Are constraints added automatically for sequence connectivity?

[elviorodriguez]

Hi! The paper says,

If a protein chain is divided into subunits (for example, domains), distance constraints are added to enforce sequence connectivity

Does this mean that the constraints are added automatically if two sequences are contiguous? Or we have to add them separately? By the way, once I have the crosslinks.txt file for my complex, how can I add it as constraints by calling it from the command line? Is there an optional argument?

[ben-shor]

Yes, connectivity constraints are added automatically if the same chain is present in different subunits, and there are residues that are less than 100 amino acids apart.

I have added an additional optional argument when running from the command line so now you can supply the crosslinks file as the last argument (make sure to pull the repository as I just made this change)