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John Pak wrote: > Hi all. > > I'm currently refining an Fab structure. All was going reasonably > well until I renumbered the PDB according to the Kabat numbering > convention. After which, REFMAC does not refine the inserted residues > properly (ie. residues 82A, 82B, 100A, 100B, 100C, etc.). It refines > these residues into a steric jumble. I think REFMAC can't recognize > that the residues are connected or something. > > So my question is, how do you refine this type of PDB in REFMAC? Or > do you just wait until the refinement is done, then change all the > residue numbers and connect entries in the header afterwards? > > Yes! - or better, let the deposition site renumber if they must.. I feel these weird numbering schemes are archaic - we can easily align sequences and see that 82A is actually 83 etc.. But that is a personal view. Eleanor