Sure they will There is no irony in what I say FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel
Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 18, 2011, at 20:01 , Phoebe Rice wrote: > 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" ($+β¬) >>> 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 * >> * * >> ===============================================================
