Hello-- > > I'm trying to use both local and global rdc restraints for RNA structure > calculation. The local restraints are coming from smaller constructs of the > upper and lower stems that are representative of full length RNA subdomain. I > can not seem to use both these rdcs from the small constructs with the imino > RDCs > from the full length RNA in a protocol similar to the dna_refi refine.py. So > I > was wondering if rigid body minimization, treating the upper and lower stem as > rigid body, fixing the local structure to the local rdcs and applying rigid > body > minimization that orients these two domains with the iminos from the full > length > RNA.
This seems like a good idea- so as to not mess up the structure components you've already determined. After you have an initial structure you should be able to relax the rigid-body grouping and refine the whole thing, taking care that the alignment tensors of the smaller constructs are distinct from each other and from that of the full length RNA. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
