Usage of the TaskOperations “RestrictToCDRsAndNeighbors”

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    • April 10, 2019 at 9:58 am #3111
      Anonymous

        Hi, I would like to include the TaskOperations “RestrictToCDRsAndNeighbors” in my xml file which is to design the CDR in an antibody-antigen interface.

        However, I do not know what to put as options under the arguments “numbering_scheme” and “cdr_definition”

        From the manual, the explanations are

        • numbering_scheme (&string): Set the antibody numbering scheme. Must also set the cdr_definition XML option. Both options can also be set through the command line (recommended). See General Antibody Tips for more info.

        • cdr_definition (&string): Set the cdr definition you want to use. Must also set the numbering_scheme XML option. See General Antibody Tips

        After reading the explanations and the General Antibody Tips I still have no idea what are the possible options to choose.

        I improvised myself and written something as the following, which didn’t work (i.e. the run stopped with no structures generated)

        <RestrictToCDRsAndNeighbors name=”to_cdrs” numbering_scheme=”AHO_Scheme” cdr_definition=”H1,H2,H3″/>

        If you have ever used RestrictToCDRsAndNeighbors, would you mind showing me the possible options for the arguments “numbering_scheme” and “cdr_definition”? 

        Thanks in advance.

      • July 10, 2019 at 5:07 pm #14838
        Anonymous

          The valid entries for numbering_scheme are “Chothia”, “Kabat”, “Enhanced_Chothia”, “AHO”, and “IMGT”. (There’s also various synonyms, e.g. where you can suffix _Scheme, like “AHO_Scheme”).

          The valid entries for cdr_definition are “Chothia”, “Aroop”, “North”, “Kabat” and “Martin”. (Refering to the respective papers and their definitions as to where the CDRs start and end.)

          Which one to use is dependent on which scheme your input files are numbered in. Depending on where you got your input from, you may need to dig around to figure out which convention they are using.

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