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Using AQUA - command overview

This file gives a short overview of the commands.

Note: not all program options are discussed here.

For more detailed information you may

Running Aqua consists of four steps:

  1. Check format of coordinate file.

  2. Convert restraints to Aqua format: command 'qconvert'.

  3. Analyze restraint violations: command 'aqpc'.

  4. Inspect results, either interactively (commands 'qsumm', 'qdbext' and 'qanal') or via Procheck-NMR.

Remarks on notation:

Check format of coordinate file

Before running AQUA, check that your coordinates are in BIOSYM or in PDB format. If you use PDB format make sure that each model is bounded by MODEL and ENDMDL records (see PDB format).

If the models are all in separate PDB files, you can use the AQUA script, joinpdb (see Appendix C), to merge them into a single PDB file.

Visualize distance and angle restraint violations with PROCHECK-NMR

See 'qhelp procheck' for more details, or read the Procheck-NMR manual.

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