###################################################################
#
# This is the May 08 2017 snapshot release of the autoPROC toolbox for
# academic users.
#
###################################################################
#
# Copyright  (C) 2005-2017 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.
#
# Authors:   G. Bricogne, C. Flensburg, P. Keller, W. Paciorek,
#            A. Sharff, O. Smart, C. Vonrhein, T. Womack
#
# Reference: C. Vonrhein, C. Flensburg, P. Keller, A. Sharff,
#            O. Smart, W. Paciorek, T. Womack & G. Bricogne
#            (2011). Data processing and analysis with the autoPROC
#            toolbox. Acta Crystallogr D 67, 293-302.
#
###################################################################

===================================================================
 Changes since the last autoPROC stable release        May 08 2017
===================================================================

* New features, fixes and improvements (released May 08 2017):


* New features, fixes and improvements (released May 05 2017):

 * Create a file with REMARK 200 content related to the STARANISO MTZ
   file produced by the AIMLESS scaling path, to have an exact
   parallel to REMARK 200 file associated to the TRUNCATE MTZ file.

 * Give "table-1" like summary for each output MTZ file at end of
   autoPROC run (bothin in stdout and summary.html as well as a file
   with ending "*.table1"): this should make it clearer what
   statistics are relevant for which MTZ file.

 * Avoid writing empty shell information in MRFANA analysis when those
   shells are bordering high-resolution limit.

 * Added support for ALS 4.2.2 detector RDI1 (CMOS_8M).

 * Support in 'imginfo' and 'GPX2' for intermediate CBF files from
   Eiger data (i.e. only those CBF files are available, although they
   were generated by a tool intended for on-the-fly conversion as
   apart of XDS processing).

 * Take care of correct permissions during installation (especially
   for Ruby installation).

 * Some clarifications in output from aP_check (oe 'process
   -checkdeps').

 * Added tool 'xparm_transform' totransform XPARM.XDS files so that
   either the rotation axis is along a lab frame axis and/or the
   detector X-axis is.

 * Added tools 'ana_cmpmat', 'aP_rotcal' and 'aP_wf_rotcal' to
   distribution: mainly useful for rotational calibration work.

 * For cases where image headers are not recording the exact settings
   of goniostat angles (Omega, Kappa/Chi, Phi), allow override via
   goniostat_{Omega,Kappa,Chi,Phi}_{axis,angle}_<ID> parameters.

 * Simplified option to use all recorded images for background
   estimation (e.g. when shadowing needs to be taken into account as
   well): setting XdsNumImagesBackgroundRange to "All" will do that.

 * Update to support latest Diamond/I23 instrument (Kappa goniostat).

 * Improved generation of STARANISO plots (reciprocal planes) with
   better legend and represenation of reciprocal cell.

 * Support for writing STARANISO-related information (analysis of
   anisotropy) as well into XML file(s).

 * Update to support latest CCP4 (version/update 7.0.036, AIMLESS
   0.5.32) and XDS (BUILT=20170215).

 * Added support for spherical/ellipsoidal statistics via MRFANA: the
   description of ellipsoid needs to be given via the '-ell'
   command-line argument.

 * Added option -L to 'find_images' tool to get arguments in form
   suitable for -Id flag of 'process' directly (reported by
   D. Reinert).

 * Added warning messages in case prediction pictures (via GPX2) could
   not be generated: this usually points to issues with headless
   cluster nodes. See also
   https://www.globalphasing.com/autoproc/wiki/index.cgi?FaqUsingGpx2OnHeadLessBox.

 * MRFANA now also computes the ellipsoidal completeness in resolution
   shells. This is the completeness within the ellipsoid fitted by
   STARANISO (to describe the anisotropy of diffraction within the
   data) for a given resolution range.

 * Some fixes to the computation of statistics within MRFANA that
   would have given small differences when comparing to other programs
   - mainly due to the inclusion of systematically absent reflections
   in those statistics and some inaccuracies when handling reflections
   at the border of resolution shells.

 * Fix when handling sparse (or very finely sliced) multi-sweep
   datasets: the unique renumbering of all datasets got confused when
   some images had no reflection centroids assigned to them.


* New features, fixes and improvements (released Dec 07 2016):

 * GPX2: automatically detect and load image files compressed with
   either gzip for bzip2. Also, for miniCBF files protect against
   missing value of Polarization.

 * Fix to the plot of misfits as function of detector position: now
   also has correct aspect ratio of detector dimensions.

 * Fixed documentation in $autoPROC_home/docs/autoproc/manual/appendix1.html
   of AutoProcScaleStatsUseMrfanaIgnoreIceRingShells (reported by
   J. Benach).

 * Fixed problem with processing compressed (.gz/.bz2) images when
   using a subset of images for background estimation.

 * Updated to support XDS Nov 1, 2016 (BUILT=20161101), pointless
   1.10.27, aimless 0.5.29 and CCP4 7.0.022.

 * Implemented workaround for problems in integrating weak data with
   XDS Nov 1, 2016 (BUILT=20161101): at least for Pilatus detectors
   setting GAIN=1 in XDS.INP seems to fix this. The problem manifests
   itself as a bias towards a non-zero intensity (we have seen values
   of +0.5 and -0.5) at high resolution when there really is no
   diffraction present. This has been reported to the XDS developers
   and the above workaround was suggested by K. Diederichs.

 * Added additional high resolution ice-ring values based on analysis
   of high-resolution datasets and comparing to [1]:

     1.524 - 1.519
     1.473 - 1.470
     1.444 - 1.440
     1.372 - 1.368
     1.367 - 1.363
     1.299 - 1.296
     1.275 - 1.274
     1.261 - 1.259
     1.224 - 1.222
     1.171 - 1.168
     1.124 - 1.122

   [1] Kumai, M. (1967). A study of hexagonal and cubic ice at low
       temperatures. Research Report 231, U.S. Army Materiel Command,
       Cold Regions Research & Engineering Laboratory, Hanover, NH.

 * Initial support for CBF files with imgCIF image headers (tested on
   Bruker Photon-II data; thanks to G. Bader, M. Benning and
   D. Reinert).


* New features, fixes and improvements (released Jul 08 2016):

 * Fixed problem with PDF-report generation when running single-sweep
   dataset without using the -d flag: it was stopping with an error
   message (and exit status) at the last step of an autoPROC job
   (reported by D. Reinert).

 * Introduced the new parameter autoPROC_CreateReportStopOnError
   (default="no") in order to not stop with an error if the PDF-report
   generation fails. Since this is a still a very new feature we don't
   want any problems to upset users automated pipelines (or our own
   Pipedream software).

 * Added (optional) auto-refresh function to the generated
   summary.html file that is active as long as it is still written to
   (suggested by P.Lukat). This feature can be activated by setting
   the parameter autoPROC_CreateSummaryUseJavaScriptAutoRefresh
   (refresh rate in seconds) to a value greater than 0.

* New features, fixes and improvements (released Jul 06 2016):

 * Change of defaults to

     AutoProcScale_RunStaraniso=yes
       => run STARANISO for each dataset

     autoPROC_CreateXml=yes
       => create ISPyB-compatible XML file for each merged dataset

     autoPROC_ScaleEarlyLateCreate=yes
       => create (if possible) amplitudes for F(early)-F(late)
          difference Fourier maps: these can then be computed
          automatically in BUSTER (setting parameter
          BusterEarlyLate=yes) to provide help in assessing the
          effects of radiation damage

 * First implementation of a PDF report generated for each merged
   datasets: the layout and content is a first design - any comments
   are very much welcomed.

 * Added support to hdf2mini-cbf (converter of Eiger HDF5 datasets
   into mini-cbf) for automatic detection of 32- versus 16-bit images.

   It now also supports GZIP compression as available as part of the
   HDF5 library (see: https://www.hdfgroup.org/HDF5/faq/compression.html).

 * Added further support to HDF5 metadata reader (in "hdf2mini-cbf" as
   well as "imginfo") for

   * reading "units" attribute for data items to ensure they are
     consistent with expectations;

   * check that sensor_thickness as written in HDF5 metadata file
     (*_master.h5) makes sense: if a value >= 320 mm is encountered,
     it will be reset to 1/1000th of this value.

     This works around a bug in images from

       * Eiger 9M at APS 21-ID-D (as of 20160426)

       * Eiger 9M at Soleil Proxima2 (known to be present between
         20160131 to at least 20160415)

   * ensure that metadata arrays are read even if the apparent number
     of images and the number of items in those data arrays don't
     match.

     This works around an inconsistency found in images from

       * Eiger 9M at Soleil Proxima2 (20160415)

 * Added automatic analysis of statistics to give indication of likely
   high-resolution limit of anomalous signal. This should help users
   in getting an initial, rough estimate of anomalous signal.

   The parameter autoPROC_AnomalousSignal_AdjustAutomatically
   (default=yes) determines if subsequent stages of data processing
   should take a detected (or determined as being absent) anomalous
   signal into account. If the user runs with -ANO or -noANO
   command-line flags, that decision will always be used and no
   adaptation is done.

 * "imginfo" will now write rotation values (angles) with greater
   precision - required e.g. for extremely fine-sliced Eiger datasets.

 * Ensure also '<' and '>' characters render correctly in
   summary.html.

 * Newer AIMLESS versions (0.5.24 and later) have a changed default
   for the SDCORRECTION card (SAME instead of INDIVIDUAL) that
   requires a switch in logic for our aP_scale scaling module.

 * A table of statistics against resolution (in 20 bins, can be
   changed via the  AutoProcScaleStatsUseMrfanaFinalNumBin parameter)
   is now also given for the AIMLESS scaling steps.

