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
=============================================
