So, are there any other common errors of annotation that one should look for?
I've just submitted seven structures (same protein) and there are some
newly introduced LINK records, but all seem correct.
eab
On 11/11/2018 02:31 PM, Robbie Joosten wrote:
Hi Tristan,
Erroneous LINK records happen quite a lot and used to be the combination of
aggressive annotation software and depositors not paying attention to the
comments from the annotators. They make up a large fraction of the bug reports
I have sent to the PDB over the years. They are usually fixed very quickly by
the annotators, as long as someone takes time to report them.
This case looks like an error in a refinement program which nevertheless should
have been caught by the depositors. What I would like to know is whether the
deposited, pre-annotation model had the LINKs or not.
LINKs are a bloody nightmare when it comes to annotation. At the moment there
is no record keeping of targets and chemical modifications in a dictionary on
the side of the PDB so there is also no standardisation. IMO mmCIF makes it
easier to store the restraints with the coordinates, but there is still no neat
mapping by LINK identfiers the way the LINKR format works in Refmac. I think
that is a missed opportunity.
Sorry for the rant, I blame the F1.
Cheers,
Robbie
Op 11 nov. 2018 19:47 schreef Tristan Croll <ti...@cam.ac.uk>:
I've seen instances like the following in roughly half a dozen deposited
structures over the past year or so. Each time I've contacted the
authors, who've been just as mystified as me by them - and certainly
didn't add them on purpose. It seems to me that some fairly
commonly-used package is erroneously turning clashes into LINK cards in
some circumstances. I just found the following clearly wrong LINKs in
6caj (deposited January this year):
LINK CD2 PHE I 266 CG2 THR I 272 1555 1555
1.47
LINK CE2 PHE I 266 CG2 THR I 272 1555 1555
1.47
... which looks like the attached image. The same bonds are also
specified in the mmCIF file, for the record.
Anyone have any clue?
Best regards,
Tristan
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