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You can try JLigand from http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html to create link and then add link record on your pdb Garib On 9 Oct 2009, at 03:40, Sampath Natarajan wrote: > Dear All, > > I’m currently refining the structure (2.0 A) with a cofactor PLP. > The PLP density is clearly indicates lysine residue is covalently > bound with PLP cofactor. But I don’t know how to link the cofactor > and lysine residue for further refinement. Any suggestions on how to > create the link between the PLP and lysine residue and do the > refinement with refmac would be greatly appreciated! > > Thanks > Sincerely, > Sampath N.