DockSorter.

0. Contact 

If you have any trouble using the software something is unclear or if you have some suggestions that you think could make the program better please contact:

deane@stats.ox.ac.uk

1. Installation

You will only need java (jre) installed. Remember to give the program appropriate write permissions in the ABiPatch folder (most common cause of an unexpected exceptions being thrown).

2. Input file preparation

It would be helpful if you look into the input files 'strA.pdb' and 'strB.pdb' in the Example folder to get the feel for the format. One needs to merge all the chains in the input file into one, call it 'A' and make sure that numbering of residues starts from '1'.

3. Usage

NB: prepare files as suggested in the previous section!

The best way to explain how the software works is to follow the example provided. It is assumed that the ABiPatch.jar is in the directory above 'example' (e.g. doing ../ in 'example' will bring you to the directory where ABiPatch.jar is).

In order to execute the example:
java -jar ABiPatch.jar -abf Example/strA.pdb -agf Example/strB.pdb 

where the options are as follows:

-abf = the antibody pdb file
-agf = the antigen pdb file

The results are written in the ABiPatch.jar directory as antibody.pdb and antigen.pdb (with obvious connotations).

4. Display Help

In order to get Help:

java -jar ABiPatch.jar -h
java -jar ABiPatch.jar --help
 
