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On Sat, March 28, 2009 5:37 am, Paul Emsley wrote: > Buz Barstow wrote: >> Dear All, >> >> I'd like to add substitute a natural base (adenine) for a non-natural >> base (2-aminopurine), in a molecular model of an RNA molecule. >> >> I'd like to do this with CCP4 and Coot. Could I ask for some help >> please? > > > The "CCP4 way" would be to use sketcher and search for aminopurines. > You will find 2,6-diaminopurine (1AP). Load this up and delete the > 6-amino group to convert to 2-aminopurine. Save the coordinates and > dictionary (give it a new name). > > Fire up coot and File -> Import CIF dictionary... > > Centre on the residue you want to substitute > > Extensions -> Modelling -> Replace residue -> 1AP (or whatever you > called it). > > (If you have a map loaded when you do this, it will try to fit to that > as a final step) > > Paul. > I may be mistaken, but I thought he was asking how to mutate from 2AP to A. (If you use simple mutate, you get a menu of 20 amino acids to choose from.) Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/