 * Added support for 'May 1, 2016' version of XDS. Please be aware
   that official XDS binaries after 20151015 up to 20160514 are known
   to show an issue in indexing (IDXREF): indexing might fail or
   produce incorrect solutions in a seemingly random way without any
   obvious reason. An updated/fixed binary (for academic users) has
   been provided by the XDS developers as of 20160517.

   If you can't update to this fixed binary, this problem can
   sometimes be averted by giving a slightly different direct beam
   position (changed by very small values - like 0.1 pixel).

 * Started adding links to autoPROC manual directly from the
   summary.html file (more will follow).

 * To avoid too much information (especially for multi-sweep
   datasets), a hide/show feature has been added to summary.html: this
   means some plots are initially hidden and can be show through
   simple clicks on a green "+" icon.

 * Plots for scaling statistics (Rmerge, completeness etc) are now
   placed after the relevant tables in summary.html.

 * Several fixes to the automatic high-resolution limit estimation via
   MRFANA: this should stabilise this feature in case of multi-sweep
   datasets.

 * Added new parameters to listing in Appendix 1 of manual
   (AutoProcScale_RunStaraniso AutoProcScale_RunStaranisoCards
   AutoProcScale_RunStaranisoHklPlotGrid AutoProcScale_RunStaranisoPqrPlotGrid
   AutoProcScale_RunStaranisoStopOnError RunIdxrefStopOnAnyError
   XdsSpotSearchNumImagesAngularRange XdsUpdateAlsoSegments).

 * Fixes to regression described at
   http://www.globalphasing.com/autoproc/wiki/index.cgi?IssuesPage201603#refinekwd.

 * Now should also work if reference MTZ file is in a directory
   without write permissions.

 * Removed out-of-date and unnecessary macros: XdsFast and
   HighRes2. The "automatic" macro is deprecated and will be removed
   in a future release.


* New features, fixes and improvements (released May 01 2016):

  * Added feature to run STARANISO directly as part of autoPROC:

    - STARANISO is a program developed by Ian Tickle at Global Phasing 
      to analyse the local mean I/sigI to then apply an anisotropic 
      cut-off and an anisotropy correction on merged intensity data.

    - This is currently only implemented for the AIMLESS scaling paths
      (i.e. the default behaviour or when running with the -M
      ScalingA3 macro) and can be activated with the

        AutoProcScale_RunStaraniso=yes

      command-line argument.

    - Data scaled in the normal way (but without applying the
      isotropic high-resolution limit determined) are given to
      STARANISO as input.

    - All analysis resulting from STARANISO is presented in the
      summary.html file, including plots showing the (potentially) 
      anisotropic nature of diffraction.

    - The reflection file after applying this anisotropic limit and 
      anisotropy correction can be used as an alternative to the 
      standard autoPROC output MTZ file for subsequent stages, 
      e.g. model refinement with BUSTER.

    - For more background information, details and examples please
      visit the STARANISO server at
      http://staraniso.globalphasing.org/.

  * fixed problem in extracting Rmerge for REMARK 200 section in
    remark200.pdb when using XSCALE path ("-M ScalingX" macro)

  * fixes to formatting of summary.html (to avoid overflow in menu
    area and correct Angstroem symbol in text)


===================================================================
 Changes included in autoPROC 1.0.4 stable             Mar 24 2016
===================================================================

* Fixes and improvements (released Mar 24 2016):

 * hdf2mini-cbf now also reports usage help when run without argument
   (reported by O. Svensson, ESRF).

 * Fixed note written by aP_convert_hdf5 regarding number of external
   link files found.

 * Added (currently) necessary imginfo wrappers for processing of
   Eiger/HDF5 datasets from following beamlines:

     Eiger 4M at ESRF, MASSIF-3
     Eiger 9M at APS 21-ID-D
     Eiger 9M at Soleil Proxima2
     Eiger 4M at Photon Factory BL1A

   For details and updates, please also check 

     http://www.globalphasing.com/autoproc/wiki/index.cgi?DataProcessingHdf5

 * A new parameter can be used to simplify masking of damaged or hot
   pixels (if those are not yet accommodated directly by the detector
   via an updated pixel-mask): autoPROC_Img2Xds_DamagedPixels can be
   set to a space-separated list of X,Y pairs a la

     process autoPROC_Img2Xds_DamagedPixels="1234,432 3210,2345" ...

   Note: pixel indexes start at (1,1) as shown by our GPX2
   viewer. Other viewers might show the first pixel as (0,0) and
   values read off those need to be adjusted by +1.


* Fixes and improvements (released Mar 04 2016):

 * Fixes to generation of XML file when running "process" without the
   -d command-line argument (reported by L. Muir, IMCA-CAT).

 * Avoid attempt to create prediction pictures when processing HDF5
   (Eiger/Dectris) datasets: GPX2 does not yet support reading HDF5
   format. This removes an irritating (and unnecessary) error message
   from standard output (reported by D. Reinert, BI).


* Fixes and improvements (released Mar 02 2016):

 * "process -checkdeps" was warning about "staraniso" not
   being present when it should have ignored this (thanks to
   K. Bataille from IMCA-CAT for pointing this out).

   There will probably be a feature in autoPROC to run STARANISO
   directly as part of processing, but for the moment the recommended
   usage of STARANISO is to use the web service at
   http://staraniso.globalphasnig.org/. For that purpose a script
   (aimless_alldata.sh) is automatically generated within the output
   directory that can be used to create a reflection MTZ file adequate
   for the web server.

 * Fixed messages from HDF5 converter script (aP_convert_hdf5).


* Fixes and improvements (released Feb 25 2016):

 * Added support for HDF5 datasets from Dectris/Eiger detector.

   * HDF5 datasets can be given to process via the new -h5
     command-line argument or as part of the existing -Id flag.

   * The tool "hdf2mini-cbf" is used for extracting separate image
     files out of the HDF5 container. It can do this for a single
     image (emulating the H5ToXds tool from Dectris) or for a series
     of images. The output CBF images contain a fully populated
     mini-cbf header and can also be written directly as compressed
     *.gz files. Conversion and writing is parallelised.

     Handling of HDF5 files written with the bitshuffle compression is
     supported on both Linux and OsX.

     A utility (aP_convert_hdf5) is provided for simple and fast
     (e.g. by submission to a cluster of workstations) data image
     extraction and conversion.

 * GPX2: emit help text when an unknown option is met.

 * Fixed regression (introduced in snapshot release 20151125)
   resulting in unnecessary runs of INTEGRATE and CORRECT steps at
   first XDS invocation.

 * Consolidated behaviour and resulting file names in summary HTML and
   XML files under different run conditions. These include running
   with or without a -d argument and - if a -d argument is given - if
   it is an absolute or relative path or points outside of the current
   directory. There could still be unresolved issues when it comes to
   working in auto-mounted filesystems or when using symbolic links -
   in which cases 'pwd' and 'pwd -P' might return different results.


* Fixes and improvements (released Dec 14 2015):

 * New feature to create early/late data values:

  * This is switched on by the new parameter
    autoPROC_ScaleEarlyLateCreate (default=no).

  * Currently this is only supported for AIMLESS scaling (default or
    ScalingA3 path) and single wavelength datasets.

  * The final MTZ file (truncate-unique.mtz etc) will contain F/SIGF
    columns with the extension "_early" and "_late".

  * For the definition of early and late datasets we use several
    points in the forward/backward completeness table. One point is of
    course the cross-over point, ie. where the two completeness curves
    cross over each other: we have to stay on either side of
    this. Optimal points for merging early/late images is then found
    by using the following parameters:

    * we want to have at least this completeness:
      autoPROC_EarlyLateCompletenessMin=0.85;

    * we stop once we reached that completeness:
      autoPROC_EarlyLateCompletenessMax=0.95;

    This means means we are now doing the early/late analysis a bit
    different to the first implementation in the previous snapshot
    release - where it was used only for marking the
    completeness-versus-batch plot.

    * the early/late border will not be shown if individual
      completeness is too low;

    * no need to divide all images into early/late if we can use much
      fewer images on either end with good completeness;

    Note: it is likely that the exact method for defining early/late
    datasets will change in future releases (additional criteria need
    to be considered).

 * Added support for RIGAKU/Eiger detectors via the new
   "RigakuEiger1M" macro.

 * Fixed regression: GPX2 was not packed up into the OSX tarball for
   the previous snapshot release.

 * Fixed generation of summary.html when job stops with an error
   message (reported by D. Reinert).

 * Improved writing of XML file:

   * new parameters autoPROC_CreateXml_ValTrue (default=1) and
     autoPROC_CreateXml_ValFalse (default=0) allow for different
     boolean types in local XML usage (True/1/true or False/0/false
     etc);

   * autoPROC.xml will be initialised with processingStatus False and
     only upon successful completion will we have True;

   * added support to inject externally defined XML elements via one of

       autoPROC_CreateXml_LocalElements="AutoProcContainer:AutoProcScalingContainer:AutoProcIntegrationContainer:Image:datasetID=12345"

     or (if value will contain spaces):

       autoPROC_CreateXml_LocalElements="AutoProcContainer:AutoProcScalingContainer:AutoProcIntegrationContainer:Image:datasetID"
       AutoProcContainer_AutoProcScalingContainer_AutoProcIntegrationContainer_Image_datasetID="12345"

 * Reworked feature to automatically select a subset of images for spot
   searching: the previous incarnation didn't really work. We now have

   * maximum number of images to use for spot-searching:
     XdsSpotSearchNumImages="999999";

   * the images used for spot searching should cover this angular
     range: XdsSpotSearchNumImagesAngularRange="360";

   * number of segments to use within XdsSpotSearchNumImagesAngularRange:
     XdsSpotSearchNumRanges="10";

   * only images within this angular range (from first image) are
     considered: XdsSpotSearchAngularRange="360";

   To use only a subset of images one could set

      XdsSpotSearchNumImagesAngularRange="10.0"
      XdsSpotSearchNumRanges=4
      XdsSpotSearchAngularRange=180

   CAVEAT: Please be aware that this might significantly hamper
           autoPROC's ability to detect multiple lattices and
           ice-rings (and take corrective measures). By using such
           settings the user might not become aware of serious
           problems with the dataset.

