Numbering failed

Member Site Forums ROSIE ROSIE – General Numbering failed

Viewing 3 reply threads
  • Author
    Posts
    • #2666
      Anonymous

        Job ID 32176 failed with this error: 


        ERROR: FR_L3 length 28 is not between 32 and 34
        Numbering failed. Exiting.

         

        Any ideas on how I can remedy this? Thank you

      • #12372
        Anonymous

          You’ve got an antibody which is outside the norm of antibodies – according to the automated annotation in ROSIE, the framework region in your light chain is too short (28 verus a standard 32 to 34). Due to the way ROSIE Antibody is set up, it can’t apply the automated proceedure to thread this onto the standard backbones.

          The first thing to check is if this antibody light chain does indeed match what it’s supposed to.  I’d highly recommend reading https://doi.org/10.1016/j.jmb.2010.10.030 and https://doi.org/10.1006/jmbi.1997.1442  and looking through the website  https://www.bioc.uzh.ch/plueckthun/antibody/  to check your antibody sequence against what is “normal” for antibodies, to see if there’s something special/funky going on with your particular light chain.

          Past that, given that your antibody is outside the norm for antibodies, you’re likely going to have to run the antibody modeling proceedure manually. So you’d download Rosetta locally, and then follow the RosettaAntibody proceedures outlined in https://doi.org/10.1038/nprot.2016.180   You’re likely going to need to tweak the alignments and settings to be able to get Rosetta to work with your “short” antibody, or to correct the misalignment that the automatic tools are doing.

        • #12893
          Anonymous

            You’ve got an antibody which is outside the norm of antibodies – according to the automated annotation in ROSIE, the framework region in your light chain is too short (28 verus a standard 32 to 34). Due to the way ROSIE Antibody is set up, it can’t apply the automated proceedure to thread this onto the standard backbones.

            The first thing to check is if this antibody light chain does indeed match what it’s supposed to.  I’d highly recommend reading https://doi.org/10.1016/j.jmb.2010.10.030 and https://doi.org/10.1006/jmbi.1997.1442  and looking through the website  https://www.bioc.uzh.ch/plueckthun/antibody/  to check your antibody sequence against what is “normal” for antibodies, to see if there’s something special/funky going on with your particular light chain.

            Past that, given that your antibody is outside the norm for antibodies, you’re likely going to have to run the antibody modeling proceedure manually. So you’d download Rosetta locally, and then follow the RosettaAntibody proceedures outlined in https://doi.org/10.1038/nprot.2016.180   You’re likely going to need to tweak the alignments and settings to be able to get Rosetta to work with your “short” antibody, or to correct the misalignment that the automatic tools are doing.

          • #13414
            Anonymous

              You’ve got an antibody which is outside the norm of antibodies – according to the automated annotation in ROSIE, the framework region in your light chain is too short (28 verus a standard 32 to 34). Due to the way ROSIE Antibody is set up, it can’t apply the automated proceedure to thread this onto the standard backbones.

              The first thing to check is if this antibody light chain does indeed match what it’s supposed to.  I’d highly recommend reading https://doi.org/10.1016/j.jmb.2010.10.030 and https://doi.org/10.1006/jmbi.1997.1442  and looking through the website  https://www.bioc.uzh.ch/plueckthun/antibody/  to check your antibody sequence against what is “normal” for antibodies, to see if there’s something special/funky going on with your particular light chain.

              Past that, given that your antibody is outside the norm for antibodies, you’re likely going to have to run the antibody modeling proceedure manually. So you’d download Rosetta locally, and then follow the RosettaAntibody proceedures outlined in https://doi.org/10.1038/nprot.2016.180   You’re likely going to need to tweak the alignments and settings to be able to get Rosetta to work with your “short” antibody, or to correct the misalignment that the automatic tools are doing.

            • #12432
              Anonymous

                I am counting 32 aa between CDR2 and 3 unless I am using a different system to assign the CDRs. Is this probably what the issue is?

              • #12953
                Anonymous

                  I am counting 32 aa between CDR2 and 3 unless I am using a different system to assign the CDRs. Is this probably what the issue is?

                • #13474
                  Anonymous

                    I am counting 32 aa between CDR2 and 3 unless I am using a different system to assign the CDRs. Is this probably what the issue is?

                  • #13524
                    Anonymous

                      The issue is with the light chain, not the heavy chain. Check all the sequences (all the loops, all the framework regions, for both chains) that are reported in the output of your ROSIE job, and see if they match up with what you think they should be.

                      Comparing different system for deliniating the start and end points of the loop (the various system in the different papers I mentioned) is a good idea, as any conflict there may point to what the issue may be with the way Rosetta is modeling things.

                  Viewing 3 reply threads
                  • You must be logged in to reply to this topic.