Step 1 - Generate Docking Interface

java -jar -Xmx500m InterfaceGeneration.jar <pdb file> -C <chain[s]

The following example will generate the docking interfaces between chains A, B, C, and D
and then save this information in a filed named 1AIP.neko:

  java -jar -Xmx500m InterfaceGeneration.jar 1AIP.pdb -C A B C D

Step 2 - Generate Embeded Interface

After the interface is generated in a 3D conformation it must be embedded into 2D space.

java -jar -Xmx500m EmbedNeko.jar <neko file> <original pdb file> <output pdb file>

The following example take the 3D interface from 1AIP.neko and create the 2D embedding.
This information, both 3D and 2D, will be appended to the original PDB file used in
Step 1.  The output is 1AIP_Interfaced.pdb.  

NOTE: THE OUTPUT PDB MUST HAVE A DIFFERENT NAME THAN THE INPUT PDB!

java -jar -Xmx500m EmbedNeko.jar 1AIP.neko 1AIP.pdb 1AIP_Interfaced.pdb

Step 3 - View Docking Interface 

The JMiV application can be started as follows.  The docking interface file
can then be loaded through the File Menu.

java -jar -Xmx500m jmiv.jar