Thank you Garib..
So you have to copy the $CLIBD/monomers/t/TYC.cif to your own directory and change the string "non-polymer" to "L-peptide" Then use that as a dictionary entry and indeed that behaves as expected - ie forms the peptide link GLY-TYC Eleanor On 16 October 2017 at 12:32, Garib Murshudov <ga...@mrc-lmb.cam.ac.uk> wrote: > These are default values. > > Decision about standard residue types are made using the info from the > dictionary. In the current version it is like: > > TYC TYC 'L-TYROSINAMIDE ' non-polymer 25 > 13 . > > I.e. it is not a peptide. Strictly speaking it is not a peptide. It would > form standard peptide link, at least on the carboxyl side. > These cases should be dealt with different types of links. > > How this residue incorporated into the protein? Is it something like > C-terminus amilation? If it is the case then better approach is to use TYR > and C-terminus amilation modification. I do not remember how it works, but > if it is the case then i can find out. > > > Regards > Garib > > > On 16 Oct 2017, at 07:06, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > > Very puzzled by this - but now I think I understand . > > Can you comment Garib please? > > In refmac there is a list of amino acids to be linked > > SUBROUTINE GET_STANDARD_RES_TYPE(MDOC,LINE,MONN,ITYPE,IERR) > ....... > C --------------------------------------------------------- > C ITYPE = 3 RES_LTYPE( 3) = 'peptide ' > C > DATA RNAME /'CYS','SER','THR','PRO','ALA','GLY','ASN','ASP' > * ,'GLU','GLN','HIS','ARG','LYS','MET','ILE','LEU' > * ,'VAL','PHE','TYR','TRP','TRY','HYP','PCA','SAR' > * ,'ORN','CSS','CSH','DAR','DPR','NLE','DAS','INI' > * ,'DGL','DGN','DHI','DIL','DIV','DLI','DSN','DSP' > * ,'ABA','BMT','MLE','MVA','DVA','MSE','PTR','DAL' > * ,'DPN','DTR','DTH','TYS','CGU','DCY','ILG','OCS' > * ,'KCX','SAH','SAM','SEP','LLP','5HP','CSO' / > > > > As you can see TYC is not in this list: > > When I change your TYC to TYS the link is formed properly, ( I have to > delete the NXT but that shouldnt matter..) > > So either TYC and all other possible peptides should be added to the RNAME > list, or better if the dictionary defines a residue as an L-peptide then > that is how it should be handled. > > > But for the present you will have to use that work-around of creating a > LINK. > > Eleanor > C > > > > > Dr Garib N Murshudov > MRC-LMB > Francis Crick Avenue > Cambridge > CB2 0QH UK > Web http://www.mrc-lmb.cam.ac.uk, > http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/ > > > >
