Since the 20160706 snapshot release, autoPROC will run STARANISO automatically (if possible) and present the results in the graphical HTML summary.

It will also provide a file aimless_alldata.mtz (or similarly named in case of multi-wavelength data) containing merged and scaled data without any resolution cutoff having been applied. This file can be uploaded and used with the STARANISO server.


Data processing, scaling and merging can produce a large number of reflection files - which can be confusing to a user. Here we are going to describe the different files produced by autoPROC (using the AIMLESS or XSCALE scaling path) - but other processing packages, pipelines or systems will create similar output, especially if using XDS as well.

Let's first look at a single sweep data processing:

Scaling path File Description Remark Useful as input to the STARANISO server?
all INTEGRATE.HKL unmerged and unscaled intensities data for unpolarised beam (so a conversion to MTZ via POINTLESS needs to take this into account); error/variance model has not been adjusted possibly (since the unmerged protocol will convert this file to a multi-record MTZ file using POINTLESS before giving it to the aP_scale module from autoPROC)
all XDS_ASCII.HKL unmerged (and scaled) intensities polarisation correction has been applied and error/variance model is adjusted; scaling and outlier rejection has been applied (depending e.g. on the choice of correction factors) yes
AIMLESS XDS_ASCII.mtz unmerged (and scaled) intensities multi-record MTZ version of XDS_ASCII.HKL (via pointless -copy xdsin XDS_ASCII.HKL hklout XDS_ASCII.mtz) yes
AIMLESS aimless_alldata_unmerged.mtz unmerged and scaled intensities, no resolution cut scale factors, absorption correction and error model adjustments determined for the isotropically significant resolution range applied to all measurements yes (if the server is being told to not re-run the aP_scale step)
XSCALE xscale_alldata.ahkl unmerged and scaled intensities, no resolution cut result from first XSCALE step yes (if the server is being told to not re-run the aP_scale step)
XSCALE xscale_alldata_unmerged.mtz unmerged and scaled intensities, no resolution cut multi-record MTZ version of xscale_alldata.ahkl yes (if the server is being told to not re-run the aP_scale step)
AIMLESS aimless_alldata.mtz merged and scaled intensities, no resolution cut merged version of aimless_alldata_unmerged.mtz yes
XSCALE xscale_alldata.mtz merged and scaled intensities, no resolution cut merged version of xscale_alldata.ahkl yes
AIMLESS aimless_unmerged.mtz unmerged and scaled intensities, isotropic resolution cut data up to the isotropic significant resolution range, i.e. this is the data the scale parameters used in AIMLESS are determined from no
AIMLESS aimless.mtz merged and scaled intensities, isotropic resolution cut merged version of aimless_unmerged.mtz no
all truncate.mtz merged and scaled intensities plus amplitudes, isotropic resolution cut result from running aimless.mtz through TRUNCATE no
all truncate-unique.mtz merged and scaled intensities plus amplitudes, isotropic resolution cut, complete data to highest resolution contains all reflections up to the highest resolution observation as well as a test-set flag no
all staraniso_alldata.mtz merged and scaled intensities plus amplitudes, anisotropic resolution cut result from running aimless_alldata.mtz through STARANISO no
all staraniso_alldata-unique.mtz merged and scaled intensities plus amplitudes, anisotropic resolution cut, complete data to highest resolution contains all reflections up to the highest resolution observation as well as a test-set flag no

Additional remarks:

  • Files named *-unique.mtz contain a test-set flag that might be random or based on a reference set provided by the user running autoPROC (in the form of a MTZ file containing amplitudes and test-set flags). In the latter case autoPROC ensures that its output reflection files from the scaling step (i.e. all files from the AIMLESS or XSCALE scaling path, including files from STARANISO and TRUNCATE) are (a) consistently indexed - if the SG allows for alternatives - relative to the reference reflection data and (b) the test set flags are transfered and complemented/restricted as required.
  • If no reference reflection data was given to a run of autoPROC, one can use the check_indexing and add_freerflag.sh tools to (a) ensure consistent indexing and (b) transfer existing test-set flags over.
  • Please note that the use of e.g. unique (provided by CCP4) will generate reflection records in a sphere up to the highest observation (limited tot the asymmetric unit of the SG). This might have unintended consequences when using anisotropically processed data from STARANISO with programs that fill in missing data e.g. with D*Fc values by default (like REFMAC - see here for a way to change that behaviour).