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:

> phenix.secondary_structure_restraints model.pdb format=pdb ss_by_chain=False

only produces intrachain beta sheets.

> phenix.secondary_structure_restraints model.pdb format=pdb ss_by_chain=False search_method=mmtbx_dssp

produces both intrachain and interchain beta-sheets.

I am fairly certain this is not KSDSSP bug per se, since output of

$PHENIX/build/ksdssp/exe/ksdssp model.pdb

contains interchain beta-sheets.

This is with 1.20.1-4487.