<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
        {font-family:Wingdings;
        panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
        {font-family:Wingdings;
        panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
        {font-family:Calibri;
        panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
        {font-family:Tahoma;
        panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
        {margin:0in;
        margin-bottom:.0001pt;
        font-size:12.0pt;
        font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
        {mso-style-priority:99;
        color:blue;
        text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
        {mso-style-priority:99;
        color:purple;
        text-decoration:underline;}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
        {mso-style-priority:99;
        mso-style-link:"Balloon Text Char";
        margin:0in;
        margin-bottom:.0001pt;
        font-size:8.0pt;
        font-family:"Tahoma","sans-serif";}
span.EmailStyle17
        {mso-style-type:personal-reply;
        font-family:"Calibri","sans-serif";
        color:#1F497D;}
span.BalloonTextChar
        {mso-style-name:"Balloon Text Char";
        mso-style-priority:99;
        mso-style-link:"Balloon Text";
        font-family:"Tahoma","sans-serif";}
.MsoChpDefault
        {mso-style-type:export-only;
        font-family:"Calibri","sans-serif";}
@page WordSection1
        {size:8.5in 11.0in;
        margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
        {page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;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?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D"><o:p>&nbsp;</o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;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?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D"><o:p>&nbsp;</o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">Thanks a lot,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">Sneha<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D"><o:p>&nbsp;</o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;"> Parthasarathy Sampathkumar [mailto:spartha2@gmail.com]
<br>
<b>Sent:</b> Thursday, October 09, 2014 2:06 PM<br>
<b>To:</b> Sneha Rangarajan<br>
<b>Cc:</b> Nathaniel Echols; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] ligand fitting<o:p></o:p></span></p>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
<div>
<p class="MsoNormal">Hi Sneha,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
</div>
<div>
<p class="MsoNormal">Easier option would be to superpose homolog-protein&#43;peptide coordinates onto your &quot;apo&quot; 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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
</div>
<div>
<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.&nbsp;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
</div>
<div>
<p class="MsoNormal">Hope this helps,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
</div>
<div>
<p class="MsoNormal">Partha<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
<div>
<p class="MsoNormal">On Thu, Oct 9, 2014 at 12:56 PM, Sneha Rangarajan &lt;<a href="mailto:rsneha@umd.edu" target="_blank">rsneha@umd.edu</a>&gt; wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">Hello everyone,</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">&nbsp;</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">I have a question about ligand fitting into density.
</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">At this point my maps look quite good with decent density for the peptide (ligand)[Rfactprs 26/31].</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">&nbsp;</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;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><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:&quot;Calibri&quot;,&quot;sans-serif&quot;;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><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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">&nbsp;</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">Is there a better way to fit the peptide into density?</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">&nbsp;</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">Thanks,</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">S</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">&nbsp;</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">&nbsp;</span><o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">
<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><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">&nbsp;<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:&quot;Calibri&quot;,&quot;sans-serif&quot;;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><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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">&nbsp;</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">S</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">&nbsp;</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;"> 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><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">&nbsp;<o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Fri, Oct 3, 2014 at 11:58 AM, Sneha Rangarajan &lt;<a href="mailto:rsneha@umd.edu" target="_blank">rsneha@umd.edu</a>&gt; wrote:<o:p></o:p></p>
<div>
<div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:11.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">I did another round of refinement with default settings (XYZ,realsp, IndB and occ) with and without
 weight optimization.&nbsp;</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:&quot;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D">Without weight opt, the Rfactors are 23/36 with RMSbonds-0.0108 and RMSangles-1.750</span><o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">&nbsp;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">One idea would be to run AutoBuild again.&nbsp; 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.&nbsp; It might help get rid of the overfitting.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">&nbsp;<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">-Nat<o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
</div>
</div>
</body>
</html>