The skeleton is produced from an electron density map by running the program bones. Atoms recieve a level code of 2 or 3 if they are thought to be side chain or main atoms, respectively. The user is free to use any system of code definition that may be applicable to the problem. Normally, a simple system would assign level 1 to be the correct main chain trace.
The colour associated with each level is defined in the datablock .bones_colour and can be any of the possible X-windows colours. The skeleton can also be used to form an envelope by associating radii to skeleton atoms of particular types. Skeletons can also be used with the Trace commands in O.
On UNIX workstations, the skeleton is calculated by the bones program (see section 8.1) which reads an electron density map, and outputs an O datastructure, that can be read with Read_formatted. The program assigns levels 3, 2 and 1 to the skeleton, depending whether it thinks the density belongs to main chain, side chain or junk, respectively.
For users using the earlier implementation of skeletons on a VAX, an O skeleton can be made from a FRODO skeleton by running a utility program oexe:o_bones on the VAX. FRODO levels USM are levels 1, 2, 3 respectively. The VAX program abones distributes with FRODO calculates levels S and M. In O, therefore, these will correspond to levels 2 and 3.