I think it is just chosen to keep the numerical range reasonable, and to
be easy to remember..
There is no signifance in any scale at the truncate stage - it will only
be properly given when the model is refined..
Eleanor
Pete Meyer wrote:
> 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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