Re: [modeller_usage] modeling two chains while preserving their structural orientation wrt each other

On 12/4/20 9:08 AM, shivu shiv wrote: > I am working on modeling a protein with two chains (heterodimer). > I have used two separate pdb files for each chain and oriented the two > template structures appropriately before the modeling. > Modeller is able to model both the chains, however not preserving the > orientation of both the chains.

If you are confident of this orientation, put the two chains in a single PDB file, as is done in the example in the manual: https://salilab.org/modeller/9.25/manual/node29.html

Modeller extracts internal distance restraints from each template separately, so if your two chains are two separate templates, there will be no inter-chain restraints.

Ben Webb, Modeller Caretaker