{
Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,
{
Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
EBIAlfaFold.addAlphaFoldPAE(al, new File(this.getPAEMatrix()), 0,