 * Allow the possibility to define pre-computed files (like
   {X,Y}-CORRECTIONS.cbf) to be reused even if they have an arbitrary
   filename.

 * Added new autoPROC_CreateGpxPicturesAtRotationAngles parameter
   (default="0 30 60 90") to define angles for GPX2/prediction pictures
   relative to first image.

 * Improved handling of reindexing requirement for multi-sweep
   datasets - when the SG symmetry allows this. This includes
   additional checks when running with or without a reference MTZ file
   and with EnsureConsistentIndexing=yes (default) or
   EnsureConsistentIndexing=no (non-default).

 * Corrections to handling of centro-symmetric spacegroups in MRFANA.

 * Ensure "xparm2simin" can be run stand-alone for multi-axis
   goniostats (as defined in our distributed
   $autoPROC_home/autoPROC/lib/kapparot.sites file)

 * The FRAME.cbf file written by COLSPOT is now saved as
   FRAME_COLSPOT.cbf: this can show some details about the
   spot-searching in XDS/COLSPOT.

 * Changed behaviour of aP_scale scaling module (invisible unless run
   explicitly with "aP_scale -id 0"):

   * by default output will have no prefix (before: "1_")

   * therefore there is no need to use "-id 0" in order to switch from
     "1_" to "" prefix. The value given with "-id" is now used as-is
     to generate "<id>_" prefix for all output files;


* Fixes and improvements (released Nov 25 2015):

 * Added support for writing of a HTML page (default = "summary.html"
   in the output directory) containing information about autoPROC
   run. This should simplify inspection of all the graphical output
   and plots produced.

   * it involves renaming some files or creating different file names
     (e.g. SPOT_never-indexed.XDS) in order to avoid the overwriting
     of files at different stages - which would confuse the HTML
     output;

   * a tarball is created (default = "summary.tar.gz" in the output
     directory) that will contain this HTML document as well as most
     files (plots etc) referenced therein;

 * Added support for XDS version "Oct 15, 2015", CCP4 6.5.018,
   POINTLESS 1.10.10 and AIMLESS 0.5.15.

 * Added support for the long-wavelength beamline I23 at the Diamond
   Light Source.

 * Added support for writing XML file(s):

   * triggered by command-line option "-xml";

   * standard file name "autoPROC.xml" (for single wavelength data) and
     "autoPROC_<lambda>.xml" for multi-wavelength data, all written
     into the output directory;

   * it follows (and expands slightly) the ISPyB examples as far as
     these are documented;

 * Changed default for GPX2 wrapper script (gpx.sh): after closing
   GPX2 the predictions will be removed. In order to keep them, the
   command-line argument "-keep" can be used.

 * Fixed bug in GPX2 wrapper script (gpx.sh): for very high-resolution
   and/or large unit cell datasets the prediction generation could
   have stop with a segmentation fault because the increase in
   stacksize limit was actually ignored.

 * Speedup generation of predictions with simcal_predict for large 
   structures by enlarging the size of hash-tables.

 * Made xds_spots2res work for curved detectors by using anaspot to 
   compute resolution of spots.

 * At the beginning of output the installation directory for autoPROC
   is now also shown.

 * Scaling module aP_scale:

   * new tool ana_mrfana gives more detailed plots as a function of
     resolution or image number (i.e. batch or dataset);

   * improved handling of data without anomalous data (-noANO flag to
     process or aP_scale): now also taken into account for XSCALE path
     and the potential conversion into *.sca files;

   * fix logic to avoid running MRFANA twice in all cases (even if not
     necessary);

 * Fixes in MRFANA regarding computations for centrosymmetric space
   groups which previously caused the printing of NaN.

 * A warning message will be displayed when using the MOSFLM path of
   autoPROC: this non-default option has not been developed or tested
   for quite some time and will be removed in one of the next
   releases.

 * The SPOT.XDS_orig file (original list of spots before doing any
   indexing) now doesn't contain any Miller indices - while SPOT.XDS
   will contain non-(0,0,0) indices for spots from the finally used
   indexing solution.

 * Added checks for consistent distance, wavelength, oscillation,
   2-theta, chi, kappa and rotation angle within a set of images
   making up a sweep.

 * Improved handling of multi-angle goniostat values when dealing with
   data from such instruments (and image headers that contain those
   settings).

 * When giving only the space group name/number to process: add
   extension to iterative indexing output files for the two cycles
   that need to be run in such cases.

 * Skip initial IDXREF step if we are doing iterative-indexing anyway.

 * Better phrasing when going into iterative indexing to describe
   accurately why this step is performed.

 * Added fully functional Gnuplot 4.6.5 to distribution to package:
   this is intended only for running from within autoPROC jobs. A user
   can still provide their own (e.g. OS-provided) binary by setting it
   explicitly on the command-line, e.g.

     process gnuplot=/where/ever/bin/gnuplot ...

 * Added new parameter autoPROC_XdsMaxDistanceJitterWarning
   (default=0.2) to give a warning if the distance refinement results
   in results outside this range (relative to the mean value).

   * the parameter autoPROC_XdsMaxDistanceJitter (default = 1.0) is
     used to automatically trigger fixing of detector position
     refinement if needed;

   * parameter refinement resulting in the crystal-detector distance
     changing by more than 0.2 mm seems too large compared to the
     typical size of a crystal (on most beamlines the crystal would
     move out of the beam if it represented physical reality);

   * large changes in distance during parameter refinement mostly
     point to problematic diffraction patterns or poor spot shapes;

 * Changed the LowResOrTricky macro so that an additional iterative
   indexing is done after processing each sweep: this can highlight
   the exact nature and relation of multiple lattices better since a
   set of refined parameters (for describing the experiment) is now
   available.

 * A new macro (HighResCutOnCChalf) is included to base automatic
   high-resolution limit decision making solely on CC(1/2) value of
   0.3.

 * A new macro (DiamondI04) for beamline I04 at Diamond is included.

 * At the start of processing (of each sweep/dataset) a short summary
   is given to show the information as read from the header of the
   first image.

 * Accommodate memory issues (either due to little physical memory or
   because of multiple jobs running simultaneously) when creating
   prediction pictures: give a warning message but don't make the full
   autoPROC job fail.


* Fixes and improvements (released Sep 23 2015):

 * Introduced new parameter autoPROC_PointlessTolerance (default =
   2.0): identical to parameter TOLERANCE as defined and used in
   POINTLESS. Increase this if the reference dataset is expected to
   deviate significantly from the dataset being processed.

 * Plots of misfits and spots now follow the usual image-viewing
   convention to be in sync with GPX2: origin is in top left corner.

 * Fix in GPX2-driving script (gpx.sh) regarding prediction file:
   ensuring it is removed after automatic picture generation and this
   removal is noticed when running the script interactively for manual
   inspection.

 * Better handling of inhouse (CuKa-wavelength) datasets when
   generating input to simcal_predict: if wavelength is between 1.5417
   and 1.5419 A the polarisation defaults to an unpolarized beam.

 * Several fixes in MRFANA to stabilise the automatic decision
   making about an adequate high-resolution limit. This includes the
   use of a Bezier curve as a basis for testing the various
   cutoff-criteria.

 * Additional fixes in MRFANA regarding computation of completeness
   (especially anomalous completeness).

 * Fixed regression from previous snapshot (internal function aP_pre
   not being defined).

* Fixes and improvements (released Aug 12 2015):

 * The computation of resolution within MRFANA has changed for MTZ
   files: instead of using the overall cell parameters the
   dataset-specific cell parameters are used now. This will have an
   effect on multi-sweep datasets, where each dataset comes with its
   own, slightly different set of cell parameters. It is then
   important to use the correct cell parameter for resolution
   computation in order to be consistent between stages (where we see
   only a single sweep or multiple sweeps simultaneously).

 * We now ensure that R-values in MRFANA (Rmerge, Rmeas and Rpim) are
   computed in the same way as in SCALA/AIMLESS. Please note that this
   is following the paper (Evans, P. (2006). Acta D62, 72-82), which
   is slightly different from others (Diederichs&Karplus/1997 and
   Weiss/1997) in the denominator. Additional information is given in
   the MRFANA output.

 * Added a table of statistics as a function of image/BATCH number in
   MRFANA.

 * Added more comments into various macro files to help user
   understanding the effect of each setting.

 * Fixed problem in analysis of iterative-indexing run (where failing
   IDXREF results were not excluded correctly and therefore sometime
   reported as a reference for the angle computation).

 * Fixed fetching of images when the user supplied an explicit image
   range (via the -Id flag): now only images within that range are
   used while before all images matching the given template were
   used. This was especially confusing during the GPX2 visualisation,
   since more images might have been presented than predictions were
   generated (if a subset of images was specified on the -Id flag).

* Fixes and improvements (released Jul 15 2015):

  * GPX2 (prediction and image visualiser):
    * now also available for OS X (version 10.7 or higher)
    * introduced new GPX2 keyboard shortcuts to simplify interaction:
        Ctrl-Left  : move to previous image
        Ctrl-Right : move to next image
        Ctrl-q     : quit program

  * Ensure that the file pointed to by the autoPROC_PointlessExtra
    parameter is also included when running POINTLESS to check for
    consistent indexing against a user-supplied reference MTZ file.

