Example for more-than-2-proteins complex estimation

[andreasntr]

The example provided for complex estimation and the make_joint_MSA_bacterial.py script refer to just 2 proteins. In the cases where more than 2 proteins must be docked (the paper talks about two or more sequences), how does the pipeline work?
Should we run make_joint_MSA_bacterial.py iteratively adding one protein at a time (after the first 2 have been docked)?

[LW-meng]

I encounter a similar problem. In my case, I need to model the complex of viruses and antibody, but antibody has two sequences(light and heavy chain).
Is there any solution for this case? Many Thanks!

[andreasntr]

This is the actual reason for which I opened the issue. Complex modeling is not feasible (looking at the provided instructions) even between two proteins if at least one them has more than one chain

[callahak]

What is the difference between bacterial and eukaryotic alignment that makes eukaryotic harder? How does a eukaryotic multi sequence alignment created from the same make_msa.py script differ from a bacterial one so that it can't be used as input for make_joint_MSA_bacterial.py?