Dear Gerard, I'm very happy for the discussion to be on the CCP4 list (or on the IUCR forums, or both). I was only trying to not create too much traffic.
All the best, Tom T >> 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 * >> * * >> =============================================================== >>