  * Clarifications to the reporting of multiple indexing solutions
    (when entering iterative indexing).

  * Fixes to the reporting of minimum angle between multiple indexing
    solutions (and also mentioning the space group used at this point
    to determine the minimum angle).

  * Added parameter autoPROC_CreateGpxPicturesAndKeepFilterFile
    (default="no") to decide if we should keep the prediction files
    that are computed during generation of images showing diffraction
    and predictions. Since those files can become rather large, not
    keeping them seems a sensible default option.

  * Use a generic gpx.sh script (to visualise predictions with
    simcal_predict and GPX2) instead of generating one on-the-fly:
    this simplifies maintenance and allows introduction of new
    features.

    * the help messages (.../gpx.sh -h) will now also report the
      possible lattices (identifier and number of spots used) when
      this script is invoked in multi-lattice cases;

    * in multi-lattice cases, GPX2 will by default (i.e. when no
      explicit "-lat" argument is used) start with all lattices shown;

    * the "-lat" argument now also supports the use of "-lat all" to
      select all lattices in a simple way;

  * Added BeamCentreFrom=header:x,y to SlsPXIII macro to avoid
    unnecessary warning message (thanks to D. Reinert for pointing
    this out).

* NEW FEATURE: incorporation of a visualisation capability for images
  and predictions (released Jun 16 2015):

  * The computation of the positions and shapes of reflections
    expected to appear on each image is performed in the newly added
    program simcal_predict. This tool is a particular use-mode of the
    simcal diffraction image simulation program written by Wlodek
    Paciorek and Claus Flensburg and extended as part of collaboration
    contract COL0044 between Global Phasing and the Diamond Light
    Source, specifically related to the I23 beamline.

  * Predicted spot positions and shapes are presented through ellipses
    superposed onto diffraction images using the new program GPX2,
    which was initially developed by Wolfgang Brehm (while in the
    group of Kay Diederichs at University of Konstanz/DE) during an
    internship with Global Phasing during the Summer of 2014 with
    generous support by the MX group (particularly PX-III) of the
    Swiss Light Source.

    At the moment, GPX2 is provided for Linux - a version of OS X is
    planned.

* NEW FEATURE: new scaling options for using "pure" AIMLESS-only or
  XSCALE-only paths within autoPROC (released Jun 16 2015):

  * the AIMLESS-only scaling path can be selected via

     process -M ScalingA3 ...

  * the XSCALE-only scaling path is chosen with

     process -M ScalingX ...

  * the hybrid path (XDS/AIMLESS) is still the default

* Updated documentation (released Jun 16 2015):

  * new sections about simcal_predict (computation of predicted
    positions and shapes) and GPX2 (display of those on top of the raw
    diffraction images)

  * new section about scaling modes implemented in scaling module
    aP_scale

  * new section "Interpreting autoPROC output"

  * enhanced examples and usage section and major reworking in all
    other parts

* Changed defaults (released Jun 16 2015):

  * The diffraction image files will not be linked into the same
    directory the actual XDS processing is run, but into a
    subdirectory (autoPROC_LinkImagesIntoSubdir parameter, default =
    "Images").

  * Ice-rings are now excluded automatically (if detected in the list
    of un-indexed spots): parameter XdsExcludeIceRingsAutomatically
    defaults to "yes".

    The width of the resolution range given to XDS for exclusion is
    enlarged slightly (parameter Xds_Spot2Res_IceRingWidthMultForXds
    with default 1.2).

  * Create pictures of diffraction images with predictions using GPX2
    (parameter autoPROC_CreateGpxPictures defaults to "yes"). The
    creation of files for visualising with MOSFLM ("ipmosflm") is now
    disabled (parameter autoPROC_CreateMosflmScript="no").

  * the parameters for divergence and mosaicity as determined by the
    XDS INTEGRATE step are reused in any subsequent integration pass
    (parameter XdsUpdateParKeepFixed="BEAM_DIVERGENCE:yes REFLECTING_RANGE:yes").

  * Instead of using REBATCH and SORTMTZ we are now using our own
    programs MRFEDIT and MRFADD (parameter UseMrfadd=yes and
    UseMrfedit=yes). These should not suffer from the same size/array
    limitations.

  * a macro to switch back to previous defaults is provided:

      process -M Version103 ...

  * the "automatic" macro has been adapted accordingly

* Clarified some command-line options in online-help given by "process
  -h" (released Jun 16 2015):

  * "-M" can also take a file name (and not only the name of a macro);
    therefore the "-D" flag is being deprecated since a duplication of
    that functionality.

  * the "-P" flag is deprecated (the MOSFLM path hasn't seen
    development for quite some time)

* Support for (released Jun 16 2015):
  - CCP4 6.5 (update 011)
  - POINTLESS 1.9.31
  - AIMLESS 0.5.9

* Removed "AutomaticChunking=yes" from "automatic" macro (released
  Jun 16 2015): if that feature is required it needs to be added
  manually as in

    process ... -M automatic AutomaticChunking=yes ...

* Added a little jiffy to create image sets based on rotation angle
  instead of image file name: ln_images.sh (released Jun 16 2015).

* Support for ALS beamline 4.2.2 including NOIR-1 detector (released
  Jun 16 2015).

* Scaling module aP_scale (released Jun 16 2015):

  * resolution limits along reciprocal cell axes as reported by
    AIMLESS now uses the same criteria for CC(1/2) and I/sigI as the
    overall isotropic high-resolution limit.

  * NEW FEATURE: support for scaling path using XSCALE; one (or
    several) XDS_ASCII.HKL files can be given via the "-hkl" argument.

  * fixed erroneous halt when encountering -mtz
    <file>:<P>,<X>,<D> syntax - found by D. Reinert

  * fixed logic for determining number of processors (to then use
    parallel AIMLESS feature) when running aP_scale standalone

  * some clean-up in the additional examples provided within the
    aP_scale.sh script generated automatically as an example for
    fine-tuning by the users

  * when re-running the scaling module aP_scale with the same
    identifier (prefix for output files): give more meaningful text so
    user knows better what to do next (thanks to S. Sheriff).

* The SPOT.*.png files produced during the indexing stage (showing
  location of indexed and non-indexed spots on the detector surface)
  now use a variable radius for points depending on spot strength
  (released Jun 16 2015).

* The remark200 tool will now also write versioning information for
  autoPROC and XSCALE into remark200.pdb file (released Jun 16 2015).

* Added support to combine XDS INTEGRATE.HKL files via 'combine_files'
  tool (released Jun 16 2015).

* When entering iterative indexing, also report angle between
  orientation matrices of each solution relative to the strongest one,
  ie the one with the most indexed spots (released Jun 16 2015).

* Don't do detailed overload analysis by default: it takes time and
  will create more large files. This is under parameter control with
  autoPROC_XdsAnalyseOverloads=no being the default (released
  Jun 16 2015).

* Added check for user-supplied -Id flags to 'process' command: ensure
  the first item (identifier) is unique (released Jun 16 2015).

* Fixed corner case in MRFANA: if the input MTZ file contained batches
  outside of the ranges defined on RUN cards, an error was
  thrown. Since those batches will never be used in later analysis
  anyway we now report and skip them (released Jun 16 2015).

* Also output CC(ano) (correlation of anomalous differences between
  random half-sets) into 'table 1' in MRFANA (released Jun 16 2015).

* Fixed handling of slightly differing wavelength values (from BATCH
  header and/or dataset information) in our REBATCH-substitute program
  MRFEDIT (released Jun 16 2015).

* Fixed spelling: parameter is called autoPROC_XdsMaxDistanceJitter
  and not autoPROC_XdsMaxDistanceChitter (released Jun 16 2015).

* The need to obtain a separate licence key for each machine on which
  the software is to be run has been removed for academic users: a
  single valid licence key will now work on any number of machines
  (released Mar 16 2015).

* Support for (released Mar 16 2015):
  - XDS version March 1, 2015
  - CCP4 6.5 (including update 005): this includes all the change in
    logic due to the final digit in the reported version now
    corresponds to the update serial number
  - POINTLESS 1.9.27
  - AIMLESS 0.5.4

* Read 'fraction of polarization' directly from Pilatus miniCBF-header
  if available (released Mar 16 2015).

* Changes to MRFANA (released Mar 16 2015):

  * Major internal re-organisation of MRFANA code: this should not be
    visible to a user.

  * Implemented the computation of CC(DANO) between halfsets in MRFANA
    similar to AIMLESS.

  * MRFANA now writes a more compact version of the merging statistics
    table. The wide-format version can be produced with the
    "-wide-format" command-line argument.

  * Better detection/distinction between XDS_ASCII.HKL, INTEGRATE.HKL
    and unmerged XSCALE output files.

* More detailed messages for POINTLESS and AIMLESS version checks
  during "checkdeps" stage (released Mar 16 2015).

* Changes in scaling module aP_scale (released Mar 16 2015):

  * by default, each AIMLESS job will also write out the XMLOUT file
    (see http://www.ccp4.ac.uk/html/aimless.html#InputOutput). To
    switch this off set the parameter autoPROC_ScaleXmlout to "no".

  * New parameter autoPROC_ScaleWithAimlessRefineSdcorrSame
    (default="no") that allows to use the same SDCORRECTION values for
    all RUNs (subkeyword SAME on SDCORRECTION card) in AIMLESS path.

  * Changed setting AutomaticChunking_MaxRuns (default = 40) only for
    SCALA path. For the default AIMLESS path it is set to 9999.

