AQUA analysis tools

Using qanal to inspect restraint violations

'Aquanal' (alias 'qanal') is a Perl script which lets you analyze the '.?rv' files which are the output of Aqua. These '.?rv' files do contain a lot of information, but are rather big, certainly when there are a lot of distance restraints and more than one structure is analyzed. To be able to analyze this huge amount of data I wrote 'aquanal'. This script can only be used if Perl5 is installed on your computer, cf. 'qhelp perl'.

The command syntax is as follows:

qanal  [VIOLATIONS_FILE]

where VIOLATIONS_FILE is the '.?rv' file produced by 'aqpc'.

For the moment the program can generate the following lists :

• Which NOE's are there between certain residues (or a range of residues) (eg which NOE's are there between residues 10-13 and 85-90)

• Highest restraint violation per structure (e.g. the 10 highest upper- and lower bound violations per structure)

• Average violation and range of violation values over all structures (eg the average, the standard deviation, the minimum- and maximum violation for a certain distance restraint for all structures when in one of the structures the violation is more then 0.5Å )

Each of these lists can be printed on the screen or saved to a file. If there is a certain type of list you would like to see added, drop me a line.

If there are questions, suggestions for new analysises, ideas for enhancements, ... mail them to Kris.Boulez@rug.ac.be.

P.S. If I find time (which might not be the first months) I plan to write a graphical shell around 'aquanal'.