In X-PLOR, the setup of pseudoatoms is accomplished by using the NOE assign statement (Section 20.1) with multiple protons in either atom selection. X-PLOR automatically adds a correction to the specified distance bounds, which it derives from the reference coordinate set (see Section 6.1). For example, for a medium NOE from an ALA methyl group to the HN proton of the next residue, one should specify the distance from the geometric center (pseudoatom) of the three methyl hydrogens to the position of the HN proton:
assign ( resid 1 and HB* ) ( resid 2 and hn ) 3.0 1.8 0.9
This assign statement sets the lower bound to 1.2 Å and the upper bound to 3.9 Å. The diameter of the methyl group is added automatically by X-PLOR as a correction, since the bounds are applied to all pairs of selected atoms in the distance geometry stage. The specification of the reference coordinate set is mandatory; otherwise a warning message will be printed and no correction applied.

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 specified explicitly.

An alternative way to replace pseudoatoms is to assign the distance restraint to the heavy atom bound to the protons, in the example above the C$^{\beta}$ carbon. In this case, one would have to add the radius of the methyl group as the correction, i.e.,

assign ( resid 1 and CB ) ( resid 2 and hn ) 3.0 1.8 1.8

Xplor-NIH 2024-06-11