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Hi Oleg,</div>
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<div class="elementToProof"><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-family: "Segoe UI", "Segoe UI Web (West European)", "Segoe UI", -apple-system, BlinkMacSystemFont, Roboto, "Helvetica Neue", sans-serif; 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="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Oleg Sobolev <osobolev@lbl.gov><br>
<b>Sent:</b> 09 January 2024 7:59 PM<br>
<b>To:</b> Reza Khayat <rkhayat@ccny.cuny.edu><br>
<b>Cc:</b> phenixbb@phenix-online.org <phenixbb@phenix-online.org><br>
<b>Subject:</b> [EXTERNAL] Re: [phenixbb] Secondary structure weights for realspace refinement</font>
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<div dir="ltr">Hi Reza,
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<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=">https://phenix-online.org/documentation/reference/secondary_structure_restraints.html</a><br>
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<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>
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<div>Let me know if you have any more questions.</div>
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<div>Best regards,</div>
<div>Oleg Sobolev. </div>
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<div dir="ltr" class="x_gmail_attr">On Mon, Jan 8, 2024 at 5:58 PM Reza Khayat <<a href="mailto:rkhayat@ccny.cuny.edu">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><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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