For REFMAC, I think you need to alter the cif file for the modified residue - such that the residue type is L-peptide rather than anything else.
Tony. Sent from my iPhone On 2 Aug 2013, at 17:08, "Arnon Lavie" <[email protected]<mailto:[email protected]>> wrote: Hi: Despite Google and several attempts, I am still having no success in getting Refmac5 to link a modified amino acid to its adjacent residues. Using sketcher, a cif file for the modified amino acid was generated. This cif file was used an input to Refmac5. The relevant part from the Refmac5 log file is shown below; note the "not be used" comment. INFO: link is found (not be used) dist= 0.776 ideal_dist= 1.332 ch:BB res: 18 GLY at:C .->ch:Ba res: 19 THN at:N . INFO: link is found (not be used) dist= 1.686 ideal_dist= 1.240 ch:BB res: 18 GLY at:O .->ch:Ba res: 19 THN at:N . I also added the link comment in the pdb file as shown below: LINK N THN B 19 C GLY B 18 LINK C THN B 19 N LEU B 20 Still, I fail to get a link between Gly18 to the modified residues THN19, and from it to the next residue Leu20. What trivial mistake am I making? Arnon -- *********************************************************** Arnon Lavie, Professor Dept. of Biochemistry and Molecular Genetics University of Illinois at Chicago 900 S. Ashland Ave. Molecular Biology Research Building, Room 1108 (M/C 669) Chicago, IL 60607 U.S.A. Tel: (312) 355-5029 Fax: (312) 355-4535 E-mail: [email protected]<mailto:[email protected]> http://www.uic.edu/labs/lavie/ ***********************************************************
