> -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Jon Wright > Sent: 08 September 2008 21:29 > To: Borhani, David > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] truncate ignorance > > Borhani, David wrote: > > ... > > but I think pretty much everyone has converged on using it for the > > past many years. > > Many small molecule crystallographers seem to refine on > intensity and so > avoid need this procedure. Towards the end of the recent > thread "Wilson > plot from truncated.mtz" it had seemed like this forum was > starting to > see that light? > > In short - if your observations are supposed to be noisy in the > "plus_or_minus sigma" sense then the peaks which are much > less than the > sigma should come out negative almost half of the time. > Truncate would > appear to be for the case where you want an estimate of the true > magnitude of the structure factor, "F", and not your > experimental data. > > Jon > >
This can't be correct, for whatever you say is true for F must also hold equally for I, in other words if you accept that the Truncate procedure is valid for getting a better estimate of the true F (and I think we're all agreed that it is valid), then logically it must also be valid for getting a better estimate of the true I. The point is that F, as the sqrt of a +ve I, is needed for computing an electron density map, whereas you don't need an improved estimate for I to do I-based refinement, since the measured I serves equally well. Note however that since the corrected I's really are better estimates, you will get lower I-based R factors (both Rwork & Rfree) from an I-based refinement (note well that the corrected I is NOT the same as the [corrected F]^2, i.e. you must NOT square the F's to do an I-based refinement, you must go back to the original I's). However as we all know (or should know by now!), getting better R factors doesn't necessarily imply that you will get a better structure, and since you have not added any more information in the Truncate procedure over and above that which you are already inputting into the refinement (namely the unit cell contents), it's very hard to see how you could get a better structure. Note also that George Sheldrick suggested in an earlier thread that the corrected I's are biased, referring to the situation where the average true I is zero, but thinking about this further I'm sure this is not correct. The reason is that if the average true I is zero, the Wilson distribution is a Dirac delta function (infinite spike) at I=0; this overrides any distribution of the measured I in the Bayes equation, so the corrected I's, and hence the average corrected I, are also exactly zero, hence there is no bias. In the general case, whilst it is true that the negative I's are increased when the correction is performed, many (not all) positive I's are decreased (because they are all shifted towards the peak of the Wilson probability density at I=0), so the net effect is that the average I is unchanged. I believe also that in an earlier posting Peter Zwart said he thought that CNS doesn't take account of the Wilson distribution when doing its version of the correction; if this is true (and I have no independent evidence that it is since I'm not a CNS user), then the above argument implies that the F's corrected by such a procedure will inevitably be biased, though the damage done may well not be significant compared with that done by using F's instead of I's in the first place. -- 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
