Hi Martin, The following works well for modified amino acids with refmac and I presume the same will work with coot. Rather than define custom links for you CYD ligand to the neighboring Val and Leu, I would edit the CYD ligand definition to make it an L-peptide (instead of the "non-polymer" default for the _chem_comp.group) then refmac (and I presume coot) will recognize the default peptide bond linkage to the neighboring residues. This way it gets the distances & angles for the standard peptide bond from the from the mon_lib_list.cif file and you do not have to define all of the individual restraints. Regards, Mitch
-----Original Message----- From: Mailing list for users of COOT Crystallographic Software [mailto:[EMAIL PROTECTED] On Behalf Of Martin Moche Sent: Friday, September 19, 2008 1:20 PM To: [email protected] Subject: [COOT] Real Space Refine Zone of modified aa 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 # ------------------------------------------------------
