Dear Edwin,

Thank you for reporting this issue.

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:

https://phenix-online.org/documentation/reference/secondary_structure.html

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

> phenix.secondary_structure_restraints model.pdb format=pdb ss_by_chain=False
$PHENIX/build/ksdssp/exe/ksdssp model.pdb

is different. They should be the same from the first look.

Best regards,

Oleg Sobolev.

On Mon, Oct 3, 2022 at 8:34 AM Edwin Pozharski <pozharskibb@gmail.com> wrote:

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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