Dear Eleanor, The method I proposed works for any amino acid, not just tyrosine. Having an amide as a separate residue may sound strange, but is it exactly how our chemists treat it as well. Best, Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Eleanor Dodson Gesendet: Montag, 16. Oktober 2017 13:40 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] Re: [ccp4bb] TYC not linked to previoys amino-acid 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<mailto: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<mailto: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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mrc-2Dlmb.cam.ac.uk&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=W10d7zbsnGPDr-U5sFcRrFm9Z_H4P4yU_c4Eq6PDyoU&s=7wCJBN-4XfEuIBGmj18zTJ_uen7yEjYGMZu0BwmWor8&e=>, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.mrc-2Dlmb.cam.ac.uk_groups_murshudov_&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=W10d7zbsnGPDr-U5sFcRrFm9Z_H4P4yU_c4Eq6PDyoU&s=w6Pt0lirXdA1Qd-CjTyAP34sQkulOy-qG8ga0OX3HhI&e=>
