Hi every one I have made a Cif file for the restraints of my ligand with Jligand, which is attached to my protein via a lysine-aldehyde Schiff base formation. The problem is that whenever I run the refmac with the Cif file with torsions and link description, it changes the distance of the Lysine and the Carbon of my ligand.
The density is there, but it does not recognize it as a C=N bond and puts them up to 2 angstrom away from each other. I do not know, if I should change the link description to make the Refmac regonize the double bond or what else I can do. This is the description of link in my Cif file: _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd LYS-MER 1 NZ 2 C18 double 1.260 0.020 I appriciate your help beforehand. Regards Sam
