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[ccp4bb]: "No Ca" petition - further clarification
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Just a quick reply to some of today's postings:
> (1) Going to the petition site, I am faced with an option to "submit" my
> name to be added to the list of people who wish to abolish the CA only
> entries in the PDB. There is no option to register a vote to retain the
> status quo. I hesitate to draw comparisons with other sorts of ballots
> where the options are limited.
your hesitation is warranted ... this is a ("grass-roots") petition, not a
plebiscite or opinion poll
> (2) I feel that there are arguments to be put for retaining CA only
> entries in the databank, These are:
nothing has been said about removing legacy entries - the petition is about
stopping future incomplete depositions at the source, i.e. before they are
accepted by the PDB. on the other hand, authors of old CA-only depositions (or
depositions without experimental information, for that matter), are of course
encouraged to complete their depositions a posteriori !
> (c) I would hesitate to erase any data from the literature. It is
i didn't have "1984" in mind, to be frank :-) again, the petition is about
changing deposition procedures, not history
> (d) My last point is, I admit, special pleading. But just suppose that
> CA only entries were to be banned, and that in a few years time a new
> super duper technique were to be invented, which allowed the accurate location
> of just the alpha carbons in a protein (lets call it ESP spectroscopy!!)
> then the world might not be able to avail itself of these results!
nothing lasts forever - if there are sound scientific reasons to change the
rules or allow exceptions, then that is fine
> I think it is important that whatever action the community takes be directed
> through the appropriate channels. The purpose of the databases, and
> particularly the PDB/RCSB is to document the literature, and *not* to pass
> judgment on the acceptability of work that has already passed peer-review.
> If a paper is published, no matter how misguided one may think it is, the
> supporting data should be deposited and available to all.
(1) most journals already pay lip service to the IUCr guidelines, but in
practice they rarely check up (the only recent exception being
Acta Cryst who now actively contact authors of old papers who have
not deposited complete data, be it coordinates or structure factors)
(2) stopping CA-only models is technically simple for RCSB/EBI to
implement (call them for what they are - "incomplete depositions").
the consequence should be that no PDB ID is issued until a
complete deposition has been provided. most often structures
are deposited before a paper is submitted or while it is out
for review. not being able to provide a PDB ID should send a
signal to the journal editor
(3) as the petition states, it will be submitted both to the IUCr and
the RCSB
(4) there is no single panacea - everybody needs to be aware of the need to
deposit models and data - students, PIs, referees, editors, and funding
agencies
finally, one of the points that got this all started was to get some
discussion going and to see what the 'communis opinio' is. judging from the
response so far, it would seem that this goal has been achieved.
--gerard
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Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
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