MODELLER modelling of a single chain
Hello,
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. I have been able to do the modelling of the one protein of interest, however I am not sure how to have MODELLER include the fixed protein in the final PDB outputs as all my current outputs only contain the modelled protein. Is this some option I can modify on running MODELLER? Or would I have to align the new structures to the old one and somehow merge files to reintroduce the other protein.
Thanks for the help! Austin
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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Modeller Caretaker