Dear Paul, Thank you for your prompt advice. The procedure you wrote worked well on my screen.
Actually, the residue is not MVA. It is N-methyl-L-Ser but its library file doesn't exist. Instead, there is N-methyl-D-Ser (DSE). I tried your procedure with the DSE.cif with an additional step of changing chirality (as below), and succeeded to refine the peptide. > Change the Group to "L-peptide" add> Change the Ciral sign to the opposite (negative -> positive) > [Triple Refine] Thank you so much. Takaaki -----Original Message----- From: Paul Emsley [mailto:paul.ems...@bioch.ox.ac.uk] Sent: Friday, January 13, 2012 9:16 PM Subject: Re: How to connect N-methylated amino acid? On 13/01/12 12:00, 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? I have never before heard of an M-peptide - I need to update Coot to handle such things properly. This is what I would do in the meantime, starting from scratch: File -> Search Monomer Library "valine" [I search list to fine the methyl-valine - MVA as you say] Click "MVA" button [Centre on the VAL to be replaced] Extensions -> Modelling -> Replace Residue -> MVA Edit -> Restraints -> "MVA" -> OK Change the Group to "L-peptide" [Triple Refine] Done. Paul.