  * Changed setting AutoProcScaleResolutionCompareDigits=3 to
    AutoProcScaleResolutionCompareDigits=0,2 to have different
    significance levels for low and high-resolution values when
    testing if convergence has been reached during scaling/merging
    with aP_scale.

  * Changed command-line argument in aP_scale from -reso to -R flag
    (more consistent with other programs/commands), but keep -reso as
    backwards compatibility (released Mar 16 2015).

  * Added check to -b flag: requires a range (<N1>-<N2>) pattern
    (otherwise stop with an error).

  * Try to catch an error in TRUNCATE (WIDTH OF BIN TOO LARGE) to then
    set the RANGES keyword explicitly (enforcing TRUNCATE to run
    through).

  * Create plots of Bdecay and Mn(k) as a function of image number as
    well.

  * Better explanation and additional checks for -x flag in aP_scale
    scaling module.

* New parameter FindImages_MaxImageNumWidth (default = 6) to handle
  image file names where the prefix and the actual image serial number
  run into each other because of a missing delimiter character
  (released Mar 16 2015).

* Added help regarding ice-ring exclusion to autoPROC reference card
  (released Mar 16 2015).

* Added option to insert call to a program/script (parameter
  XdsRunScriptAfterColspot set to full path of this program) after
  COLSPOT (released Mar 16 2015).

* New parameters UseKapparotForConsistentIndexingStopOnError (default
  = yes) and XdsGetRotationAxisViaKapparotStopOnError (default = yes)
  as a fallback to work with beamlines producing different image
  headers (e.g. with or without a mini-kappa goniostat installed). It
  should not be necessary to change these from default value (released
  Mar 16 2015).

* Better error/warning message if image header is incomplete for
  consistent indexing between scans and/or when getting ROTATION_AXIS
  via Kapparot. Only relevant for multi-axis goniostat datasets
  (released Mar 16 2015).

* anaspot: correct resolution computation for detector described with
  segments when the detector is not located at the origin (released
  Mar 16 2015).

* If the new parameter XdsUpdateCorrectionTables (default = no) is set
  to yes, we will also update {X,Y}-CORRECTIONS.cbf with the
  G{X,Y}-CORRECTIONS.cbf files from CORRECT before re-running the
  integration step (released Mar 16 2015).

* Nicer formatting of output from "imgdate.sh" jiffy: constant width
  for all file-names, dates and time-differences (released
  Mar 16 2015).

* The analysis of and (possible) warning about image header
  inconsistencies is now under parameter control:
  autoPROC_ImginfoReportWarnings with a default of "yes" (released
  Mar 16 2015).

* imginfo now also reads milliseconds from the timestamp in image
  headers if available (released Mar 16 2015).

* Also handle runs where only the space group name is given (using the
  symm=<SGname> argument) and we have to distinguish between hexagonal
  and rhombohedral settings of H3/H32 (released Mar 16 2015).

* New parameter CombineFilesRunReindexOnAll in 'combine_files' utility
  (defaulting to yes): when running REINDEX on at least some MTZ files
  (to set correct space group), we also need to run it on all to
  ensure the SG operators are given in the same (CCP4/REINDEX)
  order. Otherwise SORTMTZ will get confused and stops with an error
  (because ISYM values would be wrong). This is due to POINTLESS using
  a different, clipper-based system of symmetry operators than other
  CCP4-based programs (released Mar 16 2015).

* Also report ISa values after the XDS/CORRECT step (released
  Mar 16 2015).

* The parameter XdsExcludeIceRingsAutomatically can now also be set to
  "all" - in which case all known ice-ring ranges will have their
  resolution ranges excluded in processing, no matter if those
  ice-rings are actually present/detectable or not (released
  Mar 16 2015).

* Added more detailed notes and error messages during indexing stage
  to help spotting potential problems (released Mar 16 2015).

* Renamed P13 and P14 beamline (PetraIII) macros to avoid warning
  message from macro reading routine (released Mar 16 2015).

* Beamline macros for SLS (PX-III) and PetraIII (P13 and P14) will not
  set the silicon sensor thickness since that value is now read from
  the image header by imginfo (released Mar 16 2015).

* improved 'ana_aimless' tool to deal with difference in table format
  between AIMLESS versions up to 0.1.32 and from 0.2.11. Also added a
  plot about cumulative normal and anomalous completeness and fixed
  handling of multi-wavelength (MAD) datasets (released Jul 26 2014).

* improved the 'xds_stats' tool to give nicer plots (handling
  meaningful ranges, labels etc) and deal with old gnuplot 4.0
  versions; non-square plots now default to XdsStats_size="800,600"
  (from previously "1200,800") to make them compatible with output
  from "ana_aimless" (released Jul 26 2014).

* the 'imginfo' tool now also reads the sensor thickness (if given in
  mini-CBF header) from Pilatus-formatted images (released
  Jul 26 2014).

* the 'rigaku2xds' tool (and therefore autoPROC) should now also
  support Pilatus 300K detectors on Rigaku (AFC-11) goniostats via the
  '-M RigakuPilatus300K' macro (released Jul 26 2014).

* added support for P13 and P14 beamlines at Petra-III beamline via
  new macros (released Jul 26 2014).

* fixed 'hkl2res.sh' jiffy when DETECTOR_DISTANCE is given on same
  line as ORGX/ORGY line (released Jul 26 2014).

* fine-tuning the text when checking XDS version eg as part of the
  'checkdeps' routine (released Jul 26 2014).

* added jiffy ('imginfo_merge2cbf.sh') to process images that went
  through the XDS program MERGE2CBF (released Jul 26 2014).

* changed default for range of images used in background
  determination: autoPROC will now use 3 ranges of 10 images each
  within the first 90 degree of data (released Jun 12 2014).

* new macro (Version115) to move back to defaults for the previous
  stable version (released Jun 12 2014).

* tested with latest POINTLESS version 1.9.8 (released Jun 12 2014).

* give XDS references in standard output (released Jun 12 2014).

* fixed problem when trying to print warning message (user requested
  more threads than available on machine, released Jun 12 2014).

-------------------------------------------------------------------
<-- Below are the Release Notes for the previous stable release -->
-------------------------------------------------------------------

===================================================================
 Changes included in autoPROC version 1.0.3 stable     May 12 2014
===================================================================


===
=== New features:
===

 Installation instructions:

   * comprehensive guide how to install and test autoPROC on all major
     operating systems. These are available from the download page on
     www.globalphasing.com or included in each installation as
     $BDG_home/docs/installation/index.html (released May 07 2014).

 Parameter refinement:

   * when encountering instability of distance parameter refinement,
     detect and possible act upon it (released Mar 06 2014).

     If jitter is lower than half the autoPROC_XdsMaxDistanceChitter
     parameter value, keep it as a warning; if above this value:
     switch off distance refinement.

 Configuration:

   * a new tool ('aP_check') is available to test if all external
     dependencies (CCP4, XDS, POINTLESS, AIMLESS) are available and
     working. It can also be run via 'process -checkdeps' to give a
     short summary about those external dependencies (released
     Mar 06 2014).

   * the location of the XDS binary can be set via the environment
     variable BDG_TOOL_XDS (released Sep 13 2013).

     This is usually done in the files setup_local.sh and
     setup_local.csh located in $autoPROC_home (for a stand-alone
     installation) or $BDG_home (for all others).

     According to an existing general mechanism, this alternative way
     of specifying the location of the XDS binary can in turn be
     overridden on the command line (e.g. "process
     xds=/some/where/xds_par") or by a similar redefinition in a
     macro.

 External program support:

   * support for POINTLESS 1.92 as well as XDS "January 10, 2014
     BUILT=20140307" (released May 07 2014).

   * support for CCP4 6.4.0 (including POINTLESS 1.8.17 and AIMLESS
     0.2.17) as well as XDS "January 10, 2014 BUILT=20140211"
     (released Mar 06 2014).

   * support for POINTLESS 1.6.17, AIMLESS 0.1.24 and XDS "March 30,
     2013 BUILT 20130706" (released Sep 13 2013).

 Simplifying support:

   * in case the user didn't save the standard output of the "process"
     or "aP_scale" command, we now report the filename where a copy of
     standard output was saved at the end of a run. These files are
     often the first information we might need to ask you for in order
     to help with user issues (released Sep 13 2013).

 Analysis:

   * the new parameter AutoProcScaleStatsUseMrfanaFinalNumBin (default
     = 20) is used at a final merging statistics calculation to use a
     coarser binning that is more useful for publications or
     deposition than the fine binning used for the automatic
     determination of the high-resolution cutoff (released
     Mar 06 2014).

===
=== Changes:
===

 Reciprocal space sampling:

   * reducing the values for parameters
     NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA and
     NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA from 21 to 15, since a
     too fine sampling doesn't seem necessary and this change reduces
     memory requirements (released May 07 2014).

 Iterative indexing:

   * the iterative indexing step will now output results into a
     subdirectory by default to reduce clutter in the main output
     directory (released Mar 06 2014).

===
=== Improvements:
===

 XDS support:

   * support of latest XDS version/build "January 10, 2014" (released
     Mar 06 2014).

   * better and more extensive checks on the XDS version (and build
     date) with improved feedback to the user (released Mar 06 2014).

 Beamline/Instrument support:

   * Support for Australian Synchrotron beamlines: new macros
     AustralianSyncMX1 and AustralianSyncMX2 (released
     Mar 06 2014).

   * Support for Soleil/PROXIMA1 Pilatus 6M images that mark the gaps
     not with -1 but leave them as 0 (released Mar 06 2014).

