[phenixbb] Residue number error after autoMR or PhaserMR

[Edward A. Berry]

Nathaniel Echols wrote:
> On Wed, Apr 20, 2011 at 9:33 AM, Zhang yu<phenixzyfish at gmail.com>  wrote:
>> When I run MR in Phenix, I found that there is a numbering error in the
>> solution PDB file
>>
>> The error is that Phenix numbers residues from 0 again when the residue
>> numbers are over 999, though they belong to the same chain.
>>
>> For example
>>
>> ATOM  11513  NE2 HIS   C 999     -35.122  54.953  55.285  1.00 69.80           N
>> ATOM  11514  N   MET    C   0     -36.544  51.378  60.309  1.00 64.17           N
>> ATOM  11522  N   VAL     C   1     -37.840  53.015  63.272  1.00 69.46           N
>>
>> Does anyone has idea about it?
>
> Phaser has its own PDB parser, and it looks like it only reads
> characters 2-4 in the residue number.  This sounds like a bug, but
> there may be some reason for it - we'll check this out.
>

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