Scope of the AQUA programs

• a PDB or BIOSYM file containing one or more coordinate sets

• distance restraint file(s) in AQUA format.

Conversion scripts are available to convert DISGEO, X-PLOR, BIOSYM and DISMAN/DIANA restraint files to AQUA format. These scripts can also generate torsion angle restraint files, which are read by PROCHECK-NMR. User-defined conversion scripts can easily be linked into the master script.

Conversion from AQUA to X-PLOR, BIOSYM and DIANA format is now also available through the aq2x command.

Both "MR" and "non-MR" restraint files can be handled (MR is used here to indicate the restraint file structure currently employed by the PDB; the name was taken from the file name extension assigned by PDB).

Coordinates of pseudo-atoms are generated when necessary. Presently this is done by calculating the geometric average of the corresponding proton positions.

The output files contain a full listing of:

• Distances in all models
• Violations in all models
• Summaries:
  per model;
  per restraint;
  per residue (calculated over all models and for each individual model)
  

  These summaries list:

  number of violated restraints;
  largest violation;
  total violation;
  
  for each of three groups of restraints: upper bound violations, lower bound violations, "big" violations.
• Number of restraints for each residue

Facilities are available

• For extracting data from these files on a keyword basis
• For producing more condensed summaries (containing average and r.m.s.d. violation values; number of (violated) restraints; sorted lists of first n largest violations) per model and overall.
• For restricting the analysis to a subset of residues and/or models.

The violations and numbers of restraints can also be visualized with PROCHECK-NMR.