[Chimera-users] Text statistics from Matchmaker

nettles jnettle at emory.edu
Mon Aug 4 12:32:32 PDT 2008

I have found MatchMaker in Chimera an incredibly useful alignment  
tool. Thank you to the UCSF team!

Now, I want to do do a mutliple alignment of many structures (~100)  
off a single reference structure, and output a text record of the  
residue pairings involved in the individual alignments along with  
their RMSD.

In this particular case, I'll be looking at only small sequence  
variations of the same protein (with different drugs and cofactors).  
Accordingly,  I would also like to output the RMSD of residue pairs  
beyond the alignment cut for relatively easy  identification of  
regions having maximal variations.

Advise is appreciated,

With regard,



James Nettles, Ph. D.  Assistant Professor
Department of Pediatrics, Emory University School of Medicine

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