AQUA

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

 


HOW_TO_USE

Contents

  1. INITIALIZATION
  2. USING AQUA - COMMAND OVERVIEW
  3. FURTHER INFORMATION


1. Initialization

Before using Aqua, either interactively or from within a script, you have to initialize a serious of variables and aliases.

Define the directory root (if the system manager has not already done so) and call (substituting X.Y with the current version number):

    setenv aquaroot $YOUR_LOCATION/aquaX.Y
Prepare for interactive use with:
    source $aquaroot/aqsetupi
Prepare for use in a script with:
    source $aquaroot/aqsetup
Alternatively, you may want to store the equivalent definition in your '.cshrc' file (if the system manager has not already provided definitions). An alias for initializing the Aqua setup may also be defined there:
    setenv aquaroot $YOUR_LOCATION/aquaX.Y
    alias aqua 'source $aquaroot/aqsetupi'


Then, before running AQUA you can initialize the program simply by typing:

    aqua
I advise you not to import definitions from the 'aqsetup' script into places like '.cshrc'.


2. 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 three steps:
  1.  1. Convert restraints to Aqua format: command 'qconvert', see 2.2.
  2.  2. Analyze restraint violations: command 'aqpc', see 2.3.
  3.  3. Inspect results, either interactively (commands 'qsumm', 'qdbext' and 'qanal'; see 2.4) or via Procheck-NMR (see 2.5).
Remarks on notation:

2.1 HELP INFORMATION

    qhelp [options]
The qhelp command lists information about commands, file formats and implementation issues. Typing 'qhelp' without additional options lists the available topics.

2.2. CONVERT RESTRAINT FILE

See 'qhelp qconvert' for a description of the progam, details and command options.

2.3. COMPUTE RESTRAINT VIOLATIONS

See 'qhelp qconvert' for a description of the progam, details and command options.

2.4. INSPECT VIOLATIONS

The root names of the output files produced by AQUA are defined by the current project name, cf. previous paragraph.
The names of the output files have the following extensions, each indicating the type of data the file contains:
    summary:     .nsm (noe),  .hsm (hb),  .ssm (ss),  .dsm (dis)
    violations:  .nrv (noe),  .hrv (hb),  .srv (ss),  .drv (dis)
    counts:      .nrc (noe),  .hrc (hb),  .src (ss),  .drc (dis)
where These files are ASCII text files and can be printed out or read with any text editor.

The script 'qdbext' can be used to extract data from the '.?rv' (violations)  and '.?rc' (counts) files on a keyword basis; see 'qhelp qdbext' and  'qhelp dbas'.

Additionally, you can generate a new summary file using the 'qsumm' script. This gives a longer list of largest violations (by default only the largest three are shown for each structure). To do this, give the command:

    qsumm  VIOLATIONS_FILE  COUNTS_FILE  [MAX_LINES] [ > OUTPUT_FILE]
Also see 'qhelp qsumm'.

Another script for summarizing the results of Aqua calculations is 'qanal', written by Kris Boulez. This script can only be used if Perl5 is installed on your computer. See 'qhelp qanal'.

2.5. VISUALIZE DISTANCE AND ANGLE RESTRAINT VIOLATIONS WITH PROCHECK-NMR

See 'qhelp procheck' for more details.


3. Further information

Besides the programs and scripts mentioned above, information on various topics is available through the 'qhelp' command. Type 'qhelp' to get a list of commands and topics.

Contact the author or webmaster for help, when required.