After the molecule is read in, new names are added to the coloring categories, and assigned colors. Next, bond connectivity is established and the molecule is analyzed to identify its components, i.e., to determine which residues are protein, nucleic acids, and waters, etc. A search is then made to connect these into larger fragments of the same type, and summary information is printed to the screen. An example output for BPTI is:
Info 1) Analyzing structure ... Info 1) Atoms: 898 Bonds: 909 Info 1) Backbone bonds: Protein: 231 DNA: 0 Info 1) Residues: 58 Info 1) Waters: 0 Info 1) Segments: 1 Info 1) Fragments: 1 Protein: 1 Nucleic: 0
There are several types of fragments. Protein and nucleic fragments are homogeneous; either all proteins, or all nucleic acids. However, it is possible for a protein to be connected to a nucleic acid or some other non-protein. When this occurs, a warning message is printed, as in:
Warning 1) Unusual bond between residues 1 and 2These warnings will occur with terminal amino acids, zinc fingers, myristolated residues, and poorly defined structures.