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Xscale: Difference between revisions
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== Simple and advanced usage == | == Simple and advanced usage == | ||
[http:// | [http://xds.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_parameters.html XSCALE] is the stand-alone scaling program of the XDS suite. It scales reflection files (typically called XDS_ASCII.HKL) produced by XDS. Since the CORRECT step of XDS ''already scales'' an individual dataset, XSCALE is only ''needed'' if several datasets should be scaled relative to another. However, it does not deterioriate (over-fit) a dataset if it is "scaled again" in XSCALE, since the supporting points of the scalefactors are at the same positions in detector and batch space. | ||
One advantage of using XSCALE for a single dataset is that the user can specify the limits of the resolution shells. Another is that zero-dose extrapolation can be done. | One advantage of using XSCALE for a single dataset is that the user can specify the number and limits of the resolution shells. Another is that zero-dose extrapolation can be done. | ||
At the XDS website, there is a short and a long commented example of [http:// | At the XDS website, there is a short and a long commented example of [http://xds.mpimf-heidelberg.mpg.de/html_doc/INPUT_templates/XSCALE.INP XSCALE.INP] | ||
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FRIEDEL'S_LAW=FALSE | FRIEDEL'S_LAW=FALSE | ||
STRICT_ABSORPTION_CORRECTION=TRUE ! see XDSwiki:Tips_and_Tricks | STRICT_ABSORPTION_CORRECTION=TRUE ! see XDSwiki:Tips_and_Tricks | ||
INPUT_FILE= ../fae-rh/xds_2/XDS_ASCII.HKL | ! the star in front of the file name indicates that it is the reference wrt falloff | ||
INPUT_FILE= *../fae-rh/xds_2/XDS_ASCII.HKL | |||
FRIEDEL'S_LAW=FALSE | FRIEDEL'S_LAW=FALSE | ||
STRICT_ABSORPTION_CORRECTION=TRUE | STRICT_ABSORPTION_CORRECTION=TRUE | ||
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== Further keywords == | == Further keywords == | ||
* RESOLUTION_SHELLS= ! for the printout of R-factors, completeness, ... | * [http://xds.mpimf-heidelberg.mpg.de/html_doc/xscale_parameters.html#RESOLUTION_SHELLS= RESOLUTION_SHELLS=] ! for the printout of R-factors, completeness, ... | ||
* SPACE_GROUP_NUMBER= ! if not given, picked up from first input reflection file | * SPACE_GROUP_NUMBER= ! if not given, picked up from first input reflection file | ||
* UNIT_CELL_CONSTANTS= ! if not given, picked up from first input reflection file | * UNIT_CELL_CONSTANTS= ! if not given, picked up from first input reflection file | ||
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* DOSE_RATE= ! (optional for radiation damage correction f.i.r.) | * DOSE_RATE= ! (optional for radiation damage correction f.i.r.) | ||
* 0-DOSE_SIGNIFICANCE_LEVEL= ! (optional for radiation damage correction f.i.r.) | * 0-DOSE_SIGNIFICANCE_LEVEL= ! (optional for radiation damage correction f.i.r.) | ||
* SAVE_CORRECTION_IMAGES= ! Default is TRUE. If FALSE, don't write DECAY*.cbf MODPIX*.cbf ABSORP*.cbf | |||
== Radiation damage correction == | == Radiation damage correction == | ||
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Another example: by defining STARTING_DOSE=-78.* one would tell the program to calculate, by interpolation, those intensity values that correspond to those that would be obtained near frame 78. | Another example: by defining STARTING_DOSE=-78.* one would tell the program to calculate, by interpolation, those intensity values that correspond to those that would be obtained near frame 78. | ||
== Scaling many datasets == | |||
When scaling e.g. hundreds of partial datasets, XSCALE may finish with an error message !!! ERROR !!! INSUFFICIENT NUMBER OF COMMON STRONG REFLECTIONS . This usually indicates that one or more datasets have too few reflections. Please inspect the table | |||
XSCALE may finish with an error message !!! ERROR !!! INSUFFICIENT NUMBER OF COMMON STRONG REFLECTIONS . This usually indicates that one or more datasets have too few reflections. Please inspect the table | |||
<nowiki> | <nowiki> | ||
DATA MEAN REFLECTIONS INPUT FILE NAME | DATA MEAN REFLECTIONS INPUT FILE NAME | ||
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and check the column "ACCEPTED REFLECTIONS". Then remove the dataset(s) with fewest accepted reflections, and re-run the program. Repeat if necessary. | and check the column "ACCEPTED REFLECTIONS". Then remove the dataset(s) with fewest accepted reflections, and re-run the program. Repeat if necessary. | ||
XSCALE may also finish with the error message !!! ERROR !!! INACCURATE SCALING FACTORS. This usually indicates that one or more datasets are linearly depending on others (this happens if the ''same'' data are included more than once as INPUT_FILE), or are pure noise. | The latest XSCALE (March 1, 2015) makes it explicit which dataset(s) it cannot scale; it prints out e.g. "no common reflections with data set 197". If you get this message for many datasets, I suggest to have a line | ||
MINIMUM_I/SIGMA=2 ! reduce to 1, or 0.5, or 0.25, or 0.125, or ... to lower the cutoff | |||
after each INPUT_FILE= line, to increase the number of reflections available for scaling. However, MINIMUM_I/SIGMA= should not be decreased needlessly below its default of 3. | |||
Old versions of XSCALE may also finish with the error message !!! ERROR !!! INACCURATE SCALING FACTORS. This usually indicates that one or more datasets are linearly depending on others (this happens if the ''same'' data are included more than once as INPUT_FILE), or are pure noise. The latest version of XSCALE (March 1, 2015) copes much better with this situation; I have not seen this error message any more. | |||