Specifying the code for a query sequence is analogous to specifying the sequence itself. In addition atom based constraints may also be specified. Specifically, the distance between any two atoms, the angle between any three atoms, and the torsion between any four atoms may be defined. 1 and atom N of residue 5 to be between 2 and 3.5 Angstroms. The atom names stored in the database follow the Brookhaven convention strictly.
Any query can have any combination of all or few of the restraints.
The limit on the individual number of torsions, distances and angles is currently however limited to 20 of each. Specification of all three restraints listed above will recover sequences containing a hydrogen bond between residues 1 and 5, for example. Measurements of phi, psi, omega, chi1, chi2, chi3, chi4 and chi5 should not be specified with this option. These are accessible through the Print option. 1 and atom N of residue 5.