> -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of Pavel Afonine > Sent: 31 July 2009 03:39 > To: Jiamu Du > Cc: [email protected] > Subject: Re: [ccp4bb] question of extra high B factor > > with B~133 you uj is 3.7A which means that atom is all over > the place and meaningless
Hi I've seen this connection between B and (presumably) the implied positional uncertainty sigma(r) stated many times, and I would point out that it's actually a non-sequitur. The reason is that the RMS amplitude u = sqrt(B/8pi^2) = 1.3 Ang for B = 133 Ang^2 does not equate to the positional uncertainty. Note that I'm not just pointing out the arithmetic slip in the above calculation (how did you get 3.7 ?). The RMS amplitude pertains to the *instantaneous* atomic position arising from thermal vibration/disorder, whereas of course with X-rays we measure the *average* atomic position. If you want an estimate of sigma(r) see this paper: http://journals.iucr.org/d/issues/1999/11/00/jn0061/jn0061.pdf Using equation 1 here and assuming a O atom (note that the positional uncertainty depends on the no of electrons as well as B), I get sigma(r) = 0.81 Ang for B = 133 Ang^2 (Z = 4.1 for O at s=0.3). This of course assumes it's valid to extrapolate the equation well beyond the range for which it was derived! - but my point is that the temptingly straightforward sigma(r) = sqrt(B/8pi^2) is the *wrong* equation to use! In any case whatever value of sigma(r) (or B) you observe I would dispute that this necessarily means that the atom isn't there, what matters in the end is the electron density you see in the map. 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
