Assesing the docking

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    • December 6, 2020 at 5:19 am #3641
      Anonymous

        Hello,

        I followed the tutorial, and did docking. Now, I can see that the complex structure that I predicted is completely match the true complex structure. But, when I use TMalign and TMscore, they give me something like the following:

        Name of Chain_1: predicted.pdb

        Name of Chain_2: true.pdb

        Length of Chain_1:  289 residues

        Length of Chain_2:  579 residues

         

        TM-score= 1.00000 (if normalized by length of Chain_1)

        TM-score= 0.49914 (if normalized by length of Chain_2)

         

         

        They both have 579 residues, but I don’t why TMalign says chain one has 289.

        Any help will be appreciate.

        Thank you

      • December 6, 2020 at 2:44 pm #15640
        Anonymous

          I have a vague recollection that TMalign only works with one chain. However, I’m not familiar enough to know how it differentiates the chains as it reads the files, if it’s the TER card or a change in chain ID. Given that your second structure is read through 579 amino acids I would first try deleting the TER between the two chains. Rosetta adds this line back between all chains.

          If that doesn’t work, as a second hack, you might edit the chain IDs to match so TMalign thinks the whole complex is a single chain.

          (I looked around for the documentation that TMalign only works with one chain and couldn’t find it. That might be experiential knowledge. Good luck!)

          • December 6, 2020 at 8:14 pm #15641
            Anonymous

              I deleted the TER, and it solved the problem.

              Now, I’m getting a TM-score of 0.9948.

               

              Thank you very much for your help

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