[Pdbwiki-devel] checking remediated pdbs

Jose M. Duarte jose.m.duarte at gmail.com
Thu Jul 16 04:37:08 EDT 2009

> Jose, can you double check 1ifc (http://pdbwiki.org/index.php/1ifc) as
> you originally raised this issue? From what I can tell, looking in
> PDBase, the problem you raised looks to have been corrected in the
> remediation. i.e.
> select * from pdbx_poly_seq_scheme where entry_key = 10107;

It looks as though it is still as it was:

SELECT id, label_alt_id, label_atom_id, label_comp_id, label_seq_id FROM
pdbase.atom_site  WHERE entry_key=10107 AND label_asym_id='A' AND

The label_alt_id field is the alt loc and there are still 2 of them (A and
B) for all atoms. The latest mmCIF and PDB files also have the same alt
locs. Of course this is not really an error but more a non-standard way of
annotating things.

> The only 'format inconsistency' that I haven't checked yet is 1ifq.

That one looks also still the same in the latest mmCIF file (the one model
is tagged as 0).

By the way, not strictly related to this but important anyway. We have just
discovered this week that in the latest remediated release of the PDB
(February 2009) one of the tables of the mmCIF files is now gone:
atom_sites_alt. The table used to contain foreign keys to all atoms with alt
locs. That was actually redundant as the same info is also in the atom_site

Anyway we used to read that table in our parsers and thanks to that we've
discovered there was a problem. Hopefully there are no other major changes
in the CIF format but let's bear in mind that this kind of things can happen
(and that openMMS might become obsolete eventually...)

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