You're right. The smoothed <I> is used for the Truncate procedure,
though it is difficult in the very low resolution bins. Also it
doesn't allow for pseudo-translations, which it should.
As you say, the linear fit is only used to put data on a very rough
absolute scale. This isn't necessary, but it doesn't hurt
There's no reason why truncate shouldn't give a "best" estimate of |F|
^2 but I'm not sure why you would want this. I would think that
refinement is better done against the measured I, which may be
slightly negative
Phil
On 24 Aug 2008, at 19:23, Ian Tickle wrote:
>
> Phil
>
> OK I admit I didn't delve very deeply into the code, but looking at
> the
> printer output it obviously does do a linear fit to the Wilson plot to
> get an overall B & scale. However, looking at the man page (if all
> else
> fails read the documentation!) I see that it does say that this is
> only
> used to put the data on an approximately absolute scale. This is
> unnecessary of course - absolutely scaled data isn't needed for HA
> phasing & MR, and the refinement will give a much more accurate scale
> factor anyway.
>
> Thanks for the info.
>
> Cheers
>
> -- Ian
>
>> -----Original Message-----
>> From: [log in to unmask]
>> [mailto:[log in to unmask]] On Behalf Of Phil Evans
>> Sent: 23 August 2008 08:09
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] Wilson plot from truncated.mtz
>>
>> Actually Truncate (& ctruncate) do use a smoothed <I> in resolution
>> shell (using a spline fit), not a linear Wilson plot
>>
>> Phil
>>
>>
>>
>> On 22 Aug 2008, at 20:30, Ian Tickle wrote:
>>
>>> This indeed raises the question of whether the assumed Wilson
>>> distribution is valid, and it's another point I was in fact going to
>>> bring up. As presently constructed, Truncate fits a
>> straight line to
>>> the Wilson plot (based on Imeas) in order to determine the overall
>>> scale
>>> & B, but to avoid the problem that the low res data for a typical
>>> protein deviates markedly from the theoretical distribution, it uses
>>> resolution limits determined by the RSCALE option.
>> According to the
>>> man
>>> page, the low resolution limit is by default set to 4 Ang
>> if the high
>>> res limit is higher than 3.5 Ang. This usually means that the
>>> straight
>>> line fit is good for the high res data, but very poor for
>> the low res
>>> data, but at least this means that the assumed distribution
>> is valid
>>> at
>>> high res where most of the weak data (i.e. the data most
>> affected by
>>> the
>>> Bayes correction) is located, but not valid for any weak
>> data at low
>>> res
>>> (there will obviously be some). As you point out translational NCS
>>> invalidates these assumptions since the form of the distribution
>>> changes, but then probably only a few % of structures
>> suffer from this
>>> type of NCS.
>>>
>>> A better way to deal with this would surely be to forget about the
>>> Wilson plot and simply determine the average I in resolution shells,
>>> with perhaps spline interpolation between the bin means (this is
>>> actually the 'k-curve' method for determining E's, attributed
>>> originally
>>> to Karle & Hauptman I believe). There would still be an
>> assumption of
>>> the Wilson distribution but now only within the bins, i.e.
>> the Wilson
>>> distribution parameter would vary with resolution, when
>> previously it
>>> was a single number independent of resolution. I think
>> this would go
>>> some way towards addressing your objections.
>>>
>>> In fact my prog ECALC already uses the k-curve method to
>> determine E's
>>> and it would probably not be too much work to have it
>> optionally read
>>> the IMEAN column, perform the Bayes probability integrals and output
>>> both <F> and <F^2> (also <E> & <E^2> as now). However I've no idea
>>> whether my iteration idea for re-using the <F^2> values for the k-
>>> curve
>>> will work - it may well diverge!
>>>
>>> Cheers
>>>
>>> -- Ian
>>>
>>>> -----Original Message-----
>>>> From: [log in to unmask]
>>>> [mailto:[log in to unmask]] On Behalf Of George
>> M. Sheldrick
>>>> Sent: 22 August 2008 18:57
>>>> To: [log in to unmask]
>>>> Subject: Re: [ccp4bb] Wilson plot from truncated.mtz
>>>>
>>>> In addition to Ian's circular argument, there is the problem that
>>>> the assumed distribution is only approximately valid, indeed in the
>>>> presence of (translational) NCS it could well be a poor
>>>> approximation.
>>>> Refinement against suitably weighted measured intensities
>>>> (which may of
>>>> course be slightly negative because of experimental errors)
>>>> avoids this
>>>> problem but we still need F(obs) (and hence TRUNCATE) to
>>>> calculate a map.
