[Pdbwiki-devel] checking remediated pdbs

[Dan Bolser]

2009/7/16 Dan Bolser <dan.bolser at gmail.com>:
> Hi,
>
> I'm going through the six 'format inconsistencies' logged in PDBWiki
> (http://pdbwiki.org/index.php/Category:PDB_format_inconsistency) and
> checking if they are still problematic in the remediated PDB.
>
> Four of the five that I have checked still look problematic.
>
>
> 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;
>
>
> Should we create a new category 'issue resolved' or similar?
>
>
> The only 'format inconsistency' that I haven't checked yet is 1ifq.
>
> I'll look at the 'format errors' (11) later today and tomorrow.

Looking at the 'format errors' (11), six are simply warnings:
 'Warning! There are more than 26 chains in this PDB entry!'

http://pdbwiki.org/index.php/1p0t
http://pdbwiki.org/index.php/1s5l
http://pdbwiki.org/index.php/1z7q
http://pdbwiki.org/index.php/2axt
http://pdbwiki.org/index.php/2om0
http://pdbwiki.org/index.php/2zkr


This information was included as it can confuse people new to the PDB
(the chain code is usually a single, case insensitive character).
However, I guess they are not strictly format errors... (or are they?)
What category should this information be put in? They are certainly
less interesting than the other five 'format errors'!

I guess Category:General comment? "This category is to tag all PDB
entry annotations that do not fit into any other categories"?


Fixed in remediation!

Two of the remaining 5 'format errors' has been fixed in remediation:

http://pdbwiki.org/index.php/1b77
http://pdbwiki.org/index.php/1ob5

Should we delete the comment or somehow annotate the entry to reflect this fact?

Interestingly, the last one (1ob5) had a similar error to another
entry (1csm), which *has not* been fixed in the remediation.


Are there any 'bug tracker' extensions for MW?


> All the best,
> Dan
>