antibody_numbering_converter cannot recognize the IMGT scheme

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    • March 1, 2020 at 7:12 am #3361
      Anonymous

        To whom it may concern:

        Hi I want to convert my antibody structure from Chothia to IMGT. I use the following command and get an error “ERROR: Illegal value specified for option -antibody:output_ab_scheme : IMGT”. I am wondering is the IMGT scheme already cancelled in the number converter program? This is a 2019.35.60890 version.

        /home/rosetta_bin_linux_2019.35.60890_bundle/main/source/bin/antibody_numbering_converter.linuxgccrelease -input_ab_scheme Chothia -output_ab_scheme IMGT -s 1ahw_chothia.pdb

         

        Best regards,

        Shkai

      • March 1, 2020 at 3:27 pm #15178
        Anonymous

          This should work – but there may be a problem in the pre-processor for the options system.  It is indeed coded in there.

          For now, if you use IMGT_Scheme instead of IMGT, it should work.

        • March 1, 2020 at 3:31 pm #15179
          Anonymous

            Use IGMT_Scheme – and any time you use the coverter for now, put the _Scheme at the end.  I’ll work to debug why the ones without the _Scheme on the end are tripping up the options system.

            • March 1, 2020 at 8:40 pm #15180
              Anonymous

                Let me update,  change from -output_ab_scheme IMGT to -output_ab_scheme IMGT_Scheme works fine.

            • March 1, 2020 at 10:54 pm #15181
              Anonymous

                Awesome. Thanks for the update! I’m looking into how to fix it generally.  Hopefully will have it fixed sometime soon.

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