Thanks for the clarification. For anyone reading this in the archive, reordering of chains can easily be done using pdbtools https://github.com/harmslab/pdbtools (or biopandas https://github.com/rasbt/biopandas).
I'm building more complex versions of Coiled-coil protein origami structures (CoCoPod https://github.com/NIC-SBI/CC_protein_origami library, paper https://www.nature.com/articles/nbt.3994). 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 > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >