Hi everyone,
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?
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?
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)})
Thanks in advance,
Jan
