RosettaCommons / RosettaCommons/PyRosetta.notebooks

add acetylated N-terminus using pyrosetta

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Description

Hi team,

May I ask how to add the acetylated N-terminus and methylamidated C-terminus to a pose when using Pyrosetta? The pose is loaded from a pdb using a command like:
pose = pose_from_pdb("test.pdb").

I googled as much as I possible, but still cann't find a command that can work.
There was a command seemed to worked, but still it didn't:
pyrosetta.rosetta.core.conformation.add_variant_type_to_conformation_residue(pose.conformation(), pyrosetta.rosetta.core.chemical.ACETYLATED_NTERMINUS_VARIANT, 1)

The error was:
ERROR: Unable to find desired residue 'LYS:NtermProteinFull' with variant 'ACETYLATED_NTERMINUS_VARIANT'. Attempted to add target variant(s) to ResidueType using both ResidueType base name 'LYS' and base ResidueType. Was attempting to add new variant type 'ACETYLATED_NTERMINUS_VARIANT'

Thank you very much.

All the best.

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Research direction

Reproduce the issue in a PyRosetta notebook using pose_from_pdb("test.pdb") and the shown terminal-variant call. Investigate the residue and variant setup, then document a verified way to add both terminal modifications and the expected result.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
bioinformatics
Issue type
Documentation
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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