Hi Ben. I'm interested in using a crystal structure deposited in the PDB (structure A). However, there are two important loops missing. There is another homologous structure B from another source organism, where those loops are well defined inside electron density. I like to use the experimental data from this template B to model the missing loops in the structure A. I've tried to model the entire sequence of protein A using the B structure as a template, then cut and paste the generated loops from the model and put into the structure A. However, it did not work because many steric collisions occurred between the side chains of those loops and protein A. Carrying out loop modeling (loop.py) correct the clashes, but gives results extremely different from observed in template B. How do I model the missing loops directly in the structure A? Is it possible?
I appreciate any suggestion.
Regards
Flavio
------------------------------------- Flavio Augusto Vicente Seixas Laboratory of Structural Biochemistry Department of Biochemistry Universidade Estadual de Maringá, PR, Brazil http://www.uem.br