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Choice of Averaging

Note that all these sums are defined here for restraints created by a simple NOE ASSIgn statement. See Section 20.2.1 for an explanation of the treatment of the optional OR clauses.

For AVERage=R-6, the distance between selected sets of atoms is averaged according to

$\begin{displaymath} R = ( <R_{ij}^{-6}> )^{-1/6} \end{displaymath}$

(20.1)

where $R_{ij}$ runs through all possible combinations of distance restraints between atoms “

" in set 1 and atoms “

" in set 2.

For AVERage=R-3, the distance between selected sets of atoms is averaged according to

$\begin{displaymath} R = ( <R_{ij}^{-3}> )^{-1/3} \end{displaymath}$

(20.2)

where $R_{ij}$ runs through all possible combinations of distance restraints between atoms “

" in set 1 and atoms “

" in set 2.

For AVERage=SUM, the distance between selected sets of atoms is computed by adding up single contributions

$\begin{displaymath} R = ( \sum_{ij} R_{ij}^{-6} / n_{mono} )^{-1/6} \end{displaymath}$

(20.3)

where $n_{mono}$ is specified by the MONOmer statement. The scaling by $n_{mono}$ is required, in combination with the SUM averaging option, to scale the distances corresponding to ambiguous peaks in symmetric multimers. The difference between the R-6 option and the SUM option is subtle, and is best illustrated with an example: if two distances are involved in the average, say 3 and 10 Å, the R-6 average will produce an effective distance of 3.37 Å, and the R-6 sum a distance of 2.99 Å, which is probably the desired result for ambiguous NOESY crosspeaks. For this reason, the SUM option should be used rather than the R-6 option to treat ambiguities for observed NOEs.

For AVERage=CENTer, the distance between selected sets of atoms is set to the difference between the geometric centers of the atoms,

$\begin{displaymath} R= (r^{1}_{center} - r^{2}_{center}) \end{displaymath}$

(20.4)

Subsections

Expressing ambiguous restraints using the optional OR statement

Xplor-NIH 2024-09-13