manually defining CDRs in antibody modelling

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    • July 10, 2020 at 8:31 pm #3503
      Anonymous

        Hi all,

        I’m trying to use the antibody executable to create a model of an exisiting antibody. I have the CDR sequences that I need to model, so I created a fasta file and tried to run it. However, I get this error:

        File: src/protocols/antibody/grafting/chothia_numberer.cc:149

        ERROR: Unxpected length of h1 [length=3], length expected to be: [6, 7, 8, 9, 10, 11, 12, 13]!

        Looking through the rest of the output, I see that the code has correctly identified 3 of the 6 h1 residues. However, it is assigning the other 3 to the framework. It looks like the code gets the rest of the CDRs correct.

        Is there a way that I can manually tell the code what the h1 sequence is? Or can I modify the REGEX to either include my sequence or even hard-code it for now?

        Thanks for your help!

        Gard

      • January 20, 2021 at 4:11 pm #15688
        Anonymous

          This looks like the same issue that I posted (and solved via some help) here: https://www.rosettacommons.org/node/11094 . I realize this question is old, but maybe the solution wil help someone else.

           

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