Jmol commands for highlighting contacts

For full details, see the Jmol Scripting Documentation.

The contact command

  1. Considers two surfaces (van der Waals): of the ligand and of the rest of molecule (or specified atom sets),
  2. detects contacts and clashes (overlaps of surfaces),
  3. colours the surface according to distance between both surfaces.

contact {ligand} surface;

contact {ligand} trim;

contact {ligand} hBond;

contact {ligand} clash;

contact {ligand} connect;  

contact off;

contact on;

contact id "conIbuprofen" {IBP} trim;
contact id "conHeme" {HEM} trim;
contact id "conIbuprofen" off;
contact id "conIbuprofen" on;

hide $conIbuprofen;