[Pdbwiki-devel] checking remediated pdbs

Jose M. Duarte jose.m.duarte at gmail.com
Fri Jul 17 05:18:23 EDT 2009

2009/7/17 Dan Bolser <dan.bolser at gmail.com>

> 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"?

Agreed, General comment is probably better

> 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.

Cool! finally one of our annotations fixed! I'd go for adding a comment that
the problem has been fixed in revision so and so and then categorize it as

> Are there any 'bug tracker' extensions for MW?

Actually there is!


We should give it a go at some point!

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