Have you tried loading both the pdb and cif files for the custom residue? As far as I remember, custom ligands need both to be used in mutation -- but I rarely do that so I might be wrong... You can always revert to mutating "by hand": load pdb and cif, delete old residue, merge in new one, renumber residue, change chain ID, refine or edit torsions -- a little bit more clicks.
JED. 2012/1/18 Takaaki Fukami <[email protected]>: > Dear Paul, > > You taught me how to mutate a residue to a non-standard one. > >> [Centre on the VAL to be replaced] >> Extensions -> Modelling -> Replace Residue -> MVA > > It failed when I specify my custom monomer. > > To obtain a monomer, Coot seems to use "get-monomer", > and it was extracted from the default library file, > even if I supplied a custom cif file for the monomer. > > How do I mutate a residue to my custom monomer in Coot? > > Regards, > > Takaaki Fukami > > > > -----Original Message----- > From: Paul Emsley [mailto:[email protected]] > Sent: Friday, January 13, 2012 9:16 PM > To: 深海隆明(探索研究部蛋白構造解析Ｇ) > Cc: [email protected] > 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.
