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