PROCHECK-NMR Operating Manual
AQUA Operating Manual
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
- use the 'qhelp' command (more topics than currently in on-line manual):
qhelp [options]
The qhelp command lists information about commands, file formats and
implementation issues. Typing qhelp without additional options lists the
available topics.
- read the files in $AQUADOCDIR (equivalent of using 'qhelp').
Running Aqua consists of four steps:
- Check format of coordinate file.
- Convert restraints to Aqua format: command 'qconvert'.
- Analyze restraint violations: command 'aqpc'.
- Inspect results, either interactively
(commands 'qsumm', 'qdbext' and 'qanal') or via Procheck-NMR.
Remarks on notation:
- square brackets [] indicate an optional command switch (presence not
required)
- the order of the options is irrelevant, unless indicated otherwise
- CAPITAL letters indicate a position where you have to substitute the
name of a file (or part of a name)
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.
AQUA Operating Manual
PROCHECK-NMR Operating Manual