Tim is right. The link you want is TRANS. And if you want link between alternative position then you need to add alt codes before residue names. Llink ids must be defined in the dictionary. There are definitions for standard links in the dictionary: $CLIBD_MON/list/mon_lib_list.cif.
For templates how to use various forms of links please have a look: http://www.ysbl.york.ac.uk/refmac/data/template_link.txt If you experience further difficulties please let me know and I will try to sort this out. regards Garib 2009/8/14 Tim Fenn <[email protected]> > On Fri, 14 Aug 2009 13:24:16 -0700 > Jan Abendroth <[email protected]> wrote: > > > How can I tell refmac to maintain the peptide link? > > Here is what I tried - the numbers above just for orientation > > > > 1 2 3 4 5 6 > > 7 8 > > > 12345678901234567890123456789012345678901234567890123456789012345678901234567890 > > LINKR C ASN B 729 N GLY B 741 ASN-GLY > > > > refmac comments in the log file ... however, still pulls the residues > > apart. WARNING : description of link:ASN-GLY is not in the dictionary > > link will be created with bond_lenth = 1.260 > > > > So, in my understanding it comes down to the question: > > how is a peptide bond referenced to in the dictionary? > > > > take a look at the data_link_list loop in mon_lib_list.cif (there may > be an easier way to view this info): > > TRANS . . peptide . . peptide > default-peptide-link > PTRANS . . peptide PRO . . > default-peptide-link_pro > NMTRANS . . peptide PRO . . > default-peptide-link_cn > CIS . . peptide . . peptide > cis-peptide-link > PCIS . . peptide PRO . . > cis-peptide-link_pro > NMCIS . . peptide PRO . . > cis-peptide-link_cn > > > so you probably want TRANS. > > HTH, > Tim > > -- > --------------------------------------------------------- > > Tim Fenn > [email protected] > Stanford University, School of Medicine > James H. Clark Center > 318 Campus Drive, Room E300 > Stanford, CA 94305-5432 > Phone: (650) 736-1714 > FAX: (650) 736-1961 > > --------------------------------------------------------- >
