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When I first ran the complex structure prediction (step 4), it was outputting a model where the break between the two subunits was in the totally wrong place. After a lot of digging through the predict_complex.py file, I realized that the numbers after the "-Ls" argument needed to be changed to represent the lengths of the individual protein subunits being modeled. I finally figured this out when I saw that the lengths of the two example subunits are 218 aa and 310 aa. I imagine other people will run into this same issue until it's clarified in the README.
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