Insane: pairlist filters


Pairlist filters are used by the NMR spectrum lines, list, peaks assign and peaks make commands.The filters are defined by the following criteria:

class: pseudoatom pairs are classified as 1-3, 1-4, intraresidue, sequential, medium range (to residue ±2,3), and long range. This classification may be used to filter pseudoatom pairs via range include or exclude commands. The default is to include all classes of pairs.

contribution: If step 4 of the InSane algorithm has produced more than one potential assignment for a given peak, an attempt is made to reduce the list of candidate pseudoatom pairs by eliminating pairs which are considered to be weak contributors to the total intensity of the peak [1]. The NOE intensity contribution Ni of a pseudoatom pair i is assumed to be proportional to Ri-6, where Ri is the ensemble averaged or minimum (depending on current settings of filter parameters) of the distance between the two pseudoatoms of the pair, with a proportionality constant c which is the same for all pseudoatoms:

Ni = c Ri-6

Pseudoatom pairs are taken from the candidate list in decreasing order of Ni and accepted for the final InSane assignment, until the sum of the accepted Ni has reached a user specified fraction of the total sum of all Ni. The remaining pseudoatom pairs are rejected from the final assignment.

distance: filter to exclude pairs with distances between the two pseudoatoms above a given threshold. In an ensemble of structures the filter can be based on minimum, maximum and/or average distance. Distance filtering can be disabled by setting the upper bound to infinity. Since pseudoatoms do not have coordinates, the distance R between pseudoatoms is computed using all the inter-group proton distances Rij by the formula

intensity: upper or lower bound on raw NOE intensity. If a lower bound (intensity greater) is set, only pseudoatom pairs (A,B) with NOE intensity to noise ratio above the specified bound noise at both the "forward" (A,B) and "backward" (B,A) positions in the raw NOESY spectrum will pass the filter. Only pseudoatom pairs (A,B) for which at least one of the raw intensity to noise ratios at (A,B) or (B,A) is less than the specified threshold will pass an upper bound (intensity less) filter. Intensity filtering may be bypassed: intensity ignore.

The structures filter option can be used to restrict the calculation of the statistics (minimum, maximum, average) of pseudoatom distances to a subset of the current ensemble of structures. The default is to use all structures.

tolerance: defines how close the chemical shift coordinates of a pseudoatom pair must be to a peak position in order to be considered as a candidate for an automatic assignment in the peaks assign insane command. The tolerance is specified in points.

The filter setting are "sticky": once a filter criterion is set, it remains in use, until the criterion is modified or deactivated. The filter parameters are kept in a global data structure, i.e. the same parameter values are used for all NMR structure sets. The NMR spectrum show command can be used to view the current filter settings.

Typical settings for the automatic NOE crosspeak assignment (peaks assign insane ...):

spectrum> class include all
spectrum> distance average 10 minimum infinity maximum infinity
spectrum> structures *
spectrum> intensity greater 1
spectrum> contribution average 0.95
spectrum> tolerance 1.5

Reference:

1. M.Nilges, M.J.Macias, S.I. O'Donoghue, H. Oschkinat:
J.Mol.Biol., 269, 408-422, 1997



A.Widmer, NIBR/CPC/CSG-SB