[phenixbb] Residue number error after autoMR or PhaserMR

Nathaniel Echols nechols at lbl.gov
Wed Apr 20 12:01:09 PDT 2011

On Wed, Apr 20, 2011 at 11:45 AM, Edward A. Berry <BerryE at upstate.edu> wrote:
> There was discussion a few years back about an extended pdb format in which
> the
> fourth digit would go not just 0-9 but
> 0123456789ZBCDE...XYZabcdefghijkl....z
> (and the other digits would also if the fourth digit was greater than 9)
> So maybe the code that handles that isn't kicking in where it should?

This is Ralf's "hybrid36" format.  I think Phaser will use that
encoding for atom records, but not residues.  In any case, using the
hybrid36 format is unnecessary in this case, since the residue number
field is officially (according to the PDB) four characters long.

> The folks who want to deposit structures of whole bacteria will have to wait
> a little longer.

The PDB won't even handle ribosome structures without splitting them
into multiple files, so this has been a problem for at least a decade.
 (Phenix does not have this limitation, of course, nor do Coot,
Refmac, or CNS, as far as I know.)  Residue numbers are less likely to
overrun the official format, but I think there are structures for
fragments of proteins where the actual residue numbering starts above
9999.  I'm not sure what the PDB does to these.


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