Weekly Rosetta Bundle with PeptideDeriver Modeling Support

[debelyy-canada]

I am an academic user working on peptide–protein interface design using
the PeptideDeriver application. I currently have access to the stable
release (release-371), but I require functionality such as
-pep_output_structures, which appears to be available only in the weekly
developer builds (e.g., rosetta_bin_linux_2024.09.61533_bundle.tar.bz2).

Would it be possible to grant me access to the full weekly release
bundle that includes these features?

Thank you very much for your help

[roccomoretti]

We just opened up the site with the automatic release builds of Rosetta, at https://graylab.jhu.edu/download/rosetta/archive/release/ You should be able to get the built versions of recent Rosettas there. (Alternatively, you can clone this repo and compile from source.)

That said, it doesn't look like a -pep_output_structures option is included in recent releases. -- From what I can tell, it's never been part of Rosetta, though I might be searching for things incorrectly.

Where did you find mention of the functionality you're looking for?

[debelyy-canada]

Dear Rocco Moretti!

Thank you very much for your helpful reply and for providing the link to the new automatic release builds — that’s greatly appreciated.

Regarding the -pep_output_structures option: I came across this functionality through documentation and community discussions referring to updated versions of the PeptideDeriver application that support peptide–protein complex output. Specifically, several resources and discussions (including help from ChatGPT using up-to-date information) indicate that recent versions of PeptideDeriver support flags like:

-pep_output_structures true
-pep_output_number 5
-dump_peptide_pose true
-dump_cyclic_poses true

The functionality is described as enabling the output of docked peptide–protein structures in .pdb format directly from the PeptideDeriver run — something extremely useful for downstream modeling and design workflows.

I understand that this functionality may still be in the development branch or part of internal builds not yet reflected in the public automatic release builds. If that’s the case, could you kindly confirm whether this peptide-structure output functionality is currently supported in any branch (e.g., on the RosettaCommons GitHub)? And if so, is it accessible through a weekly developer bundle or GitHub compilation?

I’d be happy to compile from source if needed — just want to ensure I’m targeting the correct branch/version that includes this functionality.

Thank you again for your time and help — and for making Rosetta such a powerful and evolving resource.

Best regards,
Mike

[roccomoretti]

The list of PeptideDeriver specific output flags supported by the main version of Rosetta can be found at https://docs.rosettacommons.org/docs/latest/full-options-list#peptide_deriver -- That does list -dump_peptide_pose and -dump_cyclic_poses as options. Unfortunately, it doesn't look like -pep_output_structures or -pep_output_number are included in that. Nor, for that matter, does Google or Bing search show any pages with that exact string.

While it is possible there's some development version which has that or something similar, I am unaware of where to start looking for it. -- This was why I asked about where you came across mention of the options. Having a link to a specific reference, help page, or user discussion could give me a starting off place where I could start digging into things (e.g. tracking down branches). If it is just ChatGPT mentioning it, given the lack of other web presence for the search term, I'm guessing it might be an LLM hallucination.

That said, I think that it's likely -dump_prepared_pose (possibly with -dump_peptide_pose and/or -dump_cyclic_poses) that will do what you want.