Sorry I don't have instant access to Acta A here so can't comment in the light of the Flack & Shmueli paper. But it seems to me that Kevin's point is still valid, regardless of whether or not the anomalously scattering atoms have different ADPs from the average or not. I agree that this would have the complicating effects described, but I don't see that it's necessary to invoke it as an explanation. The reason is that the anomalous phasing power doesn't depend on Rano = <|delta-ano|>/<I>, it depends on the anomalous signal/noise ratio = <|delta-ano|/s.u.(delta-ano)>, or something related to it, and the standard uncertainty of course depends largely on the background). So if the fall-off due to overall thermal motion etc as described by Kevin causes the S/N ratio to dip much below 1 then the anomalous signal won't help you.
Cheers -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of Marc SCHILTZ > Sent: 13 May 2009 11:26 > To: Kevin Cowtan; CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] phasing with se-met at low resolution > > Kevin Cowtan wrote: > > This is absolutely correct - in the analysis you present, the > > non-anomalous scattering drops with resolution, but the anomalous part > > does not. And since counting noise varies with intensity, we should > > actually be better off at high resolution, since there is less > > non-anomalous scattering to contribute to the noise! (This is somewhat > > masked by the background, however). > > > > So why don't we see this in practice? > > > > The reason is that you've missed out one important term: the atomic > > displacement parameters (B-factors), which describe a combination of > > thermal motion and positional disorder between unit cells. This motion > > and disorder applies equally to the core and outer electrons, and so > > causes a drop-off in both the anomalous and non-anomalous scattering, > > over and above that caused by the atomic scattering factors. > > > > I agree with everything but would like to add the following: if we > assume an overall atomic displacement parameter, the drop-off in both > the anomalous and non-anomalous scattering is the same. Therefore, the > ratio of anomalous differences over mean intensity (which is what comes > closest to R_{ano} - in whichever way this is defined) is essentially > unaffected by atomic displacements and should still go up at high > resolution, irrespective of the values of the atomic displacement > parameter ! > > Things are more complicated if individual isotropic atomic displacements > are considered, because the anomalously scattering atoms (e.g. the Se > atoms) may have significantly larger or smaller displacement parameters > than the average. > > All this is discussed in section 4.4. of Flack & Shmueli (2007) Acta > Cryst. A63, 257--265. > > Marc > > > But your reasoning was sound as far as it went, and it is a point which > > many people haven't recognised! > > > > Kevin > > > > > > Raja Dey wrote: > > > >> Dear James, > >> > >> I don't understand why measuring anomalous differences has nothing to > do > >> with resolution. > >> > >> Heavy atoms > >> > >> scatter anomalously because the inner shell electrons > >> > >> of the heavy atom cannot be considered to be free anymore > >> > >> as was assumed for normal Thomson scattering. As a result > >> > >> the atomic scattering factor of the heavy atom becomes > >> > >> complex and this compex contribution to the structure > >> > >> factor leads to non-equality of Friedel pairs in non-centro > >> > >> symmetric systems(excluding centric zone). This feature is taken > >> advantage in > >> > >> phase determination. Since the inner shell electrons > >> > >> being relatively more strongly bound in heavy atoms > >> > >> contribute to anomalous scattering and its effect > >> > >> is more discernable for high angle reflections . Here > >> > >> the anomalous component of the scattering do not > >> > >> decrease much because of the effectively small atomic > >> > >> radii (only inner shell being effective). FOR HIGH > >> > >> ANGLE REFLECTIONS ANOMALOUS DATA > >> > >> BECOMES IMPORTANT. > >> > >> Raja > >> > > > -- > Marc SCHILTZ http://lcr.epfl.ch 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
