In X-PLOR, the setup of pseudoatoms is accomplished by the NOE ASSIgn statement (Section 18.1), with multiple protons in either atom selection. For the restraining functions (Section 18.3), X-PLOR computes either an R-6 averaged distance between the involved protons or the distance between the geometric centers of the two specified atom selections (Section 18.2). For distance geometry, X-PLOR automatically applies a pseudoatom correction to the specified distance ranges (see Section 19.2.2).
Pseudoatoms (multiple atom selections) should be used primarily for unresolved NOE cross peaks, like those of methyl groups, prochiral centers, and aromatic rings. In the case of stereospecific assignments, the distances should be exact.