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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