10.2 Basic Steps in Defining and Displaying Nonbonded Contacts

Define the types of contacts in which you are interested, e.g. all H-bonds, or H-bonds between amide NH donors and carboxylate oxygens, or Cl...Br contacts shorter than the sum of the vdW radii of Cl and Br (see Section 10.3).

Instruct Mercury to find and display contacts of the types you have defined (see Section 10.8).

Switch contacts on and off as desired, e.g. you could switch off one type of contact but continue to display the others (see Section 10.8).

If desired, build a network of molecules connected by the nonbonded contacts you have found (see Section 11).