But it is not L-peptide. And I would not like to make it L-peptide in the standard ccp4 dictionary. You can add trans link between GLY and TYC. But it would not be nice. The best solution is to use TYR and amilate C terminus.
Garib On 16 Oct 2017, at 07:40, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > 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/ > > > > 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/
