Hi,

I'm trying yo generate homology models for a protein - DNA complex. I saw the option to copy chains into my models and it works fine for the DNA chains.

I was just wondering, when I'm copying the DNA chains, are they also considered in the model generation in terms of protein side chain flexibility in this regions? Or are the chains just copied into the models without considering possible steric clashes with the protein side chains?

Thanks in advance.

Cheers,

Malgorzata