SHELXL has a nice facility for this that maybe Garib could copy. A residue may have a second (alias) residue number. This was intended for making peptide and other restraints go all the way around a cyclic peptide, but also handles the case of a continuous peptide strand that is missing residue numbers because of deletions. It is described under 'RESI' in the manual.
George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 14 Aug 2009, Jan Abendroth wrote: > Hi all, > I am hitting the wall on this one: A disordered loop has been replaced with > a short linker, which now is visible in the density. To be consistent, I > maintain the original residue numbering and get a gap of residue numbers > between the last original residue and the first residue of the loop. Refmac > thinks that these residues are not supposed to be linked, and pulls them > apart. > 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? > > Any ideas are welcome! > > Thanks! > Jan > > > -- > -- > Jan Abendroth > deCODE biostructures > Seattle / Bainbridge Island, WA, USA > work: JAbendroth_at_decode.com > home: Jan.Abendroth_at_gmail.com >