>>>>
>>>> George
>>>>
>>>> Prof. George M. Sheldrick FRS
>>>> Dept. Structural Chemistry,
>>>> University of Goettingen,
>>>> Tammannstr. 4,
>>>> D37077 Goettingen, Germany
>>>> Tel. +49-551-39-3021 or -3068
>>>> Fax. +49-551-39-22582
>>>>
>>>>
>>>> On Fri, 22 Aug 2008, Ian Tickle wrote:
>>>>
>>>>> This goes back to the issue I was raising, namely that
>>>> <F>^2 (from the
>>>>> Truncate output mtz F column) is not the same as Imeas
>> (in the IMEAN
>>>>> column) so you won't get exactly the same results from the
>>>> Wilson plot,
>>>>> particularly at high res where the average I/sigma is low.
>>>> Since the
>>>>> plot actually demands F^2 then it seems to me that
>>>> logically you need to
>>>>> use <F^2> which AFAICS is not possible using Truncate
>> since it never
>>>>> calculates that.
>>>>>
>>>>> This gets you into a circular argument because you need
>> the correct
>>>>> Wilson plot results in order to perform the Bayes
>> correction to the
>>>>> intensities (i.e. it gives you the prior distribution parameter),
>>>>> however you need the Bayes-corrected intensities to
>>>> correctly calculate
>>>>> the Wilson plot! Possibly iterating (from the initial Wilson plot
>>>>> results calculated using Imeas) will sort this out.
>>>>>
>>>>> Also referring to an earlier response by Phil, Truncate
>>>> clearly outputs
>>>>> the scaled Imeas, not <F^2>, in the IMEAN column as I had
>> originally
>>>>> assumed, since the column has a -ve min value from mtzdump
>>>> (<F^2> can
>>>>> never be < 0), and logically it's <F^2> not Imeas or <F>
>>>> that you need
>>>>> for applications (such as MR and F^2 based refinement)
>>>> which demand F^2.
>>>>>
>>>>> Cheers
>>>>>
>>>>> -- Ian
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: [log in to unmask]
>>>>>> [mailto:[log in to unmask]] On Behalf Of Eleanor Dodson
>>>>>> Sent: 22 August 2008 14:16
>>>>>> To: [log in to unmask]
>>>>>> Cc: [log in to unmask]; [log in to unmask]
>>>>>> Subject: Re: Wilson plot from truncated.mtz
>>>>>>
>>>>>> rerun truncate with input amplitudes..
>>>>>> eleanor
>>>>>>
>>>>>> James Pauff wrote:
>>>>>>> If I've lost my SCALA MTZ, and have only the truncated.mtz
>>>>>> for my dataset, which program is the quickest means of
>>>>>> obtaining a Wilson plot?
>>>>>>>
>>>>>>> Thank you again,
>>>>>>> Jim
>>>>>>>
>>>>>>>
>>>>>>> --- On Wed, 8/20/08, Eleanor Dodson
>>>> <[log in to unmask]> wrote:
>>>>>>>
>>>>>>>
>>>>>>>> From: Eleanor Dodson <[log in to unmask]>
>>>>>>>> Subject: Re: [ccp4bb] Lower completeness, decent R
>>>>>> factors, but low B factor...
>>>>>>>> To: [log in to unmask]
>>>>>>>> Date: Wednesday, August 20, 2008, 4:30 AM
>>>>>>>> James Pauff wrote:
>>>>>>>>
>>>>>>>>> Hello all,
>>>>>>>>>
>>>>>>>>> I have a refined structure at 2.6 angstroms that at
>>>>>>>>>
>>>>>>>> about 73% completeness at this resolution. The I/sigma is
>>>>>>>> about 2.0 at 2.6 angstroms, and the omit density for my
>>>>>>>> ligands is great contoured at 3.0sigma. My Rcryst is 19 or
>>>>>>>> so and the Rfree is 24.5 or so.
>>>>>>>>
>>>>>>>>> HOWEVER, my mean B value is 13.9, whereas my other 2
>>>>>>>>>
>>>>>>>> structures (at 2.2 and 2.3 angstroms, same protein, >95%
>>>>>>>> completeness) have mean B values of 22+. Any suggestions as
>>>>>>>> to what is going on here? I'm having trouble explaining
>>>>>>>> this.
>>>>>>>>
>>>>>>>>> Thank you,
>>>>>>>>> Jim
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> Have you used TLS - listed B factors will then be given
>>>>>>>> relative to the
>>>>>>>> TLS parameters. You need to run tLSANL to get a more
>>>>>>>> realistic value.
>>>>>>>> Eleanor
>>>>>>>>
>>>>>>>>
>>>>>>>> But in fact temperature factors are rather harder to
>>>>>>>> estimate at lower
>>>>>>>> resolutions than higher. Look at your <Fo> and
>>>>>>>> <Fc> curves v resolution
>>>>>>>> ( part of a REFMAC loggraph) and you can see that sometimes
>>>>>>>> the overall
>>>>>>>> scaling struggles to get a reasonable fit..
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
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> messaging traffic in compliance with its corporate email policy. The
> Company accepts no liability or responsibility for any onward
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> Therapeutics domain. Unless expressly stated, opinions in this
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