The first radiobox, Display hetatoms, applies to all Model modes, not just the special Protein Model mode. You can omit all hetatoms, or water (HOH) only.
The remainder of the settings in this dialog apply to the special Protein Model mode.
This mode, which is a 3D Drawing Mode only, only works on data imported from PDB files. It displays the bonds between protein backbone atoms as cylinders, with the radius specified in this dialog. By default, other atoms in the amino acids or residues are omitted, but you can specify a limited number of individual residues to draw in the ball-and-stick mode in this dialog. Hetatoms (non-residues) are always drawn as ball-and-stick.
The bonds drawn in this mode must be specified in the Bonds dialog in the Input1 menu. At a minimum to show the backbone there must be carbon-carbon and carbon-nitrogen bonds. Any other bonds among hetatoms and non-backbone atoms in the residues must also be specified. Usually this can be done by selecting automatic bonds in the Bonds dialog or during importing.
This mode relies on the atomic labels and residue information derived from PDB files and cannot be used without importing data in that format.
The Radius of sticks gives the size of the skeletal or stick bonds between backbone atoms - it does not apply to bonds involving hetatoms or non-backbone atoms in the residues.
Show complete residues - by number. This allows showing non-backbone atoms and associated bonds in the specified residues. Atom and bond attributes are as specified globally in the Atoms and Bonds dialogs in the Input1 menu. Note that even if a residue is selected for "full" display in this option, the backbone atoms in that residue are still shown in the standard protein way (as skeletal sticks).
In the edit box, give the residue sequence number and chain letter together, separated by spaces, commas or semicolons. You can get these numbers and letters by clicking on the atoms, or from the Atoms dialog in the Input1 menu. Thus
5A 12B
indicates that residue 5 of chain A and residue 12 of chain B are to be drawn fully. A number without a letter will be read as chain A.