> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
On
> Behalf Of Pavel Afonine
> Sent: 31 July 2009 03:39
> To: Jiamu Du
> Cc: [log in to unmask]
> 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 [log in to unmask] 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
|