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JLigand from this site http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html should be able to create link you want. And then you can add link record on your pdb as in the template: http://www.ysbl.york.ac.uk/refmac/data/template_link.txt I hope it addresses the problem you are facing. Garib On 9 Oct 2009, at 10:07, Christian Rausch wrote: > Dear Sampath! > > Refmac5's dictionary uses LLP to encode the "LYSINE-PYRIDOXAL-5*- > PHOSPHATE", a modified lysine residue with its NZ- amino group > covalently bound via a Schiff base to a pyridoxal phosphate. > See http://www.ccp4.ac.uk/html/refmac5/dictionary/list-of-ligands.html > > Have a look at the attached file "LLP.pdb" (e.g. in PyMOL). > > In Coot, move your PLP towards the NZ of the active site LYS. > Superimpose the aldehyde oxygen of PLP onto the NZ. Save both > structures and replace the ATOM coordinates of the modified LYS > with a HETATM record as you can see in the file "LLP.pdb" using the > coordinates of your LYS and PLP accordingly. > Wherever this modified LYS appears in three letter code in your PDB- > file replace it by LLP. You might need to correct the atom numbers > accordingly. The use this structure for refmac. > > > > Greetings, > Christian > Biological Chemistry, TU Munich > <LLP.pdb>