use_truncated_termini not working in combination with params files

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    • March 26, 2020 at 8:14 pm #3382
      Anonymous

        When using FastRelax with the keyword -use_truncated_termini true as expected no OXT are added if not present in the input file. However, when I run the same protocol with additional params files (-extra_res_fa), OXT are added to all chains and the -use_truncated_termini seems to be ignored. Does anyone know/suspect a reason for this and might know a workaround?

        Thanks,

        Georg

      • April 14, 2020 at 10:36 am #15240
        Anonymous

          I know you are asking from a standalone executable usage, but I do not know the solution to your problem but as nobody as replied, I thought I’d give my two pence worth. The last residue on a chain gets a patch, CtermProteinFull, which like say phosphorylations can be forced in PyRosetta, and I assume likewise in Scripts. Namely if you search CtermProteinFull in Finder/Nautilus or navigate to you will find the folder in the database where the patches are and you will find the names —always useful as it’s not straightforward. The following removes the `OXT` atom in a pose where a custom params file and ligand are present for me. 


          
MutateResidue = pyrosetta.rosetta.protocols.simple_moves.MutateResidue
          
MutateResidue(target=r, new_res='THR:protein_cutpoint_lower').apply(pose)

          I have no idea of which patch does what so I tried until I did not get a segfault. CtermTruncation, C-terminal_conjugation, THR:aryl-C-conjugated kill the process. But THR:Cterm_amidation and THR:protein_cutpoint_lower worked.

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