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It is very difficult to predict RNA tertiary structure. Eric Westhof has probably done as much as anyone to get this to work, but the successes have been modest. The best approaches seem to be emperically based, i.e., homology-modeling based upon what is in the pdb (which often means what is in the ribosome). Apart from that, the best way to do this is to obtain some electron density... By the way, I was unable to read your email except from this website: http://www.dl.ac.uk/list-archive-public/ccp4bb/msg19520.html
