<div dir="ltr">Hi Reza,<div><br></div><div>I assume that you run Phenix via command line. We have a new enhanced "ramachandran_plot_restraints" 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://doi.org/10.1016/j.str.2020.08.005">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 <<a href="mailto:rkhayat@ccny.cuny.edu">rkhayat@ccny.cuny.edu</a>> 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">
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<p>Hi,<br>
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<p>I'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://elifesciences.org/articles/38888" target="_blank">https://elifesciences.org/articles/38888</a><br>
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<p>Here is the pertinent paragraph:<br>
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<p>"T<span style="color:rgb(33,33,33);font-family:"Noto Serif",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:"Noto Serif",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:"Noto Serif",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:"Noto Serif",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:"Noto Serif",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:"Noto Serif",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:"Noto Serif",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="box-sizing:border-box;font-size:12px;line-height:0;vertical-align:baseline">mask</span></em><span style="color:rgb(33,33,33);font-family:"Noto Serif",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://elifesciences.org/articles/38888#bib37" style="box-sizing:border-box;background-color:rgb(255,255,255);color:rgb(33,33,33);text-decoration-line:none;border-bottom:1px dotted rgb(33,33,33);font-family:"Noto Serif",serif;font-size:16px" target="_blank">Richardson
et al., 2018</a><span style="color:rgb(33,33,33);font-family:"Noto Serif",serif;font-size:16px;background-color:rgb(255,255,255)">) because focusing on the fraction of residues with favored </span><em>CC<span style="box-sizing:border-box;font-size:12px;line-height:0;vertical-align:baseline">mask</span></em><span style="color:rgb(33,33,33);font-family:"Noto Serif",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://elifesciences.org/articles/38888#fig12" style="box-sizing:border-box;background-color:rgb(255,255,255);color:rgb(33,33,33);text-decoration-line:none;border-bottom:1px dotted rgb(33,33,33);font-family:"Noto Serif",serif;font-size:16px" target="_blank">Figure
12</a><span style="color:rgb(33,33,33);font-family:"Noto Serif",serif;font-size:16px;background-color:rgb(255,255,255)">, </span><a href="https://elifesciences.org/articles/38888#table2" style="box-sizing:border-box;background-color:rgb(255,255,255);color:rgb(33,33,33);text-decoration-line:none;border-bottom:1px dotted rgb(33,33,33);font-family:"Noto Serif",serif;font-size:16px" target="_blank">Table
2</a><span style="color:rgb(33,33,33);font-family:"Noto Serif",serif;font-size:16px;background-color:rgb(255,255,255)">).</span>"<br>
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<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>
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<p><br>
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<p>Best wishes,<br>
Reza<br>
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<p><br>
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<div id="gmail-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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