The COMPARE option specifies that the comparison data structures should be used for the drawing. Leaving this option causes the main structure to be used.
The TABLE option specifies that the table should be consulted to see which atoms should be plotted. In the absence of references to the table via the SCALAR or VECTOR options, the entire molecule will be plotted. However, when this option is present or when the table is referenced, the table must be an atom table, and only those atoms which are in the table will be plotted.
The CONNECT option causes the command to reconnect bonds which link atoms that are not be drawn, i.e. deleted atoms. Normally, if an atom is not drawn, any bonds to that atom are not drawn either. However, this is not always satisfactory. For example, if one wants an alpha carbon plot, one wants all the alpha carbons drawn with bonds provided they were in the same chain.
The algorithm used by the connect algorithm is simple, but it can yield strange results in certain circumstances. If a deleted atom has only one bond going to it, the bond is deleted. If it has two bonds going to it, the two atoms are bonded to each other except if they are already bonded to each other. If there are multiple bonds, then all the atoms linked to the deleted atom are rebound into a cycle. One example where this algorithm doesn't work best is if only the gamma carbon of phenylalanine is deleted. In this case, a triangle will be drawn connecting C-beta, C-delta-1, and C-delta-2.