On 10/31/2011 12:02 PM, Alexander Predeus wrote: ... > Thus, I'd like to keep the REST of A's crystal structure intact, and > only model loop L based on the structure of the same region in protein B.
It sounds like you don't really want to do "loop modeling" in the Modeller sense here (that is designed for loops where you don't know have a template structure). So really what you want to do is build a model using template A for the non-L regions, and template B for the L region. That's basically FAQ #1: http://salilab.org/modeller/9.10/FAQ.html#1
You will also want to include a little bit of the neighborhood of the L region from B, so that A and B overlap in this region. Otherwise, the loop will be poorly oriented relative to the rest of the protein.
This will build a model that resembles the A backbone, but most likely the sidechains will move. If you don't want to change the original A structure at all, select only the L region for refinement: http://salilab.org/modeller/9.10/manual/node23.html
Ben Webb, Modeller Caretaker