     The parameter autoPROC_Img2Xds_Pilatus6MGaps contains the gap
     specifications on a Pilatus 6M. With the new parameter
     autoPROC_Img2Xds_Pilatus6MIncludeUntrustedRectangle set to "yes"
     (default=no) those will be added to the list of
     UNTRUSTED_RECTANGLE.

   * improvements for non-square detectors (like the Dectris/Pilatus
     models) when the image header stores the beam centre in a
     non-standard way. The BeamCentreFrom parameter then needs to take
     this into account (released Mar 06 2014).

     On non-square detectors we swapped the (X,Y) beam-centre values
     and the NX/NY values at the same time. However, the NX/NY values
     are extremely unlikely to have been swapped by beamline software,
     since they relate directly to the fast/slow axis of the binary
     array. So now we actually calculate

       -y,-x  = NX-y,NY-x

     as a default, while before we did

       -y,-x  = NY-y,NX-x

     That latter calculation can also be used by setting the parameter
     BeamCentreFromNxNySwap to "yes".

     All this came to light from images at the Swiss-Norwegian beamline
     at the ESRF: a Pilatus 2M with the beam-centre stored as y,-x.

 Analysis:

   * MRFANA now also writes a dataset header for each merging
     statistics table: this helps identifying which images are
     included into the calculation of those statistics, what the
     average cell (and standard deviation) is etc (released
     Mar 06 2014).

   * calculation of <|DANO/sig(DANO)> in resolution shells added to
     MRFANA (released Mar 06 2014).

   * also write AIMLESS version into REMARK 200 section of
     remark20.pdb file  (released Mar 06 2014).

===
=== Fixes:
===

 Scaling

   * when working with multiple scans that contain either more than
     999 images or start with image numbers above 999: fix the
     assigning of the actual batch numbers for the final multi-sweep
     scaling run (released Mar 06 2014).

 General:

   * fix when updating XDS.INP file after POINTLESS analysis if the
     user gave an input spacegroup: the SPACE_GROUP_NUMBER keyword was
     lost  (released Mar 06 2014).

   * fix in handling new versus old format of SPOT.XDS in our ANASPOT
     jiffy (released Mar 06 2014).

   * handle multi-axis Kappa goniostats better: sometimes those are
     described with 3 or 4 angles (including/excluding the Alpha
     angle) in the header (released Mar 06 2014).

   * if there are problems during parameter refinement in XDS/CORRECT:
     ensure that updating the XDS.INP and XPARM.XDS file takes this
     into account (released Mar 06 2014).

===================================================================
 Changes relative to 1.0.1                             19 Jun 2013
===================================================================

===
=== New features:
===

 Indexing:

   * When entering 'iterative indexing', also plot number of spots
     against images for all significant solutions (as fraction into
     run_idxref_spot_hkl_histfrc.png or as absolute values in
     run_idxref_spot_hkl_hist.png).

     A new parameter RunIdxref_SpotVersusImage_MinFrac (default=0.05)
     determines the significance level for lattices (with the default
     at least 5% of the number of spots for the most populated
     lattice).

   * Added feature to run new 'anaspot' program (which analyses
     SPOT.XDS files for ice-rings etc): if we have non-default
     resolution limits given by the user we need to intervene between
     the COLSPOT and the IDXREF stage. Calling anaspot will limit the
     found spots to the set resolution based on the current, idealised
     geometry.

 High-resolution criteria:

   * Implemented CC1/2 calculation according to Karplus & Diederichs
     (2012) paper.

     Final CC1/2 criteria to determine adequate high-resolution cutoff
     defaults to 0.3 (since 0.1 is too optimistic given the intrinsic
     noise a change in random seed already shows).

 Analysis:

   * Added plot combining divergence and mosaicity (since they are
     often related in interesting ways): this will not only print the
     estimated values (per image), but also the finally used values
     for the center region of the detector.

   * MTZANA tool for analysing (merged) MTZ files (MRFANA is the
     equivalent program for unmerged, multi-record MTZ files): added
     command-line arguments -colcmpl and -nocolcmpl to print (or not)
     completeness per column (for the resolution range of that column).

   * New tool (MTZANA) to provide very similar functionality to CCP4s
     MTZDUMP program - without some of the limitations in output
     format, that often make it difficult to parse the information
     correctly.

===
=== Changes:
===

 High-resolution criteria:

   * New set of defaults - same as previous HighRes2 macro:

      setvar ScaleAnaRmergeCut_123       "99.9999:99.9999"
      setvar ScaleAnaISigmaCut_123       "0.1:0.1 0.5:0.5 0.5:1.0 1.0:2.0"
      setvar ScaleAnaRpimallCut_123      "99.9999:99.9999 0.9:0.9 0.8:0.8 0.6:0.6"
      setvar ScaleAnaRmeasallCut_123     "99.9999:99.9999"
      setvar ScaleAnaCompletenessCut_123 "0.0:0.0"
      setvar ScaleAnaCChalfCut_123       "-1.0:-1.0 0.0:0.0 0.3:0.3"

     This means that Rmerge, Rmeas and Completeness are being
     ignored as a high-resolution cutoff-criterion. Rpim and CC1/2
     are used very conservatively - and I/sigI (>= 2.0) is the main
     one.

===
=== Improvements:
===

 XDS support:

   * Put XDS parameters FIXED_SCALE_FACTOR and
     DATA_RANGE_FIXED_SCALE_FACTOR under XDS version control since
     availability depends on exact XDS version.

   * support for XDS version "March 30, 2013":

     - changes to format of XPARM.XDS file (contains all experiment
       settings): depending on the XDS version used, files generated
       by autoPROC will also follow the relevant format of this
       version.

     - additional keywords

     - changes to format of INTEGRATE.HKL (contains raw integrated
       intensities)

     - changes to various output log-files (mainly relevant to
       autoPROC are IDXREF.LP, INTEGRATE.LP)

     - changes in format of SPOT.XDS (contains list of found spots for
       indexing)

     - better versioning done by XDS (not just a version date, but now
       also a BUILT date is reported by XDS programs)

 Beamline/Instrument support:

   * Support for Pilatus images following the latest version of header
     specifications 1.3. See also

       https://www.dectris.com/technical_pilatus.html

   * Support for ALS 12.3.1 (SIBYLS) beamline. See also
     http://bl1231.als.lbl.gov/. Required settings (as of 201212) are:

     * 2-theta rotates opposite to the rotation axis:
       autoPROC_TwoThetaAxis="-1 0 0"

     * beam centre in header needs transforming:
       BeamCentreFrom="header:x,-y"

     * need to deal with beam centre in header stored including the
       2-theta offset: imginfo="imginfo_ALS_12.3.1.sh"

     Running with

       process -M Als1231 ...

     should be sufficient.

   * Support for ALS 8.3.1 beamline: macro (Als831) and imginfo jiffy
     (imginfo_ALS_8.3.1.sh). Running with

       process -M Als831 ...

     should be sufficient.

   * Support for Pilatus 6M images from ID29@ESRF: these are marked as
     'omega' scans while the current mini-CBF header from Dectris
     doesn't provide a specific Omega value. By using the EsrfId29
     macro (-M EsrfId29) an appropriate override jiffy is called to
     dynamically correct those headers.

 Image file handling:

   * to enable handling of compressed (gz and bz2) images
     automatically, the new parameter FindImages_AllowCompressedImages
     should be set to "yes".

     Note: it might be a good idea to limit the number of threads for
     XDS if using this - otherwise there will be a lot of disk I/O
     (uncompression on-the-fly) by the XDS program, e.g with

       process autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_PROCESSORS=2 ...

     Please note that 'imginfo' can already work on compressed images
     directly.

 Spacegroup determination:

   * Extract scores for each symmetry element from the POINTLESS
     analysis: this will make it easier to detect lower symmetries
     (like pseudo-orthogonal monoclinic etc).

 Scaling:

   * Changes in MRFANA (analysis of unmerged reflection files) to work
     around Pointless/Aimless bug: currently these programs write
     incorrect information into the MTZ header (Laue group instead of
     Point group) which results in wrong setup of asymmetric-unit
     handling for reflection indices - which in turn results in
     incorrect handling of anomalous statistics calculations.

   * Changed autoPROC_ExcludeBadBatchesFromCycle from 2 to 3: to avoid
     excluding batches to early when scale factors, error-model and
     high-resolution limit are still being adjusted.

   * Changed parameter AutoProcScaleMinimumCycles from 2 to 4 to do at
     least 4 scaling cycles.

   * Also extract recommended anisotropic high resolution limits from
     AIMLESS (based on I/sigI > 2.0 and CC1/2 > 0.5 criteria.

   * When running with AIMLESS (default) we will allow wider gaps
     between batches (before classifying them as separate runs): this
     is mainly useful when dealing with fine-sliced data where
     sometimes no reflection is assigned to an intermediate image
     (therefore creating a gap). Therefore, the parameter
     AutoProcScaleMaxAllowedGapSize defaults to 5 with AIMLESS and 0
     otherwise.

   * New option AutoProcScaleSetInitialHighRes (default = no) to apply
     an initial high-resolution cutoff based on <I/sigI> of -0.2 (set
     by parameter AutoProcScaleSetInitialHighResIsigI) in the final
     shell. This should ensure that scaling doesn't fail because it
     sees a very large number of supposed spots that are actually pure
     noise - eg if the crystal-detector distance was set to a
     massively over-optimistic value.

   * We now also accept -Reso or -R instead of the standard -reso for
     setting resolution limits on the command-line.

   * When stopping (due to existing files that would otherwise be
     re-used and/or overwritten), also give a list of files that cause
     that error. This will make it easier for the user to remove those
     if wanted.

