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I think the activation energy required to submit your coordinates to the PDB (filling all those forms) is much more than that required to submit that single additional file containing structure factors. I don't remember the last time I read a yeast genetics or biochemistry paper and saw the authors show their final hypothesis/model without showing any of the experimental data (gels, assaya, graphs etc.) and expected the reader to be convinced. If it isn't an accepted scientific practice elsewhere, why should the crystallographic community be rife with such abundant complacence/tolerance! Yes, I agree that there might be some dire circumstances for delaying deposition, if we could gather some examples from the community for what sorts of situations might warrant such delays. Genuine reasons to delay. I wonder.... 1) Could we send a letter to journals with gazillion authors showing support on the letter requesting that SF's ought to be deposited to complete submissions (delays, if genuine, included)? People give two hoots to a measly postdoc nobody like me hollering - so names/numbers matter in this letter! 2) Could we use the next xtallo Gordon meeting, other meetings and put this on the agenda? And, to come to a consensus? 3) Could we enforce the need to deposit data once the community has a consensus decision (inclusive of all clauses)? Then, the databases might be able to add to the requirements. Thanks. Raji ---------Included Message---------- >*** For details on how to be removed from this list visit the *** >*** CCP4 home page http://www.ccp4.ac.uk *** > > > >I would guess that there is a consensus (possibly with a very few dissenters) that it should be part of the deposition, but that nobody knows how to change the current rules. > >1) publishers don't care but will respond to the community >2) grant-awarding bodies don't know so won't apply any pressure >3) IUCR might be able to do something, but it may be that the >initiative should come from wwPDB, I don't know > >I do know that it has been discussed at many meetings but nobody >seemed to know how to change things > >I suspect the main reason for not depositing structures factors is laziness. But there is always a little suspicion that there is something to hide ... > >Phil > > >On 15 Dec 2006, at 11:28, Peter Keller wrote: > >> >> Hi Phil, >> >> On Fri, 15 Dec 2006, Phil Evans wrote: >> >>> I agree that more information to referees is desirable, & I've >>> often wanted to see the coordinates and the structure factors to >>> check things. But to follow up after publication, there are still >>> a lot of structures deposited without structure factors - why is >>> deposition of structure factors not compulsory? And who can change >>> things so that it becomes compulsory? >> >> I don't work at the EBI any longer, so I can't speak for the wwPDB >> or the MSD group, but in my understanding the answer to your second >> question is that one or more of the following three interest groups >> would have to agree to change things to make structure factor >> deposition universal: >> >> (1) Publishers: currently deposition of coordinates is required >> to get an ID code for publication. The journals could insist that >> PDB id codes quoted in the articles that they publish had to have >> both coordinates and structure factors deposited. >> >> (2) Grant-awarding bodies could insist that any structures >> determined/deposited on their funding had to be deposited with >> structure factors. >> >> (3) The "crystallographic community" (via the IUCR?) could agree >> that structure factors should always be deposited, and ask the >> wwPDB not to issue ID codes without them. This has been much >> debated in the past. I don't know whether any consensus is emerging. >> >> This is not a decision that can be made unilaterally by the wwPDB >> of course. There is also the issue of who would check that the >> policy is being followed. In scenario (3) it would be the wwPDB >> themselves, but in the other two it is not quite so clear cut. >> >> As for your first question, it would be interesting to hear some >> current views from people who don't deposit structure factors, and >> why they think that putting structure factors on hold (i.e. >> delaying their release after deposition) does not address their >> concerns. >> >> Regards, >> Peter. >> > > > ---------End of Included Message---------- Raji Edayathumangalam Postdoctoral Fellow The Rockefeller University Box 224, 1230 York Avenue New York, NY 10021
