The template for one of my models has a large region in the middle of
its sequence that shares no homology to my target sequence.
Fortunately this region does not interact with the catalytic region
in which I am interested, so I am able to remove this segment from
the model. This means than my final model is composed of two chains.
The problem I am having is with the secondary structure assignment to
the second chain of the model. Without any explicit special
secondary structure assignment the first chain of my model faithfully
replicates the secondary structures of the template, while the second
chain is lacking most if not all secondary structure. I know I could
fix this problem by adding special restraints, but would rather have
the model pick up secondary structure from the template.
I am doing this modelling with default patching off. After a lot of
testing, it seems that the N and C terminal patches are the cause of
this loss in secondary structure to only the second chain of my
model. If I comment out the patches to the protein termini but keep
the patches I'm making to the DNA in my model, then I get the results
I am looking for. Anyone have an idea why this is happening?