AQUA

Jurgen Doreleijers, Madison, jurgenfd@gmail.com
Ton Rullmann, Utrecht

 


README

Contents

  1. ACKNOWLEDGMENTS
  2. SCOPE OF PROGRAMS
  3. INSTALLING AQUA
  4. USING AQUA



1. Acknowledgments

Software contributions by the following people are acknowledged: 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: 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:

Facilities are available: The violations and numbers of restraints can also be visualized with Procheck-NMR.

New modules allow:


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.


Contact the author or webmaster for help, when required.