
By Eugene Krissinel


3.3. Surfing the coordinate hierarchy.

More than 50 interface functions offer variety of tools for surfing
the coordinate hierarchy. Generally, any model, chain, residue or atom
may be addressed directly using either of three following methods:

1) by specifying the model number, chain ID, sequence number, insertion
   code, atom name, chemical element and alternative location; these
   characteristics may be replaced by their positional equivalents,
   e.g. 2nd chain (in a model), 25th residue (in a chain), 3rd atom
   (in a residue).
2) by specifying a special path string - the "coordinate ID" (CID)
3) by looking up the hierarchy's internal reference tables.

Different methods provide different flexibility and efficiency. Access
through internal tables is the most efficient one, while using
the coordinate ID provides for maximum flexibility.

Coordinate ID is an ASCII string of the following format:

    /mdl/chn/seq(res).ic/atm[elm]:aloc
      
where mdl stands for the model number, chn - chain ID, seq - residue
sequence number, res - residue name, ic - residue insertion code,
atm - atom name, elm - chemical element ID, aloc - alternative location
indicator. Any item in coordinate ID may be replaced by a wildcard "*",
which means indefinite value for that item. The wildcard value is
automatically implied for any missing item except the chain ID,
insertion code and alternative location indicator.

