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Scaling options

autoPROC Documentation : Scaling options

Copyright    © 2015 by Global Phasing Limited
 
  All rights reserved.
 
  This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL.
Documentation    (2015)  Clemens Vonrhein, Claus Flensburg, Wlodek Paciorek & Gérard Bricogne
 
Contact proc-develop@GlobalPhasing.com


Contents


Introduction

The correct path for scaling single or multiple sweep datasets both internally as well as relative to each other (before merging the related measurements), is an area of active investigation. The best mode will depend on one or several factors:

Current default scaling mode

Each sweep is first scaled internally using the CORRECT module of XDS, producing an XDS_ASCII.HKL file of intensities. This includes all default CORRECTIONS: At this point, error estimates are adjusted, outliers (misfits) are identified and polarisation correction is applied. The resulting XDS_ASCII.HKL file for this single sweep is then scaled in AIMLESS using a smoothly varying scale factor and scaling B-factor as well as a tightly restrained (to being spherical) absorption correction. Error estimates are adjusted using SdFac and SdAdd as described in the AIMLESS manual. This results in a series of files
FileExplanation
aimless_unmerged.mtz internally scaled but unmerged intensities (a multi-record MTZ file)
aimless.mtz internally scaled and merged intensities (MTZ format)
aimless.sca internally scaled and merged intensities (Scalepack format)
The aimless.mtz file is then used to compute amplitudes and anomalous differences (plus their respective sigmas) with TRUNCATE:
FileExplanation
truncate.mtz amplitudes, anomalous differences and intensities
truncate-unique.mtz same as truncate.mtz, but including a test-set flag (if a reference MTZ file was given, those test-set flags are used and complemented if necessary)
When processing multiple sweeps within autoPROC, the separate XDS_ASCII.HKL files are combined into a multi-record MTZ file (using the combine_files tool) and then passed to AIMLESS via the aP_scale module. Here the same scaling model as above (smoothly varying scale and scaling B-factor plus restrained absorption correction) is applied, with the following characteristics: The output files will consist of
FileExplanation
aimless_unmerged_<wvl>.mtz internally and externally scaled but unmerged intensities (a multi-record MTZ file)
aimless_<wvl>.mtz internally and externally scaled and merged intensities (MTZ format)
aimless_<wvl>.sca internally and externally scaled and merged intensities (Scalepack format)
truncate_<wvl>.mtz amplitudes, anomalous differences and intensities (based on aimless_<wvl>.mtz)
truncate_<wvl>-unique.mtz same as truncate.mtz, but including a test-set flag (if a reference MTZ file was given, those test-set flags are used and complemented if necessary)

AIMLESS-only scaling path

By running "process" with the ScalingA3 macro as
process -M ScalingA3 ...
a pure AIMLESS path is provided with autoPROC. The difference to the above is that instead of using the XDS_ASCII.HKL file(s) from CORRECT, this uses the INTEGRATE.HKL file(s) directly after integration within INTEGRATE. The conversion of those reflection files into MTZ format (for use in AIMLESS via our aP_scale scaling module) is done with POINTLESS, using the correct polarisation value and description.

Those datasets for each sweep are then used in the same way as the default path described above - both for each sweep on its own as well as for the multi-sweep situation.


XDS/XSCALE-only scaling path

As an alternative to using AIMLESS as the final scaling program (either in the default/combined mode or the AIMLESS-only path), an XSCALE-only path is provided. This circumvents the use of AIMLESS completely and use only programs from the XDS package for scaling, outlier identification and error estimate adjustment. It can be activated using the ScalingX macro with
process -M ScalingX ...

Each sweep of data will be handled by the CORRECT module of XDS including all CORRECTIONS, outlier rejection and error estimate adjustment. If only a single sweep is processed by autoPROC, this internally scaled but unmerged data (XDS_ASCII.HKL) is first merged into intensities using XDSCONV and then converted into amplitudes using TRUNCATE. Therefore, the relevant output files are

If dealing with multi-sweep datasets, the various XDS_ASCII.HKL files are given to the scaling program XSCALE via our aP_scale module. All sweep datasets that are to be merged together (e.g. because they belong to the same wavelength) will be grouped under the same OUTPUT_FILE. This means that each sweep dataset within such a group "sees" data from the other sweeps of this group - while sweep datasets between groups only see each other prior to the computation of the correction factors (absorption, modulation and decay).

Common features

The above scaling modes share some common design and many common features:
Last modification: 10.06.2015