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Joint Research Group Macromolecular Crystallography

XDSAPP3 - Release notes

XDSAPP3 Version 1.9 (2023-01-12)

  • generate_XDS.INP rev 1.13 included
  • fixed a bug in myutils.py to get correctly phenix from xdsenv.py
  • fixed a bug in xdsit.py to read correctly the data collection day fron a cbf file
  • changed: XSCALE.LP file is deleted, this file caused confusion as it reported only the higher resolution shells. XSCALE (without the command line option --sx) is only used internally to define the high resolution cutoff.

XDSAPP3 Version 1.8 (2022-08-23)

  • new: in Settings tab, the checkboxed for predictions and direction cosines are grayed out, if the respective programms are not declared in xdsenv.py or not found.
  • fixed: a bug is fixed, when a .html or .txt file from the results directory was loaded, and the diffraction images where not found in the given path.

XDSAPP3 Version 1.7 (2022-07-22)

  • new: spot predictions calculated with the optionally installed generate_adx are now off  by default. They can be switched on by selecting the check box in the GUI settings tab, with the command line parameter --predictions, or in xdsenv.py by setting the parameter 'predictions' to True. GUI setting and command line option will override xdsenv.py.
  • fixed: a bug when in command line mode --all in combination with --spacegroup the spacegroup was lost.

XDSAPP3 Version 1.6 (2022-05-20)

  • generate_XDS.INP revision 1.12 (25-MAR-2022) included
  • new: in the Settings tab, Advanced Settings can be set. These are the XDS refinement parameter for IDXREF, INTEGRATE, and CORRECT, which can be individually selected. Can be set via command line options as well (command line mode only).
  • new: additional results file in cif format with entries according to PDBx/mmCIF.
  • new: command line options can be set via a text file, xdsapp3 --cmd @options.file
  • new: a new file - beamlines.py - belongs to the xdsapp3 package. Here, informations about a beamline is recorded, identified with the serial number of the detector. If a detector is recognized, this information will be incorporated in the results.cif file. The file beamlines.py may be populated with entries by time.
  • fixed: in Settings tab, the displayed values should correspond to the actual results
  • fixed a bug in creating symlinks
  • fixed an issue in plotting a Wilson plot, when values are exceedingly large negative 
  • internal: code optimisations
  • updated: help files     

XDSAPP3 Version 1.5c (2022-03-21)

  • new: xdsenv option performance['cluster'], defines the XDS.INP line CLUSTER_NODES= (experimental)
  • new: Eiger file do not need to have _data_ in name
  • fix: option -sx works and only successful data reductions are used, e.g the file XDS_ASCII.HKL is available for a data set.
  • fix: parsing of XDS.INP values nx,ny, overload corrected to be INT
  • fix: parsing of CORRECT.LP corrected
  • fix: bug in check_shutter_issue removed, this caused xdsapp3 to crash if the scaling factor in INTEGRATE.LP was uniform.
  • New HZB-Bessy logo

XDSAPP3 Version 1.5 (2021-10-25)

  • Find File dialog.: added button "Raw Data" to set base directory to data folder, in case host name is in xdsenv.py host list. This should allow a quick go to the data folder. May be useful only at HZB.
  • New "Find" "Find Next" dialog to search in log files, not in debug file (gets too large), also accessible via keyboard shortcuts ctrl-f, ctrl-g. Only active when a logfile is displyed in the "Logfiles and pictures" tab.
  • Space Group: manual setting in GUI, internal detection changed, was sometimes not reliable.
  • fixed an issue, that after "integrate and correct" summary tab and logfile CORRECT.LP was out of sync.
  • fixed an issue, that username was empty.
  • fixed an issue, that data have been written twice into the database (HZB specific)
  • fixed an issue when to many frames are empty (will issue an error message)
  • changed: XSCALE.LP is not deleted and acessible in the logs tab.
  • changed: a single internal call to  "/bin/tcsh" was changed to "/bin/bash" to reduce dpendencies on external programs.

XDSAPP3 Version 1.4b  (2021-07-26)

  • bug in preferences fixed. xdsapp3 crashed when menu preferences was used before any other action.


XDSAPP3 Version 1.4 (2021-07-05)

  • Important: if "RAW_DATA" is part of an image file path and node in xdsenv.hosts results will be stored in a corresponding subdirectory in PROCESSED_DATA: /home/my/RAW_DATA/sub1/sub1 -> /home/my/PROCESSED_DATA/sub1/sub1
  • The data selection window will now remember the last visited directory
  • In command line mode, options --image and --dir now recognises ~ (tilde) as home directory.
  • Changed the color code in the plots: red is always the current plot, blue is the previous plot.
  • A warning window will open if "!!! ERROR !!! INSUFFICIENT PERCENTAGE" in XDS output.
  • A new preference added: "Save intermediate XDS.INP". If selected, all XDS.INP files with time stamp will be saved in a subdirectory 'xdsinp_debug' (useful for debugging).
  • README file updated (tip to LC_ALL valid for all operating systems).
  • In xdsenv.py, clarified info to Albula API, info to HZB specific settings.
  • A rare bug in writing files fixed.
  • A bug in loading data in GUI mode fixed.
  • A bug in setting DIRECTION_OF_DETECTOR_X-AXIS in XDS.INP fixed
  • A bug fixed when refined detector distance after an unsuccessful indexing was not set
  • A bug in XDS_from_H5.py in setting the rotation axis fixed (for Eiger data).

