Eleanor,
Any ideas if the 0.01 in truncate is just being used as "arbitrary small
number to prevent overflow", or if it's serving another purpose? I
wasn't sure from reading truncate.f.
Thanks,
Pete
Eleanor Dodson wrote:
> Truncate doesnt "truncate" intensities or modify them in any way except
> to apply a guesstimate of the absolute likely scale based on the no of
> residues in the asymmetric unit. Truncation is only applied to the
> amplitudes for negative or very weak intensities. Obv. you cant take the
> square root of a negative number so this procedure keeps a (small)
> bvalue for the amplitude, which is better than discarding it. weak
> amplitudes/intensities provide useful information for refinement
> programs as well as strong ones
>
> If you have input I(+) and I(-) then Imean is the weighted average of
> these two, but you also retain I(+) and I(-) if you want to use these
> for later calculations
>
> Eleanor
>
>
> George M. Sheldrick wrote:
>> Well, I suppose that it doesn't qualify as a "popular refinement program"
>> but section 2.4 of the SHELX manual discusses the question of refinement
>> against amplitudes or intensities. If you are refining against
>> intesities,
>> there is no need to "truncate" the data, indeed it would be definitely
>> counter-productive to use TRUNCATE to convert I and sig(I) to F and
>> sig(F)
>> and then to convert these back to I and sig(I). For SHELXL it is also
>> not necessary to scale the data so that they are on an absolute scale.
>> I personally believe in refining against the data you actually measured
>> without compromising them in any way, but I appreciate that I am in a
>> small minority.
>>
>> 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, 7 Nov 2008, Andy Torelli wrote:
>>
>>
>>> To the CCP4 community,
>>>
>>> I have a question about ImportScaled. When I select both the "Keep
>>> the input intensities in the output file" and the "Run Truncate..."
>>> options,
>>> the output MTZ file contains IMEAN and SIGIMEAN values that are
>>> different from
>>> the input intensity file. Specifically, the values are multiplied by
>>> 1/100th
>>> of the SCALE term reported in the log file that is calculated from
>>> the Wilson
>>> Plot during the Truncate procedure. However, when the "Run Truncate..."
>>> option is not selected, the output MTZ file contains unaltered IMEAN and
>>> SIGIMEAN values that match the input file.
>>>
>>> After reading the recent CCP4 threads regarding Truncate as well as
>>> the program documentation, I still have a few questions:
>>>
>>> 1. My understanding is that this scaling of the intensities is done
>>> to bring
>>> them to an (approximate) absolute scale and therefore can only be
>>> performed
>>> when Truncate is run simultaneously (because the Wilson Plot is
>>> necessary to
>>> calculate the appropriate scale factor). However, why is the scaling
>>> equal to
>>> 1/100 of the SCALE term from the Wilson Plot (i.e. why not exactly
>>> the SCALE
>>> term)?
>>>
>>> 2. For programs that use intensities as a target for refinement, is it
>>> necessary to have the intensities scaled in this way or is it also
>>> valid to
>>> use the unaltered (scaled only) intensities?
>>>
>>> 3. On a related note, when is it best to refine against intensities vs.
>>> amplitudes? I have not been able to find recent literature that
>>> pertains to
>>> macromolecular crystallography and the documentation I've looked at for
>>> popular refinement programs that offer both targets do not provide
>>> guidelines
>>> as far as I can tell. If anyone could recommend some literature, I
>>> would
>>> really appreciate it.
>>>
>>> Thank you very much for your time,
>>> Best Regards,
>>> -Andy Torelli
>>>
>>> --
>>>
>>> =============================================
>>> Andrew T. Torelli Ph.D.
>>> Postdoctoral Associate
>>> Department of Chemistry and Chemical Biology
>>> Cornell University
>>> =============================================
>>>
>>>
>>>
>>
>>
>>
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