Hi Matthew, The superposition is a least-squares fit of the alpha-carbons of the residue pairs aligned in the sequence alignment: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ multalignviewer/multalignviewer.html#superposition I think it is reasonable to report the RMSDs in a paper if you give some indication of the number of alpha-carbon pairs that were matched (i.e. a low RMSD is less remarkable if the number of pairs matched is also low). In general, you'd only want to compare among RMSDs if they were obtained with a consistent methodology (different sets of structures) or were for the same structures (comparing methodologies). It depends what you want to convey in your paper. If you have the "Iterate" option turned on, the final RMSD and number of pairs used may both be quite low. These values are not a good measure of overall structural similarity, because they also depend on the accuracy of the starting sequence alignment: if a large proportion of pairs are pruned during iteration, it could either be because the structures are dissimilar or because those parts of the alignment were misaligned. I hope this helps, Elaine On Jul 10, 2006, at 3:26 PM, Haas, Ryan Matthew wrote:

Dear Chimera Users,

How does the matchmaker command perform its superposition? Is it a C-alpha superposition, or just backbone atoms, or all atoms? Is it appropriate to use these RMSD values obtained from “mmaker” in a manuscript?

Help is greatly appreciated.

Matthew Haas

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