Hi Frank, I would have assumed that the purpose of the experiment would have been defined in the publication associated with the deposition - not to trivialize your point, which is very important, but to put it in context. I would also assume that the sequence and ligands are as per the associated PDB deposition. So so far we are quite a way towards being able to get something useful from this data with what we have already. The relationship to associated data sets - this is harder, certainly, but not impossible. In particular, how frequently is it the case that the measurements from these 15 similar data sets actually contribute directly to the structure solution? Obviously there is a process as defined in a lab book, but you could take the stance, at least in the first instance, that they do not directly contribute if the same conclusions would be reached in their absence.
Obviously any repository must be more than an FTP site, and must allow the scientific links between structures and data to be made (for example including the model used for the successful molecular replacement.) It does seem clear to me though that we cannot set up the perfect repository in the first instance, but we do have to start somewhere. Perhaps we do not need the right answer, but one which is less wrong that not making available the data at all? Just my thoughts on this. Cheers, Graeme 2009/3/18 Frank von Delft <frank.vonde...@sgc.ox.ac.uk>: > Maybe, but images without experimental context (sequence? ligands? > purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!! > relationship to the other 15 similar datasets) are as good as no images. > And as far as I know, there's no good discussion on the table for that. At > least, no-one on the thread mentioned it, so they're probably not thinking > about it either. > > I suppose efforts like PIMS or are a start, and maybe they can even have > enough information (my feeling is they currently don't). But that's where > the discussion should start: how to index (in sense of annotate) the > datasets. The technicalities are just that: technicalities. > > Or even closer to home: does ANY detector/beamline write even timestamps > into the image header...? Never mind ring current, intensity of the beam, > size of beam, size of crystal, length of direct beam path, etc etc... > phx > > > > Gerard Bricogne wrote: >> >> Dear Bernhard, >> >> I suppose you meant "ad nauseam" ;-) . >> In any case, what is the use of discussions and recommendations >> that >> are not followed by action, and only result in making their contributors >> themselves nauseated to the point of wanting to "put this to rest"? >> As Ethan has nicely stated in his reply to Garib's double-check of >> whether we do need images, this matter should NOT be put to rest: it >> should >> be dealt with. As was argued at the end of the paper by Joosten, Womack et >> al. (Acta Cryst. D65, 176-185), the main advantage of depositing images >> would be that it would enable and stimulate the further developement and >> testing of image integration and data processing software, to the same >> degree that the deposition of structure factors has stimulated progress >> and >> testing for structure refinement software. >> >> Far from a boring issue only capable of giving headaches to Standards >> Committee members, this is a vital issue: with each undeposited set of >> images that contributed in one way or another to the determination or >> refinement of a deposited structure, there disappears an opportunity to >> test >> improvements in methods and software that would be likely to improve that >> deposited entry (and most others) at a future stage. I think we need to >> take >> a long view on this, and abandon the picture of the PDB as a static >> archive >> of frozen results: instead, it should be seen as a repository of what is >> required not only to validate/authenticate the deposited models, but to >> feed >> the continued improvement of the methods used - and hence, at the next >> iteration, the constant revision and improvement of those very models. In >> what way can this topic be a source of nausea? >> >> >> With best wishes, >> Gerard. >> >> -- >> On Wed, Mar 18, 2009 at 10:16:42AM -0700, Bernhard Rupp wrote: >> >>> >>> As Herb will attest, the need for keeping images and the various reasons >>> for it have been discussed ad nauseum and agreed upon in various imgCIF >>> meetings - I am sure Herb or Andy Howard can provide links to the >>> documents/recommendations, to put this to rest. >>> Best, BR >>> >>> Past ACA Data Standards Committee serf >>> -----Original Message----- >>> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Kay >>> Diederichs >>> Sent: Wednesday, March 18, 2009 10:02 AM >>> To: CCP4BB@JISCMAIL.AC.UK >>> Subject: Re: [ccp4bb] images >>> >> >> >
