This is a group of commands to construct molecular objects from data in the O database. Before issuing a series of zones, cover-spheres etc, the molecule to be used should be defined with the command Molecule_name. Once defined, the molecule name is maintained until changed explicitly. The name of the object to be created and viewed can be defined with Object_name, otherwise the object will have the same name as the molecule.
O uses explicit connectivity tables for each residue. When first started, the program prompts for a file containing this information. The default file connectivity draws bonds between heavy (i.e. non-hydrogen) atoms. A residue not in the connectivity list is drawn by a distance criterion to define bonds. Note that any number of generating commands ( Ca, Zone, Cover, Sphere) can be issued (possibly with different connectivity files) so that complicated objects can be constructed. If more generating commands are issued after an End_object without defining a new object, then the current object gets overwritten. The colours used are the values in the parameter block [mol]_atom_colour at the issue of the End_object command. Lines will only be drawn between atoms that have on values in their [mol]_atom_visible datablock. These values can be set by the Select commands.
Note that any number of objects can be made from one molecule, but that each object is made from only one molecule.
When an atom is picked, the default action is to label it with a small piece of text containing the residue and atom name. More information, such as the residue type, and the orthogonal coordinates of the atom, can be given in the message area at the top of the screen. The content of both the label and the message can be customized by the user. See in the example section 3.2.12 how to do this.