I'm building a homology model on a template that has a gap, but the conformation of the residues on either side of the template gap are not kept. How do I ensure that the conformation is retained?

The series of missing residues is built in as a loop, and the loop-building jobs always modify the geometry of the endpoint residues. To fix this problem, you could add a dummy residue (such as GLY) at each end of the template gap, and then use these dummy residues for the endpoints of the loop. The dummy residues will then be rebuilt, and the residues at either end of the original template gap will be used without change.

Keywords: Prime, comparative modeling

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