Reordering chains in template structure
Hi!
I have a template of four single chains, however in the target (single-chain) structure the chain segments are in a different order (as shown in the image). [image: image.png]
*Is it possible to somehow specify this correctly in the alignment file?* Currently I reorder the chains in the PDB manually, in order to be able to specify an alignment. If I make four separate entries in the alignment file (one for each chain), then the restraints between the chains are not taken into account and my structure falls apart.
Thank you & best regards, Ajasja
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
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 >
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Ajasja Ljubetič -
Modeller Caretaker