PROCHECK-NMR Operating Manual

AQUA Operating Manual

Using AQUA - command overview

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:

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:

• 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

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

AQUA Operating Manual

PROCHECK-NMR Operating Manual