mirror_ligands keyword indicates whether or not mirror images of input
ligands will be docked. There are three possible values: no, yes, and discard
(or their abbreviations n, y, and d, respectively). If mirror_ligands
is set to no, mirror images of the ligand will not be generated. This is the
manner in which DOCK has operated in the past. If mirror_ligands is set
to yes, then a mirror image of the ligand will be generated. In SEARCH mode,
when mirror_ligands is on, both chiralities are stored. Consequently,
in the top nsav ligands, the same ligand may appear twice, once for
each handedness. The different chiralities are indicated by det_rot = 1 (real
image) and det_rot = -1 (mirror image) in the ligand output file. Finally, if
the mirror image of the ligand is a better fit and if mirror_ligands is
set to discard, then this orientation of the ligand is discarded before it is
scored. This last mode may be useful when using the Critical Cluster
feature.
Note that when mirror_ligands is off, DOCK uses the Ferro-Hermans (1977) orient algorithm, the algorithm used in previous versions of DOCK. With
all other values of mirror_ligands, the Golub-Kabsch algorithm is used
(Golub, personal communication; Kabsch, 1978; Kabsch, 1976). Consequently,
there can be differences in the orientation (and scores) of ligands of the same
chirality from a DOCK run with mirror_ligands off versus a DOCK
run with mirror_ligands on.