The tutorial cofm command reports the center of mass for spec. By default, the unweighted average of the transformed coordinates of the specified atoms is reported. Untransformed coordinates are the values read from the input file, while transformed coordinates include all user-applied rotations and translations. If atoms from multiple models are specified, transformed coordinates reflect their relative positions correctly while untransformed coordinates may not (unless the model coordinates started in the same coordinate system). To get the mass-weighted center, use the weighted true option. To get the center for untransformed coordinates, use the transformed false option.
The tutorial highlight command changes the color of the atom(s) nearest the center of the specified atoms. The weighted and transformed options are the same as in the tutorial cofm command. The count option specifies the number of atoms whose color should be set. The default is one and may be as many as five.