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Hello Si-- > > ??? I tried different methods to calculate my protein. By xplor > interface, I tried sa.inp, dgsa.inp, and dg_full_embed.inp. I also > tried the scripts for python interface, like anneal.py. The dgsa > method gives the best result. However, for the scripts for python > interface, I haven't found the script including the dgsa method > yet. Could you please tell where I can find that script? To my knowledge there is no such script. I certainly have never written one. > > Another question is on the calculation including CSA. I have the anisotropy > values for amide N by using other simulation method. > The manual says the restraint list have the form: > assign (sel 00) (sel Z) (sel X) (sel Y) > ? ? ? ? ?? (sel 1) (sel 2) (sel 3) obsShift error1 [error2] > ?My question is what atoms should be chosen for selection 1,2,3? The old XPLOR DCSA term syntax is documented here: http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/node427.html and specify the atoms to be C(i-1), N(i) and HN(i), in that order. For the Python interface, you can use those atoms or N(i), C (i-1), CA(i). Or you can redefine any tensor parameters. Some discussion is given here: http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/csa-methods-marvin.pdf > Are the > observed chemical shifts the amide N chemical from spectra? the observed values are relative to the scalar chemical shift. i.e. the principal components of this chemical shift tensor sum to zero. > How can I know the error 1? I can't help you too much on this- if you're simulating CSA values perhaps you can choose some value like 5% of the maximum possible? > In xplor-nih, the chemical shift anisotropy is given by calcedShift = sum_ > {i,j} A_i*sigma_j*cos(theta_(i,j))^2. So the anisotropy values I got from > other simulations are useless here, right? > Why useless? best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkzF8KYACgkQPK2zrJwS/lZ4RACfflxe30i1oQw2Fw9vGgBXuffK sREAnRKh6PscFj65TyWrSUIck2P3Qpdm =RdaE -----END PGP SIGNATURE-----
