AQUA

Jurgen Doreleijers, Madison, jurgenfd@gmail.com

Ton Rullmann, Utrecht

README

ACKNOWLEDGMENTS
SCOPE OF PROGRAMS
INSTALLING AQUA
USING AQUA

1. Acknowledgments

Software contributions by the following people are acknowledged:

Kris Boulez, Biomolecular NMR unit, University of Ghent: qanal script [analysis of aqpc output]
Roman Laskowski, Biomolecular Structure and Modelling Group, University College, London: Range.c code [processing of file with residue/model selection info], getproj.c code [file name processing]
Mia Raves, NMR spectroscopy Utrecht: Debugging the script 'aq2xplor-tors' for converting Aqua formatted torsion angle restraint files to XPLOR format .
Gert Vriend, EMBL Heidelberg: Proton nomenclature check in WHATIF
Greg Warren, Dept. of Molecular Biophysics and Biochemistry, Yale University: New version of convXPLORdistrestr script [conversion XPLOR restraints]

We also thank all of you who contributed by reporting problems and asking questions. It really helped to improve the programs!

2. Scope of the programs

The Aqua program suite in this distribution calculates restraint violations from:

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, XPLOR, 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 XPLOR, BIOSYM, DIANA and NMR-STAR format is now also available.

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 the 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
Completeness and redundancy of the NOEs
Summaries:

per model;
per restraint;
per residue (calculated over all models and for each individual model)
per range-type (sequential, medium, long etc.)

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
Number of restraints for each range-type (sequential, medium, long etc.)

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.
For sorting restraints and violation lists.
For selecting residue ranges from PDB files and from restraint files.

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

New modules allow:

Checking and correcting the consistency of stereospecific assignments.
Checking the redundancy and completeness of NOE distance restraints.
Correcting the nomenclature of restraints and coordinates simultaneously, to comply with IUPAC definitions.

3. Installing AQUA

1. Uncompress and unpack the archive (substituting X.Y for the version you downloaded):

    tar -zxvf aquaX.Y.tar.gz

This will create a subdirectory called 'aquaX.Y' in the present working directory. If the z option doesn't work on your system you'll have to use gunzip or uncompress before the tar command.

2. Follow the instructions in the file HOW_TO_INSTALL.

4. Using AQUA

Please see the file HOW_TO_USE. After installing and initializing the 'qhelp' command gives easy access to the documentation.