc:</b> Nathaniel Echols; <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] ligand fitting<u></u><u></u></span></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Hi Sneha,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Easier option would be to superpose homolog-protein+peptide coordinates onto your "apo" structure (using SSM for example within coot), which might get the peptide closer to the binding-site of your protein, and then tweak it for better
fit.<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">OR if the peptide is not too long, and its electron density is clear one might be able to build it manually from scratch. <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Hope this helps,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Partha<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Thu, Oct 9, 2014 at 12:56 PM, Sneha Rangarajan <<a href="mailto:rsneha@umd.edu" target="_blank">rsneha@umd.edu</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Hello everyone,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></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.
</span><u></u><u></u></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].</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></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).</span><u></u><u></u></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?</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></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?</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">S</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
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<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<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"">
<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> [mailto:<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>]
<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> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] (no subject)</span><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></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><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">S</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"> </span><u></u><u></u></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" target="_blank">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" target="_blank">
phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [phenixbb] (no subject)</span><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></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:<u></u><u></u></p>
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<p class="MsoNormal"><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><u></u><u></u></p>
<p class="MsoNormal"><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><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></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.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">-Nat<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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