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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/> iEYEARECAAYFAkzhmskACgkQPK2zrJwS/lYXjQCfbo7hJQ0tv0soWOtiACeb+PeC IDsAn07sAMAIBz00bCBkNUZQ3vM2Gc+T =MVFI -----END PGP SIGNATURE-----
