Joint Research Group Macromolecular Crystallography
XDSAPP3 - Release notes
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.