Hi there,

I am trying to model a multichain protein (homodimer) using 2 templates. I have two issues,

Currently my .pir file looks like this

xxxx/

xxxx/

-------/

Firstly, my template 1 I am using both chain A and chain B, they have slightly different missing residues in the template but thats fine.

For template 2 I cant put them under the same header, modeller doesn't seem to understand that I want to use chain B of template 2 for both chain A and B of my target so I specified it separately - it seems to work fine though with this setup.

Unfortunately when I try add HETATM information ".." at the end of my target and template 1 and 2 gaps "--" for template 2 modeller says the whole sequence is out of alignment suddenly. I have specific HETATM=true in my script so it reads that part fine.

My alignment looks like this but does not work? Am I missing some obvious?