Ian Tickle wrote:
> 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,
I think that I stated that I agree with him ?
> 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.
I don't invoke it as an explanation. I simply commented on the
(first-order) independence of Bijvoet or Friedel (anomalous) intensity
ratios with respect to atomic displacement parameters. Such Bijvoet
ratios (e.g. RMS(Delta_ano)/mean(I) or the same variant with F's) are
widely advocated in the methodological SAD/MAD literature as estimates
for gauging the theoretical signal strength of anomalous scattering. Of
course we can debate over the relevance of such theoretical estimates
for practical purposes, but I really just wanted to point out that these
ratios are (to first order) independent of atomic displacements.
> The reason is that
> the anomalous phasing power doesn't depend on Rano = <|delta-ano|>/<I>,
>
I agree. R_{ano} was brought up earlier in this thread, so I just
commented on this. Personally, I also have found over the years that
R_{ano} is not a particularly useful indicator for assessing the
feasibility of SAD or MAD phasing.
I trust that the discussion of what is a good indicator would offer
enough material for another thread.
Cheers
Marc
> 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: [log in to unmask] [mailto:[log in to unmask]]
>>
> On
>
>> Behalf Of Marc SCHILTZ
>> Sent: 13 May 2009 11:26
>> To: Kevin Cowtan; [log in to unmask]
>> 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
>>
>
>
>
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--
Marc SCHILTZ http://lcr.epfl.ch
