<div dir="ltr">Hi Reza,<div><br></div><div>The parameters I mentioned previously control the weight (strength) of the SS restraints that are established. </div><div><br></div><div>To avoid rejection of your (presumably hand-curated) secondary structure annotations from PDB header, you can set</div>secondary_structure.protein.remove_outliers=False <div>Setting distance_cut_n_0 to a large number would have similar effect. Both of them can be changed if you search for them in GUI "All parameters"->"Search parameters". I would start with the remove_outliers parameter.</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, Jan 10, 2024 at 4:14 AM 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 class="msg-1659531331752959948">
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Hi Oleg,</div>
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<div><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Thank you for the help. I've defined secondary structures in the header of the PDB and
Phenix does recognize these to properly setup the .eff files for refinement. However, am I to increase/decrease
</span><span style="letter-spacing:normal;font-size:15px;color:rgb(36,36,36);background-color:rgb(255,255,255);font-weight:400">sigma,
slack, angle_sigma_scale, angle_sigma_set</span><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)"> to encourage the dihedrals towards adopting the defined secondary
structure? The pop-up bubbles in the GUI do not provide an explanation for these parameters. Alternatively, should I increase the value for distance_cut_n_0 and allow the refinement procedure to do its magic? Thanks again.</span></div>
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Best wishes,<br>
Reza</span></div>
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<div id="m_-1659531331752959948divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Oleg Sobolev <<a href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>><br>
<b>Sent:</b> 09 January 2024 7:59 PM<br>
<b>To:</b> Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu" target="_blank">rkhayat@ccny.cuny.edu</a>><br>
<b>Cc:</b> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a> <<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a>><br>
<b>Subject:</b> [EXTERNAL] Re: [phenixbb] Secondary structure weights for realspace refinement</font>
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<div dir="ltr">Hi Reza,
<div><br>
</div>
<div>There are parameters related to weights of various secondary structure restraints for each element like sigma, slack, angle_sigma_scale, angle_sigma_set for helices and sheets; planarity_sigma, parallelity_sigma, sigma for nucleic acids. The hierarchical
list of these is here: <a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline.org_documentation_reference_secondary-5Fstructure-5Frestraints.html&d=DwMFaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=6K8j3VgEJ0UG3oRcNSsZAoyWju0j2E73jDKsOYp6efvYNnWQ0FDgW2d6dnlehZaL&s=2XXvWBBG_M9vtaXmTY8VIkA1S5twtYG5r7GMTLtQVuI&e=" target="_blank">https://phenix-online.org/documentation/reference/secondary_structure_restraints.html</a><br>
</div>
<div>Some of the parameters are available via GUI on "Select atoms" -> "Secondary structure" tab.</div>
<div>For full flexibility one can run the phenix.secondary_structure_restraints command-line tool, edit the resulting parameter file and then supply it to refinement.</div>
<div><br>
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<div>Let me know if you have any more questions.</div>
<div><br>
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<div>Best regards,</div>
<div>Oleg Sobolev. </div>
</div>
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<div>
<div dir="ltr">On Mon, Jan 8, 2024 at 5:58 PM Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu" target="_blank">rkhayat@ccny.cuny.edu</a>> wrote:<br>
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Hi,</div>
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I hope all is well. Is there a way to alter the weights for secondary structure restraints? Thanks.</div>
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Best wishes<br>
Reza</div>
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<div id="m_-1659531331752959948x_m_-7570673356639600129Signature">
<div><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Reza Khayat, PhD</span></div>
<div><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">City College of New York</span></div>
<div><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Associate Professor</span></div>
<div><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Department of Chemistry and Biochemistry</span></div>
<div><span style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">Co-Director NIH G-RISE program</span></div>
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