Thanks Charles, could you let me know if the script I included is a good starting point? Removing the SAXS restraints and including the RDCs?
On Fri, May 22, 2015 at 10:09 AM, Charles Schwieters <[email protected] > wrote: > > 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 >
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