[Pdbwiki-devel] Some PDB entries from our old 'kill list'?

[Jose M. Duarte]

I've checked also 1zy8 and there's nothing too wrong about it. It uses two
alt codes for all residues of chains K, L, M and N, effectively having 2
models for them. That's not strictly an error but anyway I've added a little
comment in the wiki

Jose



2009/7/28 Henning Stehr <stehr at molgen.mpg.de>

> Hi Dan,
>
>
> I went through the kill list once already and found the same as you
> did. Almost all entries were either
> out of date or irrelevant for PDBWiki. For example,
>
> > | 1en2 | inconsistent msd residue numbering in chain A, res
>
> This refers to the MSD before it was an official mirror of the PDB.
> While they had fixed a lot of
> errors (unfortunately without documenting what they did) they also
> introduced several
> new errors such as the one mentioned above. I guess it's a good thing
> that they now joined forces
> with the PDB.
>
> Or,
> > | 1ehy | unobserved residues 138-148 in all four (identical) chains |
>
> This is something which is so common that it's neither possible nor
> desirable to
> annotate in PDBWiki.
>
> In the future, we can consider to revive our old idea of providing
> sets of say "high quality structures without unobserved residues".
>
> Henning
>
>
> On Mon, Jul 27, 2009 at 10:33 PM, Dan Bolser<dan.bolser at gmail.com> wrote:
> > Hi,
> >
> > I'm going through our old 'kill list' table and adding comments to
> > PDBWiki. Would you guys mind looking at these few cases and seeing if
> > they still warrant comments in PDBWiki?
> >
> > | 1ehy | unobserved residues 138-148 in all four (identical) chains |
> > Henning | 2007-01-25 |
> > | 1en2 | inconsistent msd residue numbering in chain A, res
> > 10,14,16,80,81 | Henning | 2007-01-31 |
> >
> > | 1xpm | inconsistent msd residue numbering in chain A | Ioannis |
> 2007-02-21 |
> >
> > | 1zy8           | inconsistent atom alt location codes in pdbase for
> > chain K | Jose      | 2007-04-02 |
> >
> >
> > The others are all either obsolete, fixed or already commented.
> >
> >
> > Cheers,
> > Dan.
> >
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