24.2 Search Command Function

This command can be performed three different close contact searches — search over all pairwise close contacts, search of close contacts to a particular atom, and searches close to a spatial point. Searches can be limited to pairs in which both atoms are in a segment or residue using INSIDSEG and INSIDRES, or to pairs in which one atom is in the segment or residue and the other is outside using OUTOFSEG and OUTOFRES. The output of a search gives distance information, and can include energies. The output can be sorted on distance or on one of the energy contributions.

The first word allows one to search the comparison structure - if not specified, we default to the main structure. If the ATOM option is specified, the search takes place with respect to the given atom. The atom is specified by segment identifier, residue identifier, and iupac name. If the POINT option is specified, the search takes place with respect to that spatial point. INSIDRES and INSIDSEG limit the search to pairs in which both atoms are in the residue or segment specified. OUTOFRES and OUTOFSEG limit the search to pairs in which one atom is in the specified residue or segment and the other is outside it. Only one type option can be specified for a search. If no option is specified, the program assumes a search over all atom pairs.

The CUT option specifies what distance is considered “close”. It defaults to 3.5 Angstroms if not specified. NSEP specifies that the residue number of any two atoms being checked must differ by at least NSEP for the pair to be considered. This is useful for omitting contacts for adjacent residues. NSEP defaults to 0. It is not used for searches within a spatial point. LIMIT gives the number of close contacts to be saved. If a search results in more that this list, the most distant contact is removed to make room for the new pair. The default for this is 1000.

The INCLUDE option allows one to add extra information to the print out. ELEC specifies the addition of the electrostatic energy; EVDW specifies the addition of Van der Waals energy; and ENB specifies the addition of the non-bonded energy. Electrostatic contributions are calculated using the method specified in the NBOND command, see Non-bonded Interactions, (an r dependent dielectric for ATOM and RESI options and a constant specified dielectric for the EXEL option). The INCLUDE option is not applicable to searches around a spatial point. The SORT option specifies that the output should be sorted by the given quantity.

The FRAC option controls the number of fractional digits used for printing any of the floating point quantities. It defaults to 3.

The output of this program consist of a title describing the search and columns of close contacts. The columns are packed onto a page automatically, so that the wider the page, the more columns that can be output.