On 11/25/20 1:59 PM, Austin Varela wrote: > I have a PDB file containing a complex composed of 2 proteins > interacting. I wish to perform homology modelling of one of these > proteins and leave the other one fixed.
To do this you would need to align both chains (i.e. 2 chains in the template aligned to 2 chains in the target) using an alignment similar to that at https://salilab.org/modeller/9.25/manual/node29.html. Then to model only one chain, override select_atoms() to select just that chain: https://salilab.org/modeller/9.25/manual/node23.html
Alternatively you could just align and model one chain, then add in the second chain to your final model using a text editor or a PDB viewer such as Chimera. But in that case you could potentially have steric clashes between the chains.
Ben Webb, Modeller Caretaker