[phenixbb] Phenix secondary structure restraints bug

[Edwin Pozharski]

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.
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