Hi Drew, Have you tried arp/wARP (the LOOPY option) or the AutoBuild option in Phenix ? If you haven't tried this you can try a complete rebuilding using you model as it stands and providing the complete sequence of your protein. At this resolution (2.1A) , they may be able to rescue your loops at least partially. There is another program called XPLEO (and a derivation of it called LoopTK) and is available from the Stanford site at the Synchrotron Linear Accelerator that has been helpful in our lab in the case of a loop region in a membrane protein.
Hope this helps. Good luck Pascal F. Egea, PhD University of California San Francisco Department of Biophysics and Biochemistry >
