Dear Coot Users, I am refining a structure with a covalently bound ligand to a cysteine residue and called cysteine+ligand for CYD. Refmac5 generates a new CYD dictionary and runs OK. Using the same dictionary in coot allows for "Real Space Refine Zone" command to be executed without crash, however the main chain C-N bonds are broken for the residues before and after my modified CYD residue. Part of my CYD dictionary is listed below but is this links not recognised by COOT?
How can I use "Real Space Refine Zone" in COOT for a covalently modified amino-acids (here called CYD). Best regards, Martin # --- DESCRIPTION OF LINKS --- # data_link_VAL-CYD # loop_ _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 VAL-CYD 1 C 2 N . 1.260 0.020 # data_link_CYD-LEU # loop_ _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 CYD-LEU 1 C 2 N . 1.260 0.020 # ------------------------------------------------------
