1. Introduction

These Operating Instructions describe how to run the AQUA and PROCHECK-NMR programs:

AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures determined by NMR spectroscopy. [Written by Ton Rullmann].
PROCHECK-NMR is a suite of programs that produce PostScript plots of the restraint violations computed by AQUA together with various analyses of the stereochemical quality of the models in the NMR ensemble. [Written by Roman A Laskowski & Malcolm MacArthur].

The inputs comprise:

the PDB file (Bernstein et al., 1977) holding the coordinates of the structure of interest, with each model in the ensemble separated by the correct MODEL and ENDMDL records (see Appendix A: Brookhaven PDB file format),
an (optional) restraint file listing the NOEs, Hydrogen-bonds, disulphides, generic distance and torsion angle restraints used in solving the structure (see Appendix B: AQUA restraint file formats),
an (optional) model- and residue-blocks file listing the model- and residue-ranges to which the analyses are to be restricted (see Selecting model- and residue-ranges).

The outputs from the programs include:

various formatted text files showing the AQUA analyses. These can be further summarised and sub-analysed using the various tools provided (see AQUA outputs and analysis tools).
PostScript files showing the PROCHECK-NMR analyses (see PROCHECK-NMR outputs). The appearance of the plots can be modified to some extent (see Customizing the PROCHECK-NMR plots).