Re: [modeller_usage] Reordering chains in template structure

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 <">> 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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