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On 07/12/11 09:47, Tim Gruene wrote: > > if you want coot to refine the bond length, you have to rename the > residue to some name coot does not yet understand and create a cif-file > which includes the restraints of the residue, the ligand, and the bond > between the two. JLigand is the way to do this. (the interface to JLigand will be in Coot 0.7). Paul