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Hi Jan-- > I've noticed a couple of previous posts that ask about ambiguous > restraints in XPLOR (or CNS) or XPLOR-NIH, but have never seen an > answer posted. The basic question again is how exactly are "or" > statements dealt with during annealing? I think this is covered here: http://nmr.cit.nih.gov/xplor-nih/doc/current/python/ref/noePot.html and here: http://nmr.cit.nih.gov/xplor-nih/doc/current/xplor/node358.html#SECTION001920000000000000000 > > Take for example, the restraint: > assign (residue 1 and name HA) ((residue 2 and name HB*) or > (residue 3 and name HB)) 2.900 1.800 4.000 > > (with a setting for the NOE averaging of "SUM") > > My understanding based on the documentation is that this would end up > requiring a R^-6 averaged satisfaction of the restraint for both > res 1 - HA -> res 2 HB* > res 1 - HA -> res 3 HB > Is this understanding correct? not precisely. Please see below. > > A supplementary, more technical, question is - how is the R^-6 > averaging carried out? I could envision two possible methods. Is this > carried out simply for each distance: > average of d(res 1 - HA res 2 - HB2) + d(res 1 - HA res 2 - > HB3) + d (res 1 - HA res 3 - HB) > > or, is this carried out such that each constraint is first averaged > and then R^-6 averaged: > average of ({average of [d(res 1 - HA res 2 - HB2) + d(res 1 - > HA res 2 - HB3)]} + {d(res 1 - HA res 3 - HB)}) > with the default settings, sum averaging gives the following expression: d = [ d(res 1 - HA res 2 - HB1)^(-6) + d(res 1 - HA res 2 - HB2)^(-6) + d(res 1 - HA res 3 - HB)^(-6) ]^(-1/6) This distance is quite similar to the shortest distance, if the next shortest distance isn't too close. So this single restraint will not restrain distances for both operands of the ``or'' statement. There is nothing special about the or - or ``and'' statement in an NOE selection- these just help choose which atoms to include in the sum. hope this help-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFEBwEGPK2zrJwS/lYRAvqRAJoDt3KlKGODb1e4I7suFCeGJ/vHhACfSyyH PwWXJpLaScnHHmzD9ovHTsQ= =JQzU -----END PGP SIGNATURE-----
