Re: [modeller_usage] MODELLER modelling of a single chain

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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