Difference between revisions of "XDSGUI"

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== Tools ==
 
== Tools ==
  
offers possibilities for running short scripts. Several such scripts are pre-defined; the user may create her own scripts. The first item offers to run [[XDS-viewer]] for displaying the predicted pattern of reflections for a user-specified frame, together with the frame itself. The other pre-defined scripts run commands that either simplify to save/restore the current data processing files to/from a "save" directory, or to manipulate [[XDS.INP]] in several ways, or to run e.g. [[pointless]] on the generated XDS_ASCII.HKL file.  
+
offers possibilities for running short scripts. Several such scripts are pre-defined; the user may create her own scripts. If scripts are modified, they are saved to ~/.xds-gui . <br>The first item offers to run [[XDS-viewer]] for displaying the predicted pattern of reflections for a user-specified frame, together with the frame itself. <br>The other pre-defined scripts run commands that either simplify to save/restore the current data processing files to/from a "save" directory, or to manipulate [[XDS.INP]] in several ways, or to run e.g. [[pointless]] on the generated XDS_ASCII.HKL file.  
  
 
As long as the XDSSTAT tab is non-functional, I suggest to put the following into a "User-defined command" of the Tools tab:
 
As long as the XDSSTAT tab is non-functional, I suggest to put the following into a "User-defined command" of the Tools tab:
  
 
  echo | xdsstat > XDSSTAT.LP; loggraph XDSSTAT.LP
 
  echo | xdsstat > XDSSTAT.LP; loggraph XDSSTAT.LP
 
If scripts are modified, they are saved to ~/.xds-gui .
 
  
 
== XDSSTAT ==
 
== XDSSTAT ==

Revision as of 15:16, 23 May 2013

XDSgui is a GUI (graphical user interface) for XDS that is supposed to help both novice and experienced users. It graphically displays the ASCII and cbf files that XDS writes, and can run useful shell commands with a simple mouse click. The design goal of the program is to enable XDS data processing without the commandline, and to supply additional graphical information.

The main window of XDSgui has the following sub-windows organized as tabs:


Projects

stores names of directories which contain files from XDS processing. If none of these is selected, the current directory is used. A new directory may be created. The list of project directories is saved to ~/.xds-gui .

Frame

to display existing 2-dimensional data frames, or to start XDS data processing by displaying a raw data frame. In the latter case, the "generate XDS.INP" button runs the generate_XDS.INP script for the raw data frame that is being displayed. The blue circles correspond to the areas of the detector that are within TRUSTED_REGION; the green circles correspond to INCLUDE_RESOLUTION_RANGE, and the red hatched regions correspond to EXCLUDE_RESOLUTION_RANGEs. The locations of the circles are not as accurate as those that XDS uses internally, because a simplified formula is used to calculate the resolution; this e.g. does not take care of detector swingout or otherwise skew geometry. Untrusted areas can be specified by the user, using two (UNTRUSTED_ELLIPSE; UNTRUSTED_RECTANGLE) or four (UNTRUSTED QUADRILATERAL) right mouse clicks. The resulting areas are shown with red outline, and the keyword/parameter pairs are shown in the XDS.INP tab.

XDS.INP

this shows the current XDS.INP file. Coloured items correspond to the circles of the Frame tab. Changes can be made with the simple editor, and the new version can be saved. A run of xds_par can be started (and killed).
The XDS.INP tab is directly connected with the Frame tab; changing a value in XDS.INP results in immediate change in the Frame tab. This means that e.g. an UNTRUSTED area that was positioned wrongly can be edited or simply removed in the XDS.INP tab.

Output from XDS

XYCORR

shows XYCORR.LP

INIT

shows INIT.LP

COLSPOT

shows COLSPOT.LP

IDXREF

shows IDXREF.LP

DEFPIX

shows DEFPIX.LP

INTEGRATE

shows INTEGRATE.LP on the left side. During the INTEGRATE step, the temporary files are displayed. On the right side, plots of the tabular quantities given for each frame, or for each batch of data are shown. For the refined quantities, only the changes are plotted.

CORRECT

shows CORRECT.LP on the left, and plots of tabular quantities on the right. The upper line in the I/sigma plot gives [math]\displaystyle{ {I/Sigma(I)}^{asymptotic} }[/math] ([Diederichs, Acta Cryst. (2010). D66, 733-740 http://dx.doi.org/10.1107/S0907444910014836]). The three lines in the Chi^2 plot are the Chi^2 values obtained during scaling, for the ABSORP, MODPIX and DECAY corrections, respectively.

Tools

offers possibilities for running short scripts. Several such scripts are pre-defined; the user may create her own scripts. If scripts are modified, they are saved to ~/.xds-gui .
The first item offers to run XDS-viewer for displaying the predicted pattern of reflections for a user-specified frame, together with the frame itself.
The other pre-defined scripts run commands that either simplify to save/restore the current data processing files to/from a "save" directory, or to manipulate XDS.INP in several ways, or to run e.g. pointless on the generated XDS_ASCII.HKL file.

As long as the XDSSTAT tab is non-functional, I suggest to put the following into a "User-defined command" of the Tools tab:

echo | xdsstat > XDSSTAT.LP; loggraph XDSSTAT.LP

XDSSTAT

As long as the tab is non-functional, put the following into a "User-defined command" of the Tools tab:

echo | xdsstat > XDSSTAT.LP; loggraph XDSSTAT.LP

XDSCONV

a simple XDSCONV.INP may be edited by the user, and saved. Upon clicking a button, xdsconv is run and if necessary a MTZ file is produced. XDSCONV.LP may be displayed.

Availability

The program is under development and has bugs. If it crashes, it should simply be restarted. A crash of the program does not interfere with the operation of XDS.

The current version of the program can be downloaded from [1] (Linux 64bit), [2] (Linux 32bit), or [3] (Mac OSX 10.7).

Dependencies

The program depends on the availability of generate_XDS.INP, XDS-viewer, and of course xds_par, xds, xdsconv, and xscale. One of the items in the Tools tab requires xxdiff. The xdsstat tab requires xdsstat.

News

program updated May 22 14:40 CEST

Known bugs / problems / workarounds

  1. TOOLS: "Show frame..." It creates everything shown in the commandline but it seem to us that everything runs in the background. Therefore xds-viewer does not open anywhere as it is not seen. Also, it would be great if this image together with the predictions would be re-directed to the Frame tab.
    On Linux, the xds-viewer window is brought to the foreground automatically, whereas on the Mac this does not seem to happen. However, an icon for xds-viewer appears in the dock (on the right) and I can double-click it to see the xds-viewer window. I have no idea how to bring xds-viewer to the foreground automatically, and I need input from people who know Macs and tell me how to do it (on the commandline!). The reason why we do not open automatically in the Frame tab is that one can have several xds-viewer windows open at the same time, and compare the patterns. As a workaround, you can manually open the resulting temp/FRAME_$X.cbf in the FRAME tab.
  2. TOOLS: "Further analyses" Again pointless runs nicely but there is no output for the user.
    Could it be that you started xds-gui by double-clicking its icon in the Finder? In that case, there is no output visible, because there is no console. Unfortunately, for all the Tools, the output is in the console window where xds-gui was started. We will try to find out how to open a window where the output is then shown. Thus, currently the workaround for this problem is to start xds-gui in a console window.