Thanks for the clarification. For anyone reading this in the archive, reordering of chains can easily be done using pdbtools (or biopandas). 

I'm building more complex versions of Coiled-coil protein origami structures (CoCoPod library, paper). 
Where sometimes the CC building blocks come in a different order than in the template structure. 

Best,
Ajasja  

PS: modeller is working great for us, thanks for maintaining it!

On Sat, 26 May 2018 at 00:10, Modeller Caretaker <modeller-care@salilab.org> wrote:
On 5/25/18 2:17 AM, Ajasja Ljubetič wrote:
> I have a template of four single chains, however in the target
> (single-chain) structure the chain segments are in a different order
...
> *Is it possible to somehow specify this correctly in the alignment
> file?*

No - your two options are (as you correctly stated) to reorder the input
PDB or to use multiple templates (losing interchain restraints in the
latter case).

That said, it's a little unusual to build a single chain model using a
multi-chain template. What are you trying to do?

        Ben Webb, Modeller Caretaker
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