I would like to run a design protocol on a protein that has, as its asymmetric unit, 2 proteins with an ion. I have done some purely AA-based symmetric design before with 2 chains controlled by separate virtual jumps and my own python-generated symdef file but I'd rather avoid doing that again :-)
My hope was that I could put (even if suboptimal) the 2 chains and the ion in a single chain and proceed as usual in symmetric design with one chain.
This works fine with the 2 proteins as a single chain but as soon as I include the metal ion in the chain, the generated symmetric structure is bad (and Vikram's metal flag doesn't help). Apparently, new jumps are created and this breaks everything.
To better understand this, would anybody have an example (pdb+symdef) of a simple symmetric structure with a metal ion at the interface of the ASU ? Or any advice otherwise.