> (& while I'm at it, freeR has nothing to do with model bias (which is > largely imaginary anyway, only a problem with low resolution molecular > replacement)) > > Phil
Phil, I understand what you're saying but 'model bias' in this context has a wider meaning than just failing to rebuild the chain correctly from an MR model at low resolution, and using this wider meaning Rfree has everything to do with model bias. For example, if I refine a high res structure with 1 Ang data using an isotropic-only B-factor model, then Rfree (& Rwork) will almost certainly be higher than you would expect using the optimal parameterisation of 3 xyz's + 6 ADPs per atom with the appropriate restraints (whatever the optimum happens to be). Bias is defined as 'difference from expectation', so the isotropic model is almost certainly biased, as reflected in the higher-than-expected Rwork & Rfree. I'm well aware that bias by itself is not necessarily a bad thing particularly when a biased estimator happens to have the least error (difference from the truth), but I doubt one can claim that in this example. 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 [email protected] 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
