[Biojava-l] advice on rmsd algorithms....

Jay Vyas jayunit100 at gmail.com
Mon Jan 24 21:38:48 UTC 2011

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

Jay Vyas

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