<div dir="ltr">Hi Reza,<div><br></div><div>If you have the new scope in the .eff file, it will be used at all times. The behavior that you observed confirms it. You have the new scope, but was putting weight_scale=300 into the old one, which was ignored. I believe you should be able to remove the old scope from the .eff file to avoid any confusion.</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span style="font-size:16px;color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif">For the </span><em style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">emsley</em><span style="font-size:16px;color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif"> target function, </span><em style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">rama_weight</em><span style="font-size:16px;color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif"> and </span><em style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">scale_allowed</em></blockquote><div>These are moved to ramachandran_plot_restraints.emsley subscope and named &quot;weight&quot; and &quot;scale_allowed&quot;.</div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span style="font-size:16px;color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif">the </span><em style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">oldfield</em><span style="font-size:16px;color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif"> target function, a grid of refinements was performed over </span><em style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">plot_cutoff</em><span style="font-size:16px;color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif"> values from 0.01 to 1.0 and </span><em style="color:rgb(0,0,0);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px">weight_scale</em></blockquote><div>These are moved to ramachandran_plot_restraints.oldfield subscope and the names are the same.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Sep 9, 2020 at 8:37 AM Reza Khayat &lt;<a href="mailto:rkhayat@ccny.cuny.edu">rkhayat@ccny.cuny.edu</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">




<div dir="ltr" style="font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255);font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi Oleg,<br>
</p>
<p><br>
</p>
<p>I figured it out, but please correct me if I&#39;m wrong. <span style="font-size:12pt">Setting </span></p>
<div><br>
</div>
<div>    peptide_link {</div>
<div>      ramachandran_restraints = False<br>
<br>
</div>
<div>and <br>
</div>
<div><span style="color:rgb(33,33,33);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)">    </span><span style="color:rgb(33,33,33);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)">ramachandran_plot_restraints
 {</span><br style="color:rgb(33,33,33);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33);font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)">      enabled = True</span><br>
</div>
<p><br>
</p>
<p>imposes the new enhanced protocol. Setting both to true does not impose the new protocol.<br>
</p>
<p><br>
Best wishes,<br>
Reza<br>
</p>
<p><br>
</p>
<div id="gmail-m_-2240139598216351031Signature">
<div name="divtagdefaultwrapper">
Reza Khayat, PhD
<div>Associate Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
<div dir="ltr" style="font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255);font-family:Calibri,Arial,Helvetica,sans-serif">
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-2240139598216351031divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a> &lt;<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-online.org</a>&gt; on behalf of Reza Khayat &lt;<a href="mailto:rkhayat@ccny.cuny.edu" target="_blank">rkhayat@ccny.cuny.edu</a>&gt;<br>
<b>Sent:</b> Wednesday, September 9, 2020 9:21 AM<br>
<b>To:</b> Oleg Sobolev<br>
<b>Cc:</b> PHENIX user mailing list<br>
<b>Subject:</b> Re: [phenixbb] [EXTERNAL] Re: Improving Ramachandran plot</font>
<div> </div>
</div>
<div>
<p>Hi Oleg,<br>
</p>
<p><br>
</p>
<p>Thanks for the response. </p>
<p>1. Yes, I am using the command line version</p>
<p>2. The run.eff file that I had included in my e-mail includes the lines you sent. I would appreciate the help in converting the old-style into the new style. ​<br>
</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
</p>
<p><br>
</p>
<div id="gmail-m_-2240139598216351031Signature">
<div name="divtagdefaultwrapper">
Reza Khayat, PhD
<div>Associate Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
<div style="color:rgb(33,33,33)">
<hr style="display:inline-block;width:98%">
<div id="gmail-m_-2240139598216351031divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Oleg Sobolev &lt;<a href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>&gt;<br>
<b>Sent:</b> Tuesday, September 8, 2020 7:43 PM<br>
<b>To:</b> Reza Khayat<br>
<b>Cc:</b> PHENIX user mailing list<br>
<b>Subject:</b> [EXTERNAL] Re: [phenixbb] Improving Ramachandran plot</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi Reza,
<div><br>
</div>
<div>I assume that you run Phenix via command line. We have a new enhanced &quot;ramachandran_plot_restraints&quot; scope to define these (similar) parameters. The previous one is there (for a short while) for backward compatibility (so users can restore old GUI jobs).
