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What about O, lsqman, lsqkab - probably most programs for superpositioning. Coot also prints a list to the terminal when using the SSM superpositioning tool, I believe. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 15 Sep 2008, todd gangelhoff wrote: > Hi, > Is there a good program that will give me the RMSD for every amino acid > compared to another structure? > > Thanks > Todd