Hi All, I am having issues with getting pseudo-amino acids to behave in refmac such that they correctly form peptide bonds with standard residues before and after them. The problem I have is that when naming atoms forming the peptide bonds, there are effectively two C-alpha atoms, as shown below, where the pseudo-amino acid is contained within the square brackets:
standard_aminoacid-[N-CA-some_stuff-CA-CO]-standard_aminoacid (both CA atoms have R groups, but I have not shown them) I have inserted the "L-peptide" line into the cif dictionary for the pseudo-amino acid, but in order to get the correct geometry, in particular the planarity of the peptide bond, the C-alpha atoms need to be called "CA", but I can only use that label once per residue. I did wonder whether it's possible to create some special TRANS definitions to use in LINKR lines in the pdb header, but I can't figure out how to do that. Any suggestions? Many thanks Dave Lawson ------------------------------- Dr. David M. Lawson Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Fax: +44-(0)1603-450018 Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk>