 The new scope looks like:</div>
<div><br>
</div>
<div>    ramachandran_plot_restraints {<br>
      enabled = True<br>
      favored = *oldfield emsley emsley8k<br>
      allowed = *oldfield emsley emsley8k<br>
      outlier = *oldfield emsley emsley8k<br>
      selection = None<br>
      inject_emsley8k_into_oldfield_favored = True<br>
      oldfield {<br>
        weight = 0.<br>
        weight_scale = 0.01<br>
        distance_weight_min = 2.0<br>
        distance_weight_max = 10.0<br>
        plot_cutoff = 0.027<br>
      }<br>
      emsley {<br>
        weight = 1.0<br>
        scale_allowed = 1.0<br>
      }<br>
      emsley8k {<br>
        weight_favored = 5.0<br>
        weight_allowed = 10.0<br>
        weight_outlier = 10.0<br>
      }<br>
    }<br>
</div>
<div>So please use this one. Notable change is that now you can restrain favored/allowed/outliers separately (or not restrain one or another).</div>
<div>Please let me know if you need to know exactly how to convert old-style parameters into new ones.</div>
<div><br>
</div>
<div>In case you are going to perform a similar study as you are mentioning, I would like to suggest adding the Rama-Z metric to the set of validation metrics. It was included particularly to judge the distribution of residues on Ramachandran plot:
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1016_j.str.2020.08.005&amp;d=DwMFaQ&amp;c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&amp;r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&amp;m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&amp;s=ptg6ZgZREaTRrW9ujd0LnZ-8kkjQnOgvn0w4NVpj8jI&amp;e=" target="_blank">
https://doi.org/10.1016/j.str.2020.08.005</a></div>
<div><br>
</div>
<div>Let me know if you have any questions.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sun, Sep 6, 2020 at 9:12 PM Reza Khayat &lt;<a href="mailto:rkhayat@ccny.cuny.edu" target="_blank">rkhayat@ccny.cuny.edu</a>&gt; wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255);font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi,<br>
</p>
<p><br>
</p>
<p>I&#39;m trying to follow the protocol described in White et al., <span style="color:rgb(115,115,115);font-family:Georgia,Times,serif;font-size:13px;font-style:italic;background-color:rgb(255,255,255)">Structural principles of SNARE complex recognition by
 the AAA+ protein NSF</span> e-life 2018 <br>
</p>
<p><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888&amp;d=DwMFaQ&amp;c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&amp;r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&amp;m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&amp;s=AL0jOsHeTv1ypmAgBkrS4fg6oj-WdYhsXDJ4qWcKh50&amp;e=" target="_blank">https://elifesciences.org/articles/38888</a><br>
</p>
<p><br>
</p>
<p>Here is the pertinent paragraph:<br>
</p>
<p><br>
</p>
<p>&quot;T<span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)">o improve the Ramachandran statistics and geometry of the models, a two-parameter grid search of real space refinements was performed in
 which 3–5 macrocycles of global minimization and local grid search were performed in the presence of secondary structure restraints. First, a grid refinement search was performed for both target functions with around 1000 refinements each. For the </span><em>emsley</em><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)"> target
 function, </span><em>rama_weight</em><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)"> and </span><em>scale_allowed</em><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)"> were
 varied from 0.01 to 300; for the </span><em>oldfield</em><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)"> target function, a grid of refinements was performed over </span><em>plot_cutoff</em><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)"> values
 from 0.01 to 1.0 and </span><em>weight_scale</em><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)"> values from 0.1 to 300. Results were judged empirically and based primarily on a balance
 between </span><em>CC<span style="font-size:12px;line-height:0;vertical-align:baseline">mask</span></em><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)"> and a minimal fraction of residues
 flagged by the program CaBLAM (</span><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888-23bib37&amp;d=DwMFaQ&amp;c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&amp;r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&amp;m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&amp;s=A-IYsxXhwe3dvl7oZ8JRr0rxyZ4W29522VR7YCPRmKg&amp;e=" style="background-color:rgb(255,255,255);color:rgb(33,33,33);border-bottom:1px dotted rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px" target="_blank">Richardson
 et al., 2018</a><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)">) because focusing on the fraction of residues with favored </span><em>CC<span style="font-size:12px;line-height:0;vertical-align:baseline">mask</span></em><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)"> and
 Ramachandran statistics alone often resulted in unrealistic models with serious problems (</span><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888-23fig12&amp;d=DwMFaQ&amp;c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&amp;r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&amp;m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&amp;s=e7ESAeeMjGInzQkzBfSgzzZPRTccskQn25ODvsw4nlQ&amp;e=" style="background-color:rgb(255,255,255);color:rgb(33,33,33);border-bottom:1px dotted rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px" target="_blank">Figure
 12</a><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)">, </span><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888-23table2&amp;d=DwMFaQ&amp;c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&amp;r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&amp;m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&amp;s=lgVCnWzCNio89ZUuhejZ7-iD0MwdtumGbIm5-yMuYLw&amp;e=" style="background-color:rgb(255,255,255);color:rgb(33,33,33);border-bottom:1px dotted rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px" target="_blank">Table
 2</a><span style="color:rgb(33,33,33);font-family:&quot;Noto Serif&quot;,serif;font-size:16px;background-color:rgb(255,255,255)">).</span>&quot;<br>
</p>
<p><br>
</p>
<p>There are no differences in the refined structures regardless of what parameters I change. Attached is the input file I use for phenix.real_space_refine (1.18.2​). Altering the oldfield weight_scale (0.1 to 300) and plot_cutoff (0.1 to 0.5) makes no difference.
 Any help is highly appreciated. <br>
</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza<br>
</p>
<p><br>
</p>
<div id="gmail-m_-2240139598216351031gmail-m_524770089551876798Signature">
<div name="divtagdefaultwrapper">Reza Khayat, PhD
<div>Associate Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
</div>
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