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

Henning Stehr stehr at molgen.mpg.de
Tue Jul 28 04:51:55 EDT 2009


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out of date or irrelevant for PDBWiki.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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