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Assesing the docking

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Assesing the docking


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

Post Situation: 
Sat, 2020-12-05 21:19

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!)

Sun, 2020-12-06 06:44

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

Sun, 2020-12-06 12:14