Hello Lisa-- > > Any official conclusion on this RDC data / Cartesian minimization issue? Is > it best for those of us using RDC data to skip that final Cartesian space > minimization? Or maybe to perform it but without the RDC potential? >
The thread was rather confused, and without proper resolution. The initial message was regarding using RDCs to try to refine a (presumably low resolution) crystal structure: > I had near perfect correlation between observed and calculated RDCs > values, which was fishy. After addition of 5Hz systematic noise to all > RDCs, i still had perfect correlation and nice convergence with no > violations(!). Initially i thought that there was something wrong with > my experimental setup (since i only used RDCs+dihedrals restrains), > but I had exactly the same result when I changed also the gb1 tutorial > RDCs values. > So to sum it up, I used the tutorial script (refine.py) and input > files for RDC refinement, regardless of how much I alter the RDCs > values (i tried up to +6Hz noise addition) I get always nice > convergence, perfect correlation obs/calc with no violations. > In this case the crystal structure was represented by dihedral restraints, and presumably these restraints were not violated when RDCs were added and subsequently overfit. The real question here is: does the addition of RDCs improve the structure when used in this fashion. Alternative approaches of refining the crystal structure would be 1) to use NCS-style restraints (using posDiffPot) or (best!) 2) use the X-ray data along with RDCs in a refinement. With either of these approaches RDC overfitting should be much less of an issue- but still something to watch for, and perhaps tuning the energy scale factors might be necessary in such protocols. This message got lost in the discussion. The thread continued with a suggestion that the default RDC energy scale factors in the eginput/gb1_rdc/refine.py script might be too large, but evidence really wasn't presented for that: the RDCs might be overfit, but that should clearly be indicated by violations or poor fit in other terms. Finally, there was a suggestion that final Cartesian minimization was somehow messing things up. Again, one must be careful- particularly of angle violations when many RDCs are used - but this step is actually useful in getting rid of bad contacts, so I would still recommend it. Other opinions welcome-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
