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We would like to use Coot to fix up the geometry between the backbone and the covalently bound chromophore within GFP variants, but our efforts to convince Coot to connect the polypeptide and the chromophore have thus far failed. This includes using MAKECIF to generate a new geometry library entry with specific LINK connections from the backbone C of Phe64 to the N (or N1) of the chromophore and likewise for the continuing connection from the chromophore C (or C3) to N of Val68. Given these definitions, Coot does refine the zone but ignores the linkage and lets the atoms involved float. A couple of uninformative error messages are issued. Coot also seems to ignore LINK cards in a PDB file. We had this working once, but something has changed in the most recent version(s) of Coot. Does anyone have a recipe for incorporating covalently bound ligands to a protein, with proper geometry? A related question is: how are the ideal bond and torsion angles defined for protein-heteroatom linkages? MAKECIF defines only the bond length. We have been unable to discover documentation describing such definitions. Thanks for any advice, Jim Remington --