[phenixbb] Phenix secondary structure restraints bug

[Oleg Sobolev]

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 at 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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