We have a 2 A dataset for a structure containing an N-methyl-peptide, and I want to refine the model with coot/refmac. I made a cif file for the peptide alone, with an unused het ID like VV0, without any difficulties.
When I refined a model with the cif file by refmac, N-methyl-peptide bonds in trans-configuration were automatically recognized and restrained as planer, however, not those in cis-configuration. There were some N-methyl-peptide bonds in the structure, in trans and cis, and all cis-N-methyl-peptide bonds were distorted (not restrained as planer, and angles around the N atoms seemed not to be restrained).
How can I make/add restraints for cis-N-methyl-peptide bonds?
I'd like to integrate the restraints in the CCP4 default library file ($CLIBD_MON/list/mon_lib_list.cif ?). Is it enough to add new _chem_link and _chem_mod entries to the file? Does Coot also read it?
Dr. Takaaki Fukami (mailto:[log in to unmask])
Discovery Research Dept. (Biostructure Gr.)
Chugai Pharmaceutical Co.,Ltd.