Hello Takaaki, Is the numbering consecutive and do you have the same chain ID? Change the definition to L-peptide in the cif file. That works at least for nucleotides and DNA
Best Sabine On 01/13/2012 01:00 PM, Takaaki Fukami wrote: > 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. >
