PRODIGY same chain issue

While we use prodigy, if the chains in both the interactors of the docked complex are same, how can we submit the file? Please help.

You will have to change the chain ID of one of the chains - that’s the only solution.

You can try to do it with our PBD-tools (local or server)


Which command line do we have to use to identify the chains in our structure through the PDBTOOLS server?

Thanks for raising this question @Antra.

The issue is that PRODIGY requires you interactors to be in different chains. If you check in your PDB file, you’ll have both the same chain (A in your case).

To split them, you need to identify where one begins and where the other ends. There is no simple way to do that because it depends on how you merged them.

If you know at which number the interactor 2 starts, you can try to use pdb_selres.

The full explanation about each of the commands available in pdb-tools is available in the web interface manual.