XDSAPP3 Version 1.3 (2021-04-20)

  • Improved data selection window, now displays data file list, but not selectable.
  • New Help menu entry: Check for updates
  • New option --auto: prefix "auto_" to result files <project>.mtz, etc, may be useful in scripted autoprocessing.
  • Changed option --database [username], accepts a username to write this into the database (only for HZB use).


XDSAPP3 Version 1.2 (2021-04-12)

  • New data selection dialog
  • Fixed a bug in CORRECT_last_table view.

XDSAPP3 Version 1.1  (2021-03-15)

  • In xdsenv.py new entry hosts, this defines special local settings (see README).
  • Command line option --image accepts absolute and relative path names.

XDSAPP3 Version 1.0  (2021-03-01)

  • New code basis: Python 3.6+, PyQt5, Matplotlib.
  • Dectris Eiger detectors are supported (suffix ".h5"). To read Eiger data files, it is strongly recommended to use the XDS plugins dectris-neggia or durin-plugin (DLS) in combination with generate_XDS.INP. It is also possible to use the Dectris Python API or the converter eiger2cbf, but this is not recommended.
  • The setup file xdsenv.py has additional sections, performance parameters like number of cpus or processes can be pre-determined here. See comments in the file itself.
  • In the CORRECT plots tab, plots for I/SigI, CC1/2, R_meas, SigAno, AnoCor, and Completeness can be displayed with x-axis as "Resolution" or "1/R2", this can be chosen in the Preferences menu.
  • XDSAPP3 can be used in a command line mode without the dependencies on PyQt5 and Matplotlib (useful for integration in scripted data analysis).
  • New selection "CORRECT Completenes & Quality"  in the "Logfiles and pictures" tab, showing only the last table from the CORRECT run.
  • New Help menu in the GUI. 
  • The overall program stability has been improved.

XDSAPP2, XDSAPP1 Release Notes

Version 2.0  (07/05/2015)

  • Automated detection of anomalous signal and setting of "strict absorption correction" in CORRECT.
  • The fraction of R_free reflections has been changed: instead of 5%, the program now uses 5% if there are less than 42000 unique reflections in the data set, else a maximum 2100 reflections are flagged as R_free. It is checked that at least 1% of the total unique reflections are flagged to avoid later problems with phenix.refine.
  • You can now choose the location of the output directory.
  • In the refinement of the detector distance, the keyword POSITION has been added for compatibility with both old and new XDS versions.
  • If images are created using merge2cbf, it is possible to provide missing header information in a file EXP.INP (XDS format) in the images folder.
  • The overall program stability has been improved.


Version 1.02  (03/06/2014)

  • Hot fix for Pointless, necessary since CCP4-6.4.0 update 014.
  • Fixed output inconsistency between left column and summary tab of the GUI window.
  • Minor bugs corrected in relation with Pointless, XDS alien rejection and manual space group input for the command line version.

Version 1.01  (29/04/2014)

  • Ubuntu fix for compability with the default shell link.
  • Compability with newer generate_XDS.INP script from Kay Diederichs (version 22/04/2014).
  • Support for Rigaku (.osc) detectors (test data set kindly provided by Peter J. Stogios). Crysalis .pck files are now listed in the possible extensions (test data set kindly provided by Vito Calderone), but not supported by generate_XDS.INP. Unless you use a modified version of the script (at your own risk), XDSAPP will not be able to work with those files.
  • Four new fields have been added in the Settings tab to take into account different diffractometer geometries.

Version 1.0  (25/02/2014)

  • New graphical user interface using Python2.6 or higher & Qt4.
  • Use of the script generate_XDS.INP from Kay Diederichs to determine the data collection parameters automatically. No template is needed anymore.
  • Separation of processing and intensities analysis to avoid recalculations during "step-by-step" processing.
  • When loading already processed data sets, a summary of the previous results is shown in the summary tab and the values can be used for further processing.
  • The new button "Default parameters" in the "Settings" tab allows the internal deletion of parameters in case a new processing with different parameters is needed.
  • Fully automatic command line based data processing mode.

Version 0.21

  • Error for PILATUS 6M images with four digits fixed.
  • Image names can now consist of more than one dot (e. g. ab.cd.01_0001.img
  • Spacegroup determination in POINTLESS is now "symmetry-based" instead of "cell-based": space group 18 will always be P21212 irrespective of axis lengths and C2 will always be C2 (instead of I2 in case of an less oblique cell).

Version 0.2

The XDS release of March 15, 2012 replaced Rmrgd-F by a correlaction factor CC(1/2) between random half-datasets and changed the format for reporting SigAno and AnomalCorr in CORRECT.LP (see XDS Release Notes). Unfortunately, XDSAPP 0.1 can not deal with the new format of CORRECT.LP. XDSAPP 0.2 can handle the new format as well as the old one and generates a plot for CC(1/2) within the "CORRECT" tab if XDS Version March 15, 2012 is installed.