Dear Nat, You are making an excellent point, that I would like to supplement with another drawn from an intermediate stage between making compulsory the deposition of coordinates (to which you are referring) and the discussion we are having right now about moving towards the deposition of diffraction images - namely, the deposition of "structure factor" data.
At first that idea seemed to many to be just as far-fetched as the current one is seen by many. I can remember an impassioned e-mail to this BB by Gerard Kleywegt with subject line "SOS: save our structure factors!", pleading the case for that deposition to be made cmpulsory so as to be make it possible to have as objective a picture as possible of the quality of the electron density on which the model was based; and he went on to produce the Electron Density Server, the usefulness of which few would now dispute. There are probably few instances in which the EDS could be proven to have led to "significant new biological insights", but it is undeniable that it must have provided very useful means of checking deposited structures to see whether there might be questionable bits in crucial regions, whereas previously one would have had to believe indiscriminately everything that was modelled. This structure factor deposition also led to the possibility of large-scale testing of new developments in refinement algorithms which played a huge role in helping improvements in those to be throroughly evaluated, and the programs to be made robust. This led in turn to being able to see more detail or more corrections in old pdb entries via the EDS, culminating in such initiatives as PDB-redo that, if not revolutionising the biological information content of the pdb, has certainly helped make its contents much more assessable. Through the effect on the improvement of refinement programs, it can be said that the greatest beneficiaries of the deposition of structure factors yesterday are not so much the people who deposited the associated structures at the time, but everyone who refines structures today and will do so tomorrow with the much improved programs it has helped produce. We are simply today at the logical next step, i.e. depositing the images that the structure factors came from. For many reasons that have been described by many people, images often contain much more information about the reliability (or otherwise) of the structure factors derived from them (I have repeatedly mentioned the corruption by reflexions from parasitic lattices). Such images will not only provide the foodstuff for new developments aimed at dealing better with the problem: once those developments have taken place, more reliable data will be obtainable from them, that may frequently clean up dubious features of the previous maps or bring into question certain parts of the previous models. I think that Adrian's rather dismissive comment that developers can get the job done from a few scraps of bad images gleaned from colleagues in distress is simply a sign of a lack of experience in developing software. We should not, therefore, be too blinkered and ask only "What will it do for my structure if I deposit my images", but instead ask "What will depositing my images do to improve the processing and refinement programs of tomorrow" (I am not trying to sound like JFK here ...). The answer is: an awful lot! These improvements will then help everybody, including the sceptical depositor in question in his or her next tough project; but as usual they will be taken for granted by those who thought that depositing images was a waste of time ... . I hope this elicits more comments from doubters and detractors: their voices and arguments should certainly be heard. With best wishes, Gerard. -- On Thu, Oct 27, 2011 at 02:11:28PM -0700, Nat Echols wrote: > On Thu, Oct 27, 2011 at 1:47 PM, Adrian Goldman > <adrian.gold...@helsinki.fi>wrote: > > > 1) this is not a matter of science, but science (internal) policy, and so > > the majority actually SHOULD count. > > > > It's worth keeping in mind that there was once strong opposition to the > current rules on PDB deposition - the best example I could find is here: > > http://www.nature.com/nsmb/journal/v5/n6/pdf/nsb0698-407.pdf > > Notably, nearly a third of scientists polled thought they should be allowed > to publish without releasing coordinates. If this had been a majority, > should the journal editors have meekly submitted and allowed the old policy > of 1-year holds to continue? Admittedly, the issue of archiving raw images > is not the same, since they are of much less use to the community, but it's > a good example of why some opinions should be ignored. > > -Nat -- =============================================================== * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===============================================================