Professor Sheldrick,

	My apologies for the wording of my statement about popular refinement 
programs, I regret I was not clear that I had only looked at some of the 
manuals for available programs that happen to also be popular :)
	Thank you for your reply to my question.  I'm glad that your response 
confirmed some of my understanding of the proper treatment of the data. 
  Indeed part of the reason for my questions was because I was concerned 
that my original intensities were overwritten with post-Truncate, scaled 
values.
	With regards to refining against amplitudes or intensities, I looked at 
section 2.4 in the SHELXL manual, but I'm still not sure when to choose 
refinement against amplitudes or refinement against intensities if you 
have the option of both.  Let me ask the question a different way. Are 
there particular programs, phasing/methods or stages of refinement that 
benefit from refining against intensities vs. amplitudes for programs 
that offer both options?

Thanks again,
-Andy Torelli

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
>> =============================================
>>
>>

-- 

=============================================
Andrew T. Torelli Ph.D.
Postdoctoral Associate
Laboratory of Steven E. Ealick
Department of Chemistry and Chemical Biology
Cornell University
=============================================