Clearly that was a problem. Another issue may be if you have very large couplings you may also create very large forces on the atoms, and you will need to rebalance (probably lower) the RDC force constants. You may need to make the time step shorter, and refine longer, similar to Choy et al. Journal of Biomolecular NMR, 21: 31-40, 2001.
Cheers, Geoff On 11/15/10 4:40 PM, "Charles at schwieters.org" <Charles at schwieters.org> wrote: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello Jos-- > I am trying to refine a structure of ubiquitin using some very large > RDCs (several > 100 Hz). During refinement, the rdc energy becomes > very large, and final structures are yielding 10 out of 40 rdcs > violated. Looking at the list, all violated residues have observed RDC > greater than 100 and a calculated RDC of exactly 100, so it looks like > you have a maximum value limit in place. All other RDCs are modeled > quite well. > > Is there indeed an upper limit restriction on RDC_calc, and is there a > way that I can increase it? I haven't spotted an appropriate keyword > in the examples and docs yet. > There is indeed an upper bound for Da which can be adjusted using the setDaMax method of VarTensor. For example, the setup of the alignment tensor object in eginput/gb1_rdc/refine.py can be modified as below to set a maximum Da value to 200 Hz. This is documented here: http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/varTensor.html and the default value of DaMax is 50. best regards-- Charles # medium Da rhombicity for (medium,Da,Rh) in [ ('t', -6.5, 0.62), ('b', -9.9, 0.23) ]: oTensor = create_VarTensor(medium) oTensor.setDaMax(200) oTensor.setDa(Da) oTensor.setRh(Rh) media[medium] = oTensor pass -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/><http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkzhmskACgkQPK2zrJwS/lYXjQCfbo7hJQ0tv0soWOtiACeb+PeC IDsAn07sAMAIBz00bCBkNUZQ3vM2Gc+T =MVFI -----END PGP SIGNATURE----- _______________________________________________ Xplor-nih mailing list Xplor-nih at nmr.cit.nih.gov http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih -- Geoffrey A. Mueller, Ph.D. Staff Scientist, NIEHS 919-541-3872 mueller3 at niehs.nih.gov
