Hi, Sorry for the long post - this stirred some memories. Feel free not to read below this line :)
--this line-- The suggestion to store frozen crystals brings to mind an old (and bad!) Soviet science fiction novel (The Seller of Air) - only instead of storing liquified oxygen, we're looking at the rise of the Protein Crystal Authority: a massive underground structure with interior facilities that are maintained at LN2 temperature, and where support staff gingerly roams the frozen halls in modified space suits. A change of shift conversation between two serious, mustachioed, pipe-smoking men comes to the mind's eye: "How're things today, Roger?" "Oh not too bad Frank - we shipped out 1671 crystals with only two empty loops so far. Which reminds me - please get the cryo-team to cut two flash-frozen interns out of sector 17, the robots keep bumping into them" I can also see the following scenario unfold: a specific crystal is retreived from storage - but it does not diffract (or better yet, it's a ball of ice). Now ask yourself - is it an honest issue - storage problems, X-ray induced decay, or something -- or the intelligent fraudster simply submitted some known junk crystals to the repository, knowing that nothing can be proven definitively one way or another? Let's also consider difficult cases such as GPCRs where the full dataset may be derived from 20-30 crystals each of which only survived 30 seconds of exposure. What do we do then? Ask the experimenters to submit 35 more crystals, just in case there are questions later? --- As far as I know, it is standard practice to assume that authors are innocent, until sufficient evidence is produced to the contrary. Burden of proof is on the investigating parties - simply because for every 1 case of dishonesty there are hundreds of thousands of honest papers. Would you make all of us store used-up crystals? As long as people publish most of the details necessary to reproduce the materials (protein samples and crystals) used in structure determination - the crystals may be reproduced 'by persons skilled in the art'. There is no need to even store or distribute specific plasmid/clone DNA samples any more as long as relevant DNA sequences are retained (thank you, synthetic DNA providers!). In my opinion the real problem in biology (and increasingly in chemistry) is that people often do not publish enough details for the work to be easily reproducible. This is to a great degree the result of journals allowing 'materials and methods' sections that elicit a reflex "golly, a whole paragraph of text!" response and are printed in font size 3. No need to point fingers - we all know which journals let this happen. In their partial defense - supplementary materials are supposed to be the new destination of methods and such, but not everyone uses them and even those are often incomplete or sloppy. We cannot practically hope for the return of the halcyon years when certain German chemistry publications insisted that synthetic procedures are successfully reproduced in an independent lab prior to publication. This obviously isn't going to happen - it'd be impractical, expensive, and slow. However, when we review papers (especially papers describing truly novel and interesting results) we have all the right to insist on publication of detailed methods. Artem --- When the Weasel comes to give New Year's greetings to the Chickens no good intentions are in his mind. -----Original Message----- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Lijun Liu Sent: Saturday, March 21, 2009 1:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] images Now that there is possibility that images could be fake, which means the first and automatic FFT in crystallography could be falsified. All those depositions later than this would be just nothing but wrong, if images were fake. To keep the first and most important FFT not contaminated, I would suggest the deposition of crystals. 0) Crystal is harder to be fake than images; From crystal to images, maybe only 1 hour needed; 1) Protein crystals could be stored in LN2 for probably more than 1000 years; 2) There normally are small and not a big space occupier; 3) They can be easily maintained by simply feed LN2 and controled by computer; 4) You do not need buy hard drives, DVDs, .. and no need in suffering from different format of files, ... 5) Crystallography keeps moving forward though slow. It is possible that future people can get better data from the almost same crystal, better than using softwares to deal with images, ... 6) Temporarily I suggest the generous 3rd generation synchrotron facilities round out some space for saving those crystals, because there are normally located far from downtown and have enough land around... 7) ... Lijun > Kay Diederichs wrote: > >>In this case the structure factors were deposited, but these do not >>have a column for the anomalous signal. Re-refinement with these >>structure factors was inconclusive. >> >>If I could have downloaded the images, I could have investigated >>this easily, because there's a large difference in the f" of those >>two metals. >> >>So to me access to images sometimes may help to answer a scientific >> question. > > > I would add a plea to those considering an image deposition system: > accept MAPS too! > > At the very least it would be nice to see the initial and final maps > the crystallographer used. Even if I have the structure factors I'm > not necessarily an expert on the ins and outs of what someone had to > do to refine a twinned or otherwise troublesome structure, and I > don't want to have to learn the specific refinement program you used > to be able to reproduce the exact map you saw. (For very old > structures, it may no longer be possible to compile the specific > version of the refinement software on new processors/OSes, or someone > may have used a commercial refinement package.) And of course, there > are non-crystallographers who use structures and it is absurd to > expect them to learn x-ray refinement to see the relevant map for a > twinned structure that EDS couldn't process. > > I love EDS. But even though it usually has a map for a given > structure, seeing the actual map generated by the crystallographer > who was the expert on the project would be better. Once a system is > designed that is large enough to handle images, maps would not > significantly increase the required storage space. I've poked a > couple people to suggest that even now the PDB ought to be accepting > maps. > > > -- > -Eric >
