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<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="Signature">
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
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 tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Oleg Sobolev <osobolev@lbl.gov><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 "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://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1016_j.str.2020.08.005&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=ptg6ZgZREaTRrW9ujd0LnZ-8kkjQnOgvn0w4NVpj8jI&e=">
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">
<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'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&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=AL0jOsHeTv1ypmAgBkrS4fg6oj-WdYhsXDJ4qWcKh50&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>"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="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://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888-23bib37&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=A-IYsxXhwe3dvl7oZ8JRr0rxyZ4W29522VR7YCPRmKg&e=" target="_blank" style="background-color:rgb(255,255,255); color:rgb(33,33,33); border-bottom:1px dotted rgb(33,33,33); font-family:"Noto Serif",serif; font-size:16px">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="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://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888-23fig12&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=e7ESAeeMjGInzQkzBfSgzzZPRTccskQn25ODvsw4nlQ&e=" target="_blank" style="background-color:rgb(255,255,255); color:rgb(33,33,33); border-bottom:1px dotted rgb(33,33,33); font-family:"Noto Serif",serif; font-size:16px">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://urldefense.proofpoint.com/v2/url?u=https-3A__elifesciences.org_articles_38888-23table2&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=CC98DLroSZABXnlwA93ckm5Bfu3Zx893dguNRHGVqJE&s=lgVCnWzCNio89ZUuhejZ7-iD0MwdtumGbIm5-yMuYLw&e=" target="_blank" style="background-color:rgb(255,255,255); color:rgb(33,33,33); border-bottom:1px dotted rgb(33,33,33); font-family:"Noto Serif",serif; font-size:16px">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>
</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_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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