<div dir="ltr">Dear Edwin,<div><br></div><div>Thank you for reporting this issue.</div><div><br></div><div>I'm afraid there is a slight misunderstanding of the parameter because of lack of description in our documentation. The ss_by_chain flag only affects "from_ca" search_method. It has no effect when you choose any other methods. For the sake of completeness, from_ca_conservative, max_rmsd, use_representative_chains and max_representative_chains also only affect "from_ca" method. I'll adjust the description of parameters that can be seen at the bottom of this page:</div><div><a href="https://phenix-online.org/documentation/reference/secondary_structure.html">https://phenix-online.org/documentation/reference/secondary_structure.html</a><br></div><div><br></div><div>It would be helpful if you could share (off-list) the model.pdb you were experimenting with, so I can look deeper into why output of</div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">> phenix.secondary_structure_restraints model.pdb format=pdb ss_by_chain=False <br>$PHENIX/build/ksdssp/exe/ksdssp model.pdb</blockquote></div><div>is different. They should be the same from the first look.</div><div><br></div><div>Best regards,</div><div>Oleg Sobolev.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 3, 2022 at 8:34 AM Edwin Pozharski <<a href="mailto:pozharskibb@gmail.com" target="_blank">pozharskibb@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">When using phenix.secondary_structure_restraints (from command line, not sure if it's different in GUI) ss_by_chain flag is ignored when using default method (ksdssp, even if explicitly selected). Works fine when mmtbx_dssp is used though. Details:<div><br></div><div>> phenix.secondary_structure_restraints model.pdb format=pdb ss_by_chain=False <br></div><div><br></div><div>only produces intrachain beta sheets.</div><div><br></div><div>> phenix.secondary_structure_restraints model.pdb format=pdb ss_by_chain=False search_method=mmtbx_dssp<br></div><div><br></div><div>produces both intrachain and interchain beta-sheets.</div><div><br></div><div>I am fairly certain this is not KSDSSP bug per se, since output of </div><div><br></div><div>$PHENIX/build/ksdssp/exe/ksdssp model.pdb</div><div><br></div><div>contains interchain beta-sheets.</div><div><br></div><div>This is with 1.20.1-4487.</div></div>
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