   * Create additional plots using "ana_aimless" command (in PNG
     format via gnuplot) that are useful: scaling B-factor (vs
     image/batch) and Rmerge (vs image/batch). The name of the created
     output files (prefix; default = "ana_aimless") can be set with
     the new (optional) argument -o.

   * Write script (aP_scale.sh) with actually used commands run: this
     should make it easier for a user to re-run the final scaling
     step.

   * Added parameter XdsScaleRunMultipleCriteria (default=no):
     additional scaling-only runs (in new aP_scale.sh) are thus
     switched off or on.

   * Using new MTZANA program instead of MTZDUMP: faster, better
     formatting and under our control (so easier to react and avoid
     surprises).

 Analysis:

   * Major reworking of the 'mkmovie' command (see -h output for
     details): usage of ffmpeg/avconv for encoding and MOSFLM/ADXV for
     image-generation still needs some testing and work.

     In general this is more a proof-of-concept than a robust way of
     generating movies for a set of diffraction images.

   * Improved generation of profile plots and movies in the 'mkmovie'
     command - including generation of gnuplot files that allow
     interactive handling (rotation) of 3D profile representations.

     Added command-line argument "-profile_only" to generate those.

   * New parameter XdsStats_StopOnGnuplotError (default=no) to control
     handling of errors during gnuplot: when set to "yes" autoPROC
     will stop if one of the plot-generating steps fails because of a
     gnuplot inconsistency.

   * Various changes to look-n-feel of plots: hopefully resulting in
     nicer plots.

   * Added diagnostic to warn if refined distance parameter moves more
     than autoPROC_XdsMaxDistanceChitter=1.0 mm from the mean. In
     those cases something else is most likely going on and at least
     the distance should be held fixed during integration (followed by
     several cycles of post-refinement and integration, eg. using the
     "-M LowResOrTricky" macro).

 General:

   * work around bug in AIMLESS/POINTLESS: unmerged MTZ files written
     by those programs (as of 20130517) have wrong content in the
     SYMINF record of the MTZ file header (Laue instead of Point group
     name). Contacted Phil Evans and CCP4 about that.

   * Extract POINTLESS program version via new generic function.

   * Better dealing with binning (for RSTATS-based statistics; shown
     when running with '-v' flag): setting

       CheckIndexing_RstatsBinningMaxNum to 50 (from 10)
       CheckIndexing_RstatsBinningMinWidth to 0.0001 (from 0.01)

     and adding

       CheckIndexing_RstatsBinningNumBin=10
       CheckIndexing_RunMtzana="no"

     Also added command-line argument "-n <nbin>" to set the number of
     bins to be used (beware: depending on completeness the actually
     used bins might still be different).

     Setting CheckIndexing_RunMtzana="yes" will run the data through
     the statistics part of MTZANA and calculate various CC values via
     this route too.

   * Better way to deal with differences between versions of
     POINTLESS: a generic function to extract version number from
     POINTLESS standard output will allow handling different versions
     of POINTLESS (and the different input they accept and output they
     produce).

   * Changed default conversion factor between XDS mosaicity (sigma)
     to MOSFLM (FWHM): from 2.0 to 2.3548 - which it should be for a
     Gaussian.

   * When updating parameters in XDS.INP file using "xds_update_pars"
     module: take different behaviour of XDS versions into account
     (see Version July 4, 2012 in XDS release notes at
     http://xds.mpimf-heidelberg.mpg.de/html_doc/Release_Notes.html).

   * Started adding support for generating commands that will use our
     new visualiser (gpx) to display diffraction images and
     predictions. This is still under construction and must await the
     release of the visualiser and prediction generator before it
     becomes fully functional.

   * Make sure some temporary files are removed to keep things tidy.

===
=== Fixes:
===

 Indexing:

   * When dealing with distributed background images: avoid problems
     if processed images don't follow a simple numbering (from 1 to N).

     Also: create pseudo-contiguous images for this part in
     subdirectory (to avoid confusion).

   * Fixed problem in getting the correct number of indexed spots out
     of an IDXREF.LP file (when this was reported with two different
     numbers in two places). This resulted in the wrong percentage
     being reported on standard output.

 Spacegroup determination:

   * Deal with a change in POINTLESS XML-output that caused the
     reindexing operator not being fetched correctly within
     "ana_pointless".

 Scaling

   * In MRFANA: fix to ensure correct sorting of ASCII files from XDS
     (INTEGRATE.HKL, XDS_ASCII.HKL or XSCALE output) to avoid wrong
     calculation of anomalous statistics like completeness.

   * Always set VRSET to -999999999 (SortmtzVrsetValue parameter) in
     calls to SORTMTZ: this should avoid errors - for datasets that
     have most likely some issues with detector areas (beam stop, dead
     modules or such).

   * Fixes to automatic adjustment of image ranges (-b argument): to
     deal with multi-scan experiments that are not using different
     filename templates, but rather a continuation of image numbers
     (e.g. when using different spots on the crystal).

   * Fixes to setting arguments for scaling module (aP_scale): to deal
     with multi-scan experiments that are not using different filename
     templates, but rather a continuation of image numbers (e.g. when
     using different spots on the crystal).

   * In MRFANA: fix initialisation in calls to CCP4 library. This
     should avoid bogus warning messages from the CCP4 library about
     LRIDX.

   * Write correct scaling software (SCALA or AIMLESS) into REMARK 200
     section of automatically generated remark200.pdb files.

 High-resolution criteria:

   * In high-resolution cutoff criteria: explicitly set R-values (to
     be ignored) to 99.9999 to be in sync with MRFANA program (where
     this is the value to mark a value that can't be calculated).

 General:

   * Try to get the command-line arguments into a better formatted
     string (for reporting).

   * Clarified warning message when giving only symm card (without
     cell).

   * Give detailed information regarding the number of threads used at
     various stages (and for XDS or MOSFLM path). Also telling the
     user how to set or modify the automatic settings for the
     different stages.

   * Fixes in "check_indexing" to avoid different resolution limits
     being used for different re-indexing operators.

   * Fix problem where the final summary information (about cell,
     spacegroup, resolution etc) was given based on a wrong MTZ file
     (present in current directory and not subdirectory).

     Also fix extraction of resolution limits. Previously, overall
     limits of reflections was given, but now resolution limits of
     actually measured amplitudes is reported.

   * Fixed a bug which may cause the scaling module aP_scale to fail
     with no meaningful error message on some systems if mtzana is not
     available. For more details see:

       https://www.globalphasing.com/beta/wiki/index.cgi?SoftwareReleases201211KnownIssues#autoprocapscale

     Additional checks have been implemented to work around this issue.


New features:

 * support for scaling with AIMLESS to support larger datasets (more
   than 5000 images).

   This is now the default (if AIMLESS is available in the users
   PATH), but can be switched off (to use SCALA instead) with
   autoPROC_ScaleWithAimless=no. This requires CCP4 version 6.3.0
   onwards!

   By default, the scaling will run with multiple threads (can be
   controlled by the -nthreads command-line argument to 'process' or
   through the OMP_NUM_THREADS environment variable).

 * new jiffy add_freerflag.sh (to add existing test-set flags from one
   MTZ file to another)


Improvements:

 * added AutoProcScaleMinimumCycles (default=2) parameter to the
   scaling module (aP_scale): this gives more control in macros like
   the HighRes2 one mentioned below)

 * give warning if only resolutions below 4A were used for
   space-group determination in POINTLESS. Users are advised to check
   the correct or most likely spacegroup in such cases of low
   resolution or poor diffraction by hand.

 * added new ways of using macros:

   - using 'process -M show' will not only give a description for a
     particular macro, but show also the detailed settings. This can
     help users fine-tune some of the distributed macros.

   - a user can now also give a filename as argument to '-M', so that
     own macros can be given without the need of setting the
     environment variable autoPROC_MacroDirs. The file still needs to
     follow the standard macro-format.

 * two new macros (HighRes2 and NoHighResCut) to either use only I/sigI
   and Rpim as high-resolution criteria or none at all.

 * new macro (LowResOrTricky) with a few settings that could help
   low-resolution and/or messy diffraction data: mainly trying to
   stabilise parameter refinement during integration.

 * easier way to keep mosaicity fixed during integration in XDS:
   setting the parameter XdsUpdateMosaicityScale to a positive
   (non-zero) value will keep the mosaicity constant and fixed during
   the second (and following) integration path. The actual value is
   the value recommended by XDS (as reported in INTEGRATE.LP) scaled
   by the XdsUpdateMosaicityScale value.

 * support for latest XDS version (September 26, 2012)

 * added parameter autoPROC_TestSetFraction (default=0.05) to the
   scaling module (aP_scale). This will be used when calling uniqueify
   to generate a fresh test-set.

 * imginfo tool now also deals with DATE items in ADSC images of
   format, such as 'DATE=Fri Apr 23 18:12:09 PDT 2010;'

 * support for POINTLESS 1.6.18 (from CCP4 6.3.0 release)

 * added plot showing detector position of misfits (according to XDS
   definition)

 * improvements in the generation of plots via new parameters
   XdsStats_sizeSquare, XdsStats_MaxSize, XdsStats_PositionInMm and
   XdsStats_PlotMissingImages

 * support for MOSFLM 7.0.9 (in CCP4 6.3.0 release)

 * extract additional information from POINTLESS step about potential
   twinning

 * added parameter ExpectLargeAnomalousSignal (default="no") and
   XdsSetStrictAbsorptionChiSquareCut (default=1.5): those are used
   to adjust settings in the CORRECT step - to deal better with
   datasets showing very large anomalous signals (e.g. with metal 
   clusters at low resolution).

