Hi guys . I noticed that I get a different RMSD using the biojava alignCE methd, (CeMain), as compared to MolMol, another popular molecular visualization tool. Any idea why ? The rmsd appears to be 2.54 (biojava CEMain) as compared to 13.5 (molmol). Im using the gap size of -1 as in the biojava examples..... -- Jay Vyas MMSB/UCHC