Dear Colin, I think you understood perfectly what George was saying regarding the loss of information, but he will probably answer better than I.
In any case, and for the ones that did not understand it, what George was telling is related to the fact that a data collection made with a continuous crystal rotation contains more information than when this information is transformed into frames... The loss of information that we are referring to has the same meaning as when we calculate electron density maps with different grid sizes. The finer the grid, the greater is the information on the map. But you are right saying that the shorter the interval between produced frames, the lower the loss of information. However, the procedure that you are suggesting should have some limits... otherwise the amount of information would grow dramatically. All the best, Martin ________________________________________ Dr. Martin Martinez-Ripoll Research Professor xmar...@iqfr.csic.es Department of Crystallography & Structural Biology www.xtal.iqfr.csic.es Telf.: +34 917459550 Consejo Superior de Investigaciones Científicas Spanish National Research Council www.csic.es -----Mensaje original----- De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] En nombre de Colin Nave Enviado el: jueves, 27 de octubre de 2011 0:49 Para: CCP4BB@JISCMAIL.AC.UK Asunto: Re: [ccp4bb] IUCr committees, depositing images Dear George, Martin I don't understand the point that one is throwing away information by storing in frames. If the frames have sufficiently fine intervals (given by some sampling theorem consideration) I can't see how one loses information. Can one of you explain? Thanks Colin -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martin M. Ripoll Sent: 26 October 2011 22:50 To: ccp4bb Subject: Re: [ccp4bb] IUCr committees, depositing images Dear George, dear all, I was just trying to summarize my point of view regarding this important issue when I got your e-mail, that reflects exactly my own opinion! Martin ________________________________________ Dr. Martin Martinez-Ripoll Research Professor xmar...@iqfr.csic.es Department of Crystallography & Structural Biology www.xtal.iqfr.csic.es Telf.: +34 917459550 Consejo Superior de Investigaciones Científicas Spanish National Research Council www.csic.es -----Mensaje original----- De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] En nombre de George M. Sheldrick Enviado el: miércoles, 26 de octubre de 2011 11:52 Para: CCP4BB@JISCMAIL.AC.UK Asunto: Re: [ccp4bb] IUCr committees, depositing images This raises an important point. The new continuous readout detectors such as the Pilatus for beamlines or the Bruker Photon for in-house use enable the crystal to be rotated at constant velocity, eliminating the mechanical errors associated with 'stop and go' data collection. Storing their data in 'frames' is an artifical construction that is currently required for the established data integration programs but is in fact throwing away information. Maybe in 10 years time 'frames' will be as obsolete as punched cards! George On Wed, Oct 26, 2011 at 09:39:40AM +0100, Graeme Winter wrote: > Hi James, > > Just to pick up on your point about the Pilatus detectors. Yesterday > in 2 hours of giving a beamline a workout (admittedly with Thaumatin) > we acquired 400 + GB of data*. Now I appreciate that this is not > really routine operation, but it does raise an interesting point - if > you have loaded a sample and centred it, collected test shots and > decided it's not that great, why not collect anyway as it may later > prove to be useful? > > Bzzt. 2 minutes or less later you have a full data set, and barely > even time to go get a cup of tea. > > This does to some extent move the goalposts, as you can acquire far > more data than you need. You never know, you may learn something > interesting from it - perhaps it has different symmetry or packing? > What it does mean is if we can have a method of tagging this data > there may be massively more opportunity to get also-ran data sets for > methods development types. What it also means however is that the cost > of curating this data is then an order of magnitude higher. > > Also moving it around is also rather more painful. > > Anyhow, I would try to avoid dismissing the effect that new continuous > readout detectors will have on data rates, from experience it is > pretty substantial. > > Cheerio, > > Graeme > > *by "data" here what I mean is images, rather than information which > is rather more time consuming to acquire. I would argue you get that > from processing / analysing the data... > > On 24 October 2011 22:56, James Holton <jmhol...@lbl.gov> wrote: > > The Pilatus is fast, but or decades now we have had detectors that can read > > out in ~1s. This means that you can collect a typical ~100 image dataset in > > a few minutes (if flux is not limiting). Since there are ~150 beamlines > > currently operating around the world and they are open about 200 days/year, > > we should be collecting ~20,000,000 datasets each year. > > > > We're not. > > > > The PDB only gets about 8000 depositions per year, which means either we > > throw away 99.96% of our images, or we don't actually collect images > > anywhere near the ultimate capacity of the equipment we have. In my > > estimation, both of these play about equal roles, with ~50-fold attrition > > between ultimate data collection capacity and actual collected data, and > > another ~50 fold attrition between collected data sets and published > > structures. > > > > Personally, I think this means that the time it takes to collect the final > > dataset is not rate-limiting in a "typical" structural biology > > project/paper. This does not mean that the dataset is of little value. > > Quite the opposite! About 3000x more time and energy is expended preparing > > for the final dataset than is spent collecting it, and these efforts require > > experimental feedback. The trick is figuring out how best to compress the > > "data used to solve a structure" for archival storage. Do the "previous > > data sets" count? Or should the compression be "lossy" about such > > historical details? Does the stuff between the spots matter? After all, > > h,k,l,F,sigF is really just a form of data compression. In fact, there is > > no such thing as "raw" data. Even "raw" diffraction images are a > > simplification of the signals that came out of the detector electronics. > > But we round-off and average over a lot of things to remove "noise". > > Largely because "noise" is difficult to compress. The question of how much > > compression is too much compression depends on which information (aka noise) > > you think could be important in the future. > > > > When it comes to fine-sliced data, such as that from Pilatus, the main > > reason why it doesn't compress very well is not because of the spots, but > > the background. It occupies thousands of times more pixels than the spots. > > Yes, there is diffuse scattering information in the background pixels, but > > this kind of data is MUCH smoother than the spot data (by definition), and > > therefore is optimally stored in larger pixels. Last year, I messed around > > a bit with applying different compression protocols to the spots and the > > background, and found that ~30 fold compression can be easily achieved if > > you apply h264 to the background and store the "spots" with lossless png > > compression: > > > > http://bl831.als.lbl.gov/~jamesh/lossy_compression/ > > > > I think these results "speak" to the relative information content of the > > spots and the pixels between them. Perhaps at least the "online version" of > > archived images could be in some sort of lossy-background format? With the > > "real images" in some sort of slower storage (like a room full of tapes that > > are available upon request)? Would 30-fold compression make the storage of > > image data tractable enough for some entity like the PDB to be able to > > afford it? > > > > > > I go to a lot of methods meetings, and it pains me to see the most brilliant > > minds in the field starved for "interesting" data sets. The problem is that > > it is very easy to get people to send you data that is so bad that it can't > > be solved by any software imaginable (I've got piles of that!). As a > > developer, what you really need is a "right answer" so you can come up with > > better metrics for how close you are to it. Ironically, bad, unsolvable > > data that is connected to a right answer (aka a PDB ID) is very difficult to > > obtain. The explanations usually involve protestations about being in the > > middle of writing up the paper, the student graduated and we don't > > understand how he/she labeled the tapes, or the RAID crashed and we lost it > > all, etc. etc. Then again, just finding someone who has a data set with the > > kind of problem you are interested in is a lot of work! So is figuring out > > which problem affects the most people, and is therefore "interesting". > > > > Is this not exactly the kind of thing that publicly-accessible centralized > > scientific databases are created to address? > > > > -James Holton > > MAD Scientist > > > > On 10/16/2011 11:38 AM, Frank von Delft wrote: > >> > >> On the deposition of raw data: > >> > >> I recommend to the committee that before it convenes again, every member > >> should go collect some data on a beamline with a Pilatus detector [feel free > >> to join us at Diamond]. Because by the probable time any recommendations > >> actually emerge, most beamlines will have one of those (or similar), we'll > >> be generating more data than the LHC, and users will be happy just to have > >> it integrated, never mind worry about its fate. > >> > >> That's not an endorsement, btw, just an observation/prediction. > >> > >> phx. > >> > >> > >> > >> > >> On 14/10/2011 23:56, Thomas C. Terwilliger wrote: > >>> > >>> For those who have strong opinions on what data should be deposited... > >>> > >>> The IUCR is just starting a serious discussion of this subject. Two > >>> committees, the "Data Deposition Working Group", led by John Helliwell, > >>> and the Commission on Biological Macromolecules (chaired by Xiao-Dong Su) > >>> are working on this. > >>> > >>> Two key issues are (1) feasibility and importance of deposition of raw > >>> images and (2) deposition of sufficient information to fully reproduce > >>> the > >>> crystallographic analysis. > >>> > >>> I am on both committees and would be happy to hear your ideas (off-list). > >>> I am sure the other members of the committees would welcome your thoughts > >>> as well. > >>> > >>> -Tom T > >>> > >>> Tom Terwilliger > >>> terwilli...@lanl.gov > >>> > >>> > >>>>> This is a follow up (or a digression) to James comparing test set to > >>>>> missing reflections. I also heard this issue mentioned before but was > >>>>> always too lazy to actually pursue it. > >>>>> > >>>>> So. > >>>>> > >>>>> The role of the test set is to prevent overfitting. Let's say I have > >>>>> the final model and I monitored the Rfree every step of the way and can > >>>>> conclude that there is no overfitting. Should I do the final > >>>>> refinement > >>>>> against complete dataset? > >>>>> > >>>>> IMCO, I absolutely should. The test set reflections contain > >>>>> information, and the "final" model is actually biased towards the > >>>>> working set. Refining using all the data can only improve the accuracy > >>>>> of the model, if only slightly. > >>>>> > >>>>> The second question is practical. Let's say I want to deposit the > >>>>> results of the refinement against the full dataset as my final model. > >>>>> Should I not report the Rfree and instead insert a remark explaining > >>>>> the > >>>>> situation? If I report the Rfree prior to the test set removal, it is > >>>>> certain that every validation tool will report a mismatch. It does not > >>>>> seem that the PDB has a mechanism to deal with this. > >>>>> > >>>>> Cheers, > >>>>> > >>>>> Ed. > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > >>>>> Julian, King of Lemurs > >>>>> > > > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