 * when dealing with datasets that have slight gaps (empty or
   non-existing images) together with automatic 'chunking': make use
   of new parameter AutoProcScaleMaxAllowedGapSize (default=0) to
   avoid weird chunking due to those gaps.

 * when working with multi-scan datasets that will get merged into
   separate files (e.g. multi-wavelength MAD): added parameter
   AutoProcScaleCombineCrystalDatasetInCrystal (default=yes) to work
   around CCP4 library feature (that will lose cell parameters for a
   specific dataset, since it assigns cell on a per-crystal basis).

   This should avoid problems with the iterative scaling (in SCALA),
   merging statistics and high-res recommendation (in MRFANA) -
   otherwise the calculation of resolution for a given HKL uses
   slightly different cells and would therefore be out-of-sync.

 * more sensible message about images with different scale factors:
   still based on global statistics, but at least doesn't get confused
   by missing images or image numbers above 999

 * imginfo:

   - additional checks for odd Pilatus headers (wavelength values in A but
     unit in nm, distance given in mm without a unit or with 'm' unit)

   - added checks for weird wavelength value (below 0.5A) and distance
     value (>100m or <1mm) to automatically adjust these header
     specification issues

   - catch Proxima1/Soleil case where we have Kappa and Chi values but
     no Omega (and Chi is identical to Starting_angle): pretend that
     this is a Kappa goniostat

     This is due to Proxima1's capability of doing both Omega- and
     Phi-scans on a Kappa goniostat when the Pilatus header
     specification doesn't provide an entry for Omega (so the starting
     Omega value is stored in the Chi parameter). This might change
     with updates to software by Dectris and the Proxima1 beamline.

   - handle negative zero values in angles (reset to 0.0): otherwise
     the KAPPAROT tool to enforce consistent indexing and/or calculate
     general rotation axis (eg. phi-scans on multi-axis goniostats)
     gets confused.

 * when combining several reflection files (within autoPROC or with
   the command-line tool 'combine_files'): take value of
   EnsureConsistentIndexing into account to prevent POINTLESS from
   wrongly re-indexing the data into an equivalent (but not identical)
   setting.

 * new parameter SpacegroupIndistinguishableGroups to allow better
   message for I23/I213 and I222/I212121 cases

 * new parameter FindImages_ExcludeLastImage (default=no) to exclude
   the last image of a found scan: deals e.g. with sync issues at
   SLS-PXIII regarding shutter-closure

 * support for:

   - SLS-PXIII (Prigo) beamline configuration and Pilatus headers
     through macro:

       % process -M SlsPXIII ...

   - Soleil-Proxima1 (Kappa) beamline configuration and Pilatus headers
     through macro:

       % process -M SoleilProxima1 ...

   - NSLS-X25 (initial Pilatus 6M headers) through imginfo-wrapper:

       % process imginfo=imginfo_NSLS_X25.sh ...


   - support for Pilatus 6M images from ID29@ESRF: these are marked as
     'omega' scans while the current mini-CBF header from Dectris
     doesn't provide a specific Omega value. By using the EsrfId29
     macro an appropriate override jiffy is called to dynamically
     correct those headers:

       % process -M EsrfId29 ...

 * New tool (MTZANA) to provide very similar functionality to CCP4s
   MTZDUMP program (without some of the limitations in output format,
   that often make it difficult to parse the information correctly).

 * make sure some temporary files are removed to keep things tidy.

Fixes:

 * handle multi-scan cases where one (or several) scans had more than
   999 images (which could previously give an error in the final,
   multi-scan scaling step).

 * explicitly set VRSET in SORTMTZ to avoid odd failures when
   combining several MTZ files for scaling. However, those failures
   usually meant very poor or wrong beamstop masking, leading to
   wrongly integrated intensities behind the shadow.

 * added checks in MRFANA to avoid memory corruption.

 * added safety margin for low-resolution limit suggestion from
   MRFANA: avoids 'losing' low-resolution reflections due to slightly
   different methods of calculating resolution and/or rounding errors.

   This should also speed-up the scaling job (aP_scale) since it
   avoids unnecessary additional cycles of scaling with updated
   resolution limits.

 * fixed some wrong amounts of white-space in REMARK 200 generation
   (remark200.pdb file)

 * when combining files (using combine_files utility), take care to
   get correct batch numbering offset - relevant for large
   scans/datasets with more than 999 images.

   In the same combine_files utility, some reporting regarding
   necessary reindexing has been fixed (previously it might have
   reported reindexing when in fact it didn't do any).

 * better support for GnuPlot 4.4 (used in creating plots in PNG
   format)

 * fixes during indexing when iterative indexing is used
   (automatically determined or user-requested) and several indexing
   stages are necessary anyway (e.g. the user only supplied spacegroup
   but not cell parameters): pick the correct master list of spots for
   detection of (partially) empty datasets.

 * better messages when analysing indexed spots for potential
   high-resolution limit

 * fixed bug in the aP_scale module (when combining different analysis
   tools regarding automatic adjustment of high-resolution limits):
   the explanations why a certain high-resolution limit was picked
   were sometimes out-of-sync.

 * added check in iterative indexing to avoid continuing with
   obviously wrong solution: sometimes IDXREF seems to succeed whereas
   only very few spots were actually used for the indexing
   solution. The parameter XdsIndexingStopIfSpotsLessPercent
   (default=2) is used for that check.

===================================================================
 Changes relative to 1.0.0                             20 Jul 2011
===================================================================

New features:


Improvements and changes:

 * imginfo:

   - added support for Pilatus headers I03@Diamond

   - added support for ADSC/Rigaku combo headers

   - allow APS1 prefix in header items

   - additional checks when encountering odd/duplicate oscillation
     axis definitions

 * added some jiffies:

   - beam8.sh will report all 8 possible beam centre settings

   - imgdate.sh can be used to analyse collections of images based on
     the timestamp in the image header

 * better method for getting completeness (for overload analysis) from
   reflection files

 * added option autoPROC_XdsAcceptOverloads (default=no) to generate
   a second set of files with overloaded reflections being accepted
   instead of ignored. This is only meant to be a desperate and last
   measure!

 * MRFANA (merging statistics calculation):

   - better order of inclusion criteria of reflexions (resolution
     check now before sysabs) resulting in significant speedup.

   - ice-ring treatment improved through (among several changes):

     a) using ice-ring limits instead of mid-point (with fixed width)

     b) using experimentally observed values for ice-ring resolution
        limits from large number of JCSG datasets

     This results in much more reliable treatment of
     ice-rings. Statistics used in applying the various cut-off
     criteria (for the high-resolution limit) now use an interpolation
     across those ice-ring resolution shells.

 * aP_scale (scaling module):

   - significant speedup through changes in MRFANA (see above) and a
     faster invocation of MTZDUMP (to read header information from MTZ
     files)

   - changed default so that MRFANA will assume by default that the
     data could contain ice-rings
     (AutoProcScaleStatsUseMrfanaIgnoreIceRingShells=yes)

   - new command-line option (-noice) to revert back to previous
     default, ie. no ice-rings present in data

 * find_images should give nicer identifier values (by removing
   trailing '0' characters in obvious cases).

 * changed from old XDS keyword 'MINUTE' to new 'SECONDS'

 * unless the user saves standard output already, write a (uniquely
   named) log-file to ensure that standard output is not lost.

 * new option to distribute background images over larger range of
   images (in chunks): DistributeBackgroundImages (default="no"). This
   should give a better initial background (BKGINIT.cbf file from the
   XDS INIT step), while avoiding using a very large number of images
   (which would be slower).

 * added analysis for empty images: we now require at least 2
   (XdsSpotSearchMinNumSpotsPerImage) spots per image but allow 5
   (XdsSpotSearchNumAllowedEmptyImages) empty images within the range
   of images used for spot searching.

 * lowered starting value for automatic backstop masking in XDS
   (DEFPIX step) to 5000 (XdsOptimizeDefpixStart), to deal with very
   weak images.

 * added option (XdsSetHighResFromIndexedSpots=no) to set
   high-resolution limit based on indexed spots.

Fixes:

 * add protection against dash failing on 'empty' .autoPROC files

 * avoid setting reslow/reshigh outside normal command-line system

 * MRFANA:

   - corrected bug in accessing cached values of completeness (per
     resolution bin), therefore avoiding duplication of calls -
     resulting in further speedup.

 * fixed wrong reporting of reindexing requirements (due to changes in
   POINTLESS log-file format)

 * ensure that 'process' exits with status 0 if all went well

 * fixed problem in passing empty strings (of non-zero length) into
   parameters, eg.

     refine autoPROC_XdsKeyword_REFINE_INTEGRATE=" " ...

   will now work.

 * when analysing the low- and high-resolution limit of indexed spots:
   ensure that the correct set of parameters is used when the
   iterative indexing was used (because of multiple lattices,
   ice-rings etc).

 * deal with scans of more than 999 images (when creating plots of
   scale, divergence and mosaicity)

#### NOTES

  The 32-bit Linux distributions of Global Phasing's software will
  work on systems running relatively old kernels (versions
  2.4.x). Most mainstream server and desktop Linux distributions that
  are currently under active maintenance are based on the newer 2.6.x
  kernel series.

  The current 32-bit release will be the last to support Linux systems
  based on the 2.4.x kernel. Future distributions (including patches
  and minor updates) of our software for all Linux systems released
  after this one can only be relied on to work on systems running
  kernels from the 2.6.x series.

  This is only a significant change for our 32-bit distribution: our
  64-bit distributions for Linux have always required kernel version
  2.6.x

  To check the version of the kernel on a particular system, run the
  following command:

      uname -r        

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

Any feedback and remarks should be send to the autoPROC developers:

               proc-develop@globalphasing.com

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