Dear Coot experts, I'm working on a peptide with an N-methyled amino acid in the middle. How can I connect this residue to previous/next residues?
To simplify the problem, first I changed the residue to MVA (N-methyled-L-VAL), because its library file (MVA.cif) exists in $CCP4/lib/data/monomers/, in which it is defined as M-peptide as below. data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level MVA MVA 'N-METHYLVALINE ' M-peptide 21 9 . # I prepared coordinates of the residue and make Coot read the MVA.cif file, then "refine zone" around the residue MVA, but MVA won't connect to neither previous/next residues. Doesn't coot recognize the M-peptide as with L/D-peptide? How can I define the connectivity between a special residue and standard amino acids? Thank you in advance. Takaaki Fukami ----- Discovery Research Dept. (Biostructure Gr.) Chugai Pharmaceutical Co.,Ltd.
