Obviously, most of the definitions and examples in this section are taken from the original SYBYL Theory Manual.
Objects
The highest level object you can manipulate within SYBYL is the molecule work area. The areas are work spaces in which you 'hold' the structures. They have been given aliases which are compesed of the letter M followed by an integer. Since SYBYL can work with an unlimited number of work areas simultaneously, you may have any number of work areas defined at any time. They would have been named M1, M2, etc. automatically, but they may be created in arbitrary order.
SYBYL allows you to manipulate several basic types of objects whose definitions and characteristics are intuitive: molecules, substructures, atoms, bonds, rings, etc.. Others are less intuitive: sets and features. An overview of most objects can be found following this link.
When selecting objects for a command, some general naming conventions should be followed. For example, try to limit names of atoms and substructures to 7 characters, and sets and features to 31 characters, although there is no strict limit on the number of characters used. Molecules can have arbitrarily long and complex names and should be placed between double quotes when special characters or spaces are included (or when starting with a numeric character). When selecting Wild characters can be used to indicate multiple objects: the asterisk (*) matches any number of characters of any type, the at sign (@) matches a single character of any type. Examples of how to designate various objects can be found following this link.
Return to the main SYBYL tutorial page.