Dear Gerard,Tom and Bernhard, Thankyou for highlighting the IUCr Diffraction Data Deposition Working Group and Forum.
Dear Colleagues, I am travelling at present and apologise for not replying sooner to the CCP4bb, and also am with intermittent email access until later this week when I 'return to office'. The points being raised in this CCP4bb thread are very important and the IUCr also recognises this. The role of the IUCr Working Group that has been set up is to bring to a focus information and to identify steps forward. We seek to make progress towards archiving and making available all relevant scientific data associated with a publication (or a completed structure deposition in a validated database such as the PDB). The consultation process is being formalised via the IUCr Forum pages. The Working Group and a wider Group consisting of IUCr Commissions and consultants has been established for discussion and planning. We are also aiming at a community consultation via the Forum approach and we will launch the Forum for this asap. The IUCr invites as wide as possible inputs, from the various communities that the IUCr Commissions serve, on the diffraction data deposition future, which can surely be improved. Thus this Forum will help to record an organised set of inputs for future reference. The Forum is being set up and will require registration, which is a straightforward process. Details will follow shortly. Members of the Working Group and its consulted representatives are listed below. Best wishes and regards, Yours sincerely, John Prof John R Helliwell DSc Chairman of the IUCr Diffraction Data Deposition Working Group (IUCr DDD WG). IUCr DDD WG Members Steve Androulakis (TARDIS representative) John R. Helliwell (Chair) (IUCr ICSTI Representative; Chairman of the IUCr Journals Commission 1996-2005) Loes Kroon-Batenburg (Data processing software) Brian McMahon (IUCr CODATA Representative) John Westbrook (wwPDB representative and COMCIFS) Sol Gruner (Diffuse scattering specialist and SR Facility Director) Heinz-Josef Weyer (SR and Neutron Facility user) Tom Terwilliger (Macromolecular Crystallography) Consultants: Alun Ashton (Diamond Light Source (DLS); Data Archive leader there) Herbert Bernstein (Head of the imgCIF Dictionary Maintenance Group and member of COMCIFS) Frances Bernstein (Observer on data deposition policies) Gerard Bricogne (Active software and methods developer) Bernhard Rupp ( Macromolecular crystallographer) IUCr Commissions (Chairs and/or alternates). On Sat, Oct 15, 2011 at 1:32 AM, Gerard Bricogne <g...@globalphasing.com> wrote: > Dear Tom, > > I am not sure that I feel happy with your invitation that views on such > crucial matters as these deposition issues be communicated to you off-list. > It would seem much healthier if these views were aired out within the BB. > Again!, some will say ... but the difference is that there is now a forum > for them, set up by the IUCr, that may eventually turn opinions into some > form of action. > > I am sure that many subscribers to this BB, and not just you as a > member of some committees, would be interested to hear the full variety of > views on the desirable and the feasible in these areas, and to express their > own for everyone to read and discuss. > > Perhaps John Helliwell can elaborate on this and on the newly created > forum. > > > With best wishes, > > Gerard. > > -- > On Fri, Oct 14, 2011 at 04:56:20PM -0600, 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 >> >> > > -- > > =============================================================== > * * > * 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 * > * * > =============================================================== > -- Professor John R Helliwell DSc
