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Hi Haydyn-- > > Sorry to send this to you directly but I'm having trouble sending it > to the mailing list. My apologies. are the messages bouncing? If so, please send the bounce error messages directly to me. > I'm currently trying to refine a homology model of a small protein with > measured RDCs according to the method of Chou et. al. (JBNMR v18 200). > My question is in regard to the use of an NCS term in the initial > regularisation protocol. > > Q. If you have a structure that is monomeric, how do you set up an NCS > term to hold the backbone relatively constant during the regularisation? > > I've superficially tried this sort of thing: > --> > evaluate ($k_ncs = 5.00) > ncs restraints > initialize > group > equi (resid 5:85) > weight = $k_ncs > end > ? > end > --- > > and then set up the force constant stuff in the usual way, and make sure > an ncs statement is called in the flags: > > flags > exclude * > include bonds angl impr vdw noe rama carb cdih coup ncs plan sani coll > end > > This set-up doesn't work, so either I read the paper (Calmodulin > example) incorrectly and the NCS term is used in that particular case > only due to the symmetry of calmodulin, or I've not set-up the NCS term > correctly. I'm betting on the latter. probably. I think you need to first duplicate those coordinates which you which to restrain: so you could make a second copy of the structure, fix one structure, and then the ncs restraints group statement should have two equi entries: one for the fixed structure, and one for the version you wish to refine. Actually, there are two other options: the IVM will allow you to rigidly fix the entire backbone (while still allowing its translation, rotation). Also, within the python interface, there is another ``NCS'' potential term which does the same as above, but does not require the structure copying step. Please let me know if you're interested in this last option, and I'll scare up an example. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.1 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQE/N5WAPK2zrJwS/lYRAog7AJ93iPxPFP58eq1Aks39jwzWbERJ4ACeOyeO t5itLeNbgJCrIAIVucoetRE= =kHCn -----END PGP SIGNATURE-----
