Remodel and the depracated EMPTY NC

[Anonymous]

I am using Remodel and I wanted to use a non-canonical amino acid. However, EMPTY NC XXX in the blueprint no longer works as I get an error (below), with a suggestion to use a PackerPalette via a PackerTask or TaskFactory.

I am using Remodel in Pyrosetta 4 2020.49 release (a stable)  for 3.7, but I believe my problem is Rosetta in general one, not a Pyrosetta one. RemodelMover does not accept a task. Furthermore, the pose index numbers change relative to the initial pose so I am not quite sure how such a task would look like.

Looking further afield, RemodelDesignMover does accept a task but it gets called by RemodelMover().apply half way down the RemodelMover.cc file and there is a lot of stuff before and after it. Sure, it is tempting as the before part is prepping for it, hence its unique arguments (RemodelData and RemodelWorkingSet), which would probably circumvent adding Options, but this seems like a totally non-trivial task and the errors come from RemodelData.

Consequently, is there a way to make RemodelMover use a NCAA? Or should I simply use a different mover?

EMPTY NC NME

ERROR: Error in ResfileContents::check_for_deprecated_commands(): The “EMPTY” command has been deprecated.  Please refer to the documentation on PackerPalettes (https://www.rosettacommons.org/docs/latest/rosetta_basics/structural_concepts/PackerPalette) for details on how to properly use PackerPalettes to create a set of ResidueTypes with which one will design, and TaskOperations to prune away ResidueTypes that are not desired at a particular location.

NC NME

ERROR: Error in ResfileContents::check_for_deprecated_commands(): The “NC” command has been deprecated.  Please refer to the documentation on PackerPalettes (https://www.rosettacommons.org/docs/latest/rosetta_basics/structural_concepts/PackerPalette) for details on how to properly use PackerPalettes to create a set of ResidueTypes with which one will design, and TaskOperations to prune away ResidueTypes that are not desired at a particular location.

PIKAA [NME]

ERROR: Error in RemodelData::get_loops_to_build_from_blueprint(): Line “[NME]” could not be parsed.  PIKAA statements cannot contain noncanonicals in the context of Remodel, since Remodel foolishly re-implements core functionality instead of calling core functions.  If this is a problem, contact possu@stanford.edu.

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