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
