Sorry if this message reads a bit out of date, it has been sent two days ago without success, I am trying to sent it one more time.
XDS 发件人: gsw...@pku.edu.cn 收件人: Felix Frolow <mbfro...@post.tau.ac.il>, CCP4BB@JISCMAIL.AC.UK, x...@pku.edu.cn 已发送邮件: Tue, 18 Oct 2011 10:36:51 +0800 (CST) 主题: Re: [ccp4bb] IUCr committees, depositing images Dear All, Since John has responded to the issues raised by Tom and several responders, and he has just described the overall goal of IUCr DDD WG (Diffraction Data Deposition Working Group), I will just second on this important issue particularly for the future biological macromolecular crystallography. In my opinion, the reasons for raw data deposition can be summarized as following (overlapping with others) * Keep permanent experimental records; this may not be done well for all crystallographers. * Make it possible for rigorous thorough check by reviewers as FF suggested in this mail; in fact this has been a problem for some structures published prestigious journals, particularly for low-resolution results, and these low-resolution structures tend to become more and more. * Minimize falsification and other types of mistakes and misconducts in structural biology. * Make it easier for validations/collaborations, I bet many structures in PDB are wrong, but there is no way to find out by the current data deposition. * Good for methods developers; I also agree that there are essentially no much technical problem for the raw image(data) depostion, this is especially true if we leave the deposition at or near the synchrotron sites. I hope we will join in John's forum on this important issue at: http://forums.iucr.org/ XDS Xiao-Dong Su, Professor Chairman of the Commission on Biological Macromolecules (CBM), International Union of Crystallography (IUCr); School of Life Sciences, Peking University 100871 Beijing, China Phone: +86-10-62759743 FAX: +86-10-62765669 E-mail: x...@pku.edu.cn ----- 原始邮件 ----- 发件人: Felix Frolow <mbfro...@post.tau.ac.il> 收件人: CCP4BB@JISCMAIL.AC.UK 已发送邮件: Mon, 17 Oct 2011 03:31:52 +0800 (CST) 主题: Re: [ccp4bb] IUCr committees, depositing images On the deposition of raw data: Committees, wherever you are! I guess that abstaining from storing the raw diffraction data in the form of frames is not very wise whatever its size is. I regret that for some PDB entries I do not have diffraction data (needless to say that authors do not submitted even structure factors). I maintain a bit more than 1.2 T diffraction data starting from 2001 and all is nicely resides on two small WD pocket disks (needless to say that I have several copies of the data). Generally I have all data I ever collected going back to beginning of 80's, but I am to lazy to reform DAT tapes. Sure, running Pilatus for an olympic record, we will go home with several T of data after 24 h (will we?). But this is an abuse of the system. The final goal is the structure determination, and there are much less good crystals everywhere in one year that one Pilatus could collect in one week. But to decide fast if the crystal diffraction data from Pilatus is good for storage or even for measurement whatever the speed of data collection is, good data processing software is needed. I personnaly think that there is only one, the one. Anyhow, I think if the author wish to publish his structure, and it is important, and I am a reviewer, and it is going to prestigious journal, I will reprocess his data and will check his way to the final crystal structure solution from the beginning. It is as in mathematics. If someone claim that he solved a long-staing problem from the past, he will not go away from his envious colleagues, who will drop everything and will sit and check, until they will find a mistake. What a pleasure!!! And if there are no mistakes - chapeau !!! 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 16, 2011, at 20:38 , 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 >>>>
