> -----Original Message----- > From: Vellieux Frederic [mailto:frederic.velli...@ibs.fr] > Sent: 19 October 2009 19:31 > To: Ian Tickle > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] how to improve Rfree? > > Hi Ian (& ccp4bb'ers), > > NCS ties reflections in reciprocal space by the interference G-function > effect. Nothing more. So you get an R-free value that is lower than if > you don't have NCS. One should be aware of that, and referees should be > aware of that.
Hi Fred That may be true (though not always), but I was actually referring to the problem of 'predicting' (usually after the fact!) what is the expected value of Rfree for an optimally refined structure, given Rwork (without knowing Rwork it's impossible!) and basic information about the data, the structure and the refinement protocol. This is (partly) a question of working out the observation/parameter ratio; then the big question arises as to how you count the NCS restraints. This calculation is tricky even in non-NCS cases, but as I said NCS really fouls things up (and I don't have a satisfactory solution)! Without having the expected value of Rfree as a basis for comparison how can you argue with the referees that the value of Rfree that you actually observed demonstrates that your model is free of bias or overfitting? My previous example of model bias in a 1 Ang isotropic B-factor refinement may have seemed remote and even irrelevant to many people struggling with 3 Ang data, but I would point out that model bias and the concomitant higher-than-expected Rfree is ubiquitous. If that were not true we wouldn't need to refine or model-build any MR solutions - just calculate structure factors and publish! The fact that Rfree never (well hardly ever) drops immediately to its final value but requires a lot of work model-building/refining is testament to the model bias still remaining in all the intermediate models between the initial MR model and the final refined structuure. Cheers -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
