One more consideration: Since organization is not one of my greatest talents, I would be absolutely delighted if a databank took over the burden of archiving my raw data for me. Phoebe
===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp ---- Original message ---- >Date: Tue, 18 Oct 2011 18:17:14 +0100 >From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> (on behalf of Gerard >Bricogne <g...@globalphasing.com>) >Subject: Re: [ccp4bb] IUCr committees, depositing images >To: CCP4BB@JISCMAIL.AC.UK > >Dear Enrico, Frank and colleagues, > > I am glad to have suggested that everyone's views on this issue should >be aired out on this BB rather than sent off-list to an IUCr committee >member: this is much more interactive and thought-provoking. > > There would seem to be clear biases in some of the positions - for >instance, the statement that we overvalue individual structures and that >there is value only in their ensemble has to be seen to be coming from >someone in a structural genomics centre ;-) . However, as Wladek pointed >out, when an investigator's project is crucially dependent on a result >embodied in a deposited structure, it would be of the greatest value to that >investigator to be able to double-check how reliable some features of that >structure (especially its ligands) actually are. > > On the other hand Enrico, as a specialist of crystallisation and >modelling, sees value only in improving those contributors to the task of >structure determination. This is forgetting (1) an essential capability of >crystallography: that, through experimental phasing, it can show you what a >protein looks like even if you have never seen nor modelled one before, >through the wondrous process of producing model-free electron-density maps; >and (2) an essential aspect of the task of structure determination: that it >doesn't aim at producing a model with perfect geometry, but one that best >explains the measured data and neither under- nor over-interprets them (I >realise, though, that Enrico's statement "Data just introduces experimental >errors into what would otherwise be a perfect structure" is likely to be >tongue-in-cheek ...). > > When it comes to making explicit the advantages of archiving at least >the raw images that yielded the data against which a deposited PDB entry was >refined, many good reasons have been given, but I feel that > > (1) there is an over-emphasis on the preservation of diffuse scattering >that has a tendency to give this archiving a nuance of "blue-skies" research >and thus to detract from its practical urgency; time will come for diffuse >scattering to be fully appreciated, but at the moment its mention acts as a >bit of a distraction, if not a turn-off in this context for people who not >not love it already; > > (2) as far as I see it, the highest future benefit of having archived >raw images will result from being able to reprocess datasets from samples >containing multiple lattices ("non-merohedral twinning"). Numerous >structures are determined and refined against data obtained by integrating >only the spots from the major lattice, without rejecting those that are >corrupted by overlap by a spot from a minor lattice. This leads to >systematic errors in these data that may only be incompletely taken out by >outlier rejection at the merging stage, and will create noise or confusing >residual features in difference maps, if not false features in the main map >and therefore its interpretation by the model. In my opinion it will be the >development of methods for dealing with overlapped lattices and for the >proper treatment of such data in scaling and refinement (as is already >possible with small molecules) that will bring about the major possibility >of substantially improving deposited results by reprocessing the raw images >co-deposited with them; > > (3) there is also the more immediate possibility of better removing ice >rings, or ligand powder rings, from images, than by having to throw away >certain thin shells of merged data in the structure factor file. > > I see the case for raw image deposition as absolutely compelling, >especially in view of the auto-catalytic process through which their >availability will speed up the development of precisely the new methods and >software to extract better data from them and better refine models against >them. The impact of structure factor deposition on the development of better >refinement programs is there to prove that this paradigm of a chain reaction >makes total sense. > > Various arguments tend to be fired off as decoys - "get better >crystals", why not "get a better post-doc"? - but they are unhelpful in the >way they prolong procrastination when what we need is to bite the bullet. >The IUCr Forum that John Helliwell pointed at already contains draft plans >for a pilot run of a reasonable scheme. > > > With best wishes, > > Gerard. > >-- >On Tue, Oct 18, 2011 at 06:19:27PM +0200, Enrico Stura wrote: >> Dear Peter, >> >> How many crystallographers does it take to transform bad data into good >> data? >> None, you need a modeller. Only a modeller can give you a structure with >> perfect >> geometry. Data just introduces experimental errors into what would >> otherwise be a perfect >> structure. >> >> If you have good data do you need crystallographers? >> ... >> >> Of course there all the cases in between. That ... you are right, is the >> other half of the story. >> >> From a biological point of view, only borderline cases make "cents" ($+€) >> to store. >> The experimenter in consultation with a beamline scientist at an SR >> facility is the best >> small commitee suitable to evaluate what is worth keeping. I am sure that >> the images >> that are worth storing for a long long time would fit on a few Tb at a >> reasonable cost. >> Storing everything would make it harder to find something worth improving >> in the future. >> >> Enrico. >> >> >> On Tue, 18 Oct 2011 17:12:42 +0200, Peter Keller >> <pkel...@globalphasing.com> wrote: >> >>> Dear Enrico, >>> >>> Please don't get me wrong: what you are saying is not incorrect, but it >>> is only half the story. >>> >>> On Tue, 2011-10-18 at 15:13 +0200, Enrico Stura wrote: >>>> With improving techniques, we should always be making progress! >>> >>> Yes, of course! >>> >>>> If we are trying to answer a biological question that is really >>>> important, >>>> we would be better off >>>> improving the purification, the crystallization, the cryo-conditions >>> >>> You have left X-ray crystallography out of this list. It is a technique >>> like the others, and can also be improved :-) >>> >>> It may be true that the number of crystallographers that are working on >>> improving instrumental methodology and software is small compared to the >>> number working on improving wet-lab techniques, but that number is not >>> zero, and the contribution is significant. The rest of you benefit from >>> that work! >>> >>>> instead of having to rely on >>>> processing old images with new software. >>>> >>>> I have 10 years worth of images. I have reprocessed very few of them and >>>> never made any >>>> sensational progress using the new software. Poor diffraction is poor >>>> diffraction. >>> >>> Maybe so, but certain types of datasets are useful for methods and >>> software development, even if no new biological insights could be gained >>> by reprocessing them. These datasets are often hard to get hold of in >>> practice, especially when they are in someone's lab on a tape that >>> no-one has a reader for any more. >>> >>> Obtaining protein, growing crystals and collecting new data in such a >>> way that the interesting features of those datasets are reproduced can >>> be much much harder than curating the images would be. This is >>> especially true for software-oriented people like us who don't have >>> regular access to wet-lab facilities. >>> >>>> Money can be better spent buying a wine cellar, storage works for wine. >>> >>> Images have already been lost that ought to have been kept. The >>> questions are: how to select the datasets that are potentially of value, >>> and how to make sure that they don't disappear. >>> >>> Regards, >>> Peter. >>> >> >> >> -- >> Enrico A. Stura D.Phil. (Oxon) , Tel: 33 (0)1 69 08 4302 Office >> Room 19, Bat.152, Tel: 33 (0)1 69 08 9449 Lab >> LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE >> http://www-dsv.cea.fr/en/institutes/institute-of-biology-and-technology-saclay-ibitec-s/unites-de-recherche/department-of-molecular-engineering-of-proteins-simopro/molecular-toxinology-and-biotechnology-laboratory-ltmb/crystallogenesis-e.-stura >> http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html >> e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71 > >-- > > =============================================================== > * * > * 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 * > * * > ===============================================================
