These scripts help generate input files for peptide extension protocol.
Run without args for usage.

addDummyAlanines.pl
   Will add placeholder alanines with zero coords to a pdbfile. They mark 
   the spot where the extension will go. The output pdbfile will be 
   renumbered sequentially (atoms and residues) Note that if your input 
   pdbfile is not sequentially numbered for residues, some odd things 
   may happen.

makeLoopLibraryFromVall.pl 
 AND
makeLoopLibraryFromPDBlist.pl
   As the names suggest, these scripts will generate loop library format
   files from either a vall style file, or from a list of idealized pdbs.
   You may use this loop library for your favourite loop modelling protocol
   and it is also the correct format for peptide extensions.
