XDSGUI: Difference between revisions

* the simple editor operating in the tabs understands ctrl-X (cut), ctrl-c (copy), ctrl-v (paste), ctrl-z (undo) and ctrl-Z (redo).

* ctrl-+ (control-plus) and ctrl-- (control-minus) enlarge or decrease the font size of characters.

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 to create a first XDS.INP from the header of the raw data frame that is being displayed. (Note: this button needs to be used only once per dataset; all later changes to XDS.INP are done by different means - manually or scripted) The blue circle(s) delineate(s) the area(s) of the detector within TRUSTED_REGION; the green circles correspond to INCLUDE_RESOLUTION_RANGE, and the red [[XDSGUI#Technical aspects of XDSGUI usage|hatched]] regions correspond to EXCLUDE_RESOLUTION_RANGEs. The locations of the circles are not as accurate as those that XDS uses internally, because only values from XDS.INP, not the refined ones from XPARM.XDS) are used to calculate the resolution, and do not currently account for segmented or curved detectors. After XDS has indexed spots, they can be visualized with the *predictions* button.

* "Load" a data file (e.g. FRAME.cbf) or, in case of Eiger HDF5 data, a frame based on a *master.h5 file to have it displayed. The pane can be "dragged" with the left mouse button; the mouse wheel zooms. The parameters in the XDS.INP tab are taken for resolution calculations (i.e. the frame header is not being interpreted in any way). For HDF5 data, the *master.h5 file must be loaded; this will automatically show its first frame (note that for this to work, the path to the correct [[XDSGUI#Technical aspects of XDSGUI usage|"generic library"]] must be specified in Menu/Settings). The frame number can be chosen with the selection box on the right, or the up-down arrows.

The right side of the tab shows the indexed (black) and not-indexed (red) reflections of [[SPOT.XDS]].

XDSGUI depends on [[generate_XDS.INP]], [[XDS-viewer]], and of course [[XDS]] (both the xds and xds_par binaries!), [[XDSCONV]], and [[2cbf]]. The ''statistics'' tab requires [[XDSSTAT]] and [[XDSCC12]]. For visualization of the raw data frames in the ''Frame'' tab, [[Eiger]] data processing requires either the [https://www.dectris.com/features/features-eiger-x/h5toxds/ <code>H5ToXds</code>] binary or the [https://www.globalphasing.com/autoproc/wiki/index.cgi?DataProcessingHdf5 <code>hdf2mini-cbf</code>] binary (needs autoPROC license). Only the latter works for the .h5 files produced at Diamond Light Source; if hdf2mini-cbf should be used, it needs to be symlinked under the name H5ToXds (because XDSGUI has the name H5ToXds hardwired). ([https://github.com/biochem-fan/eiger2cbf <code>eiger2cbf</code>] does not seem to work with Eiger2 .h5 files.)

The program can be downloaded, by academic users, as binary for Linux [https://{{SERVERNAME}}/pub/linux_bin/xdsgui 64bit] (compiled on RHEL7) and for Mac ([https://{{SERVERNAME}}/pub/mac_bin/xdsgui_mac_intel.dmg Intel] and [https://{{SERVERNAME}}/pub/mac_bin/xdsgui_mac_silicon.dmg Apple Silicon], respectively).  

  xdsgui: error while loading shared libraries: libQtGui.so.4: cannot open shared object file: No such file or directory

or similar for libQtCore.so.4 or libQtOpenGL.so.4 , you should install the Qt5 version which is now the default on Linux.

# ''Problem description: On the Mac, after loading frames, by clicking “generate XDS.INP”, the program gives some strange symbol “” in XDS.INP. And the more you click “save” button, the more “” appeared. This looks like <br>SPACE_GROUP_NUMBER=0  ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90  .''<br> The problem is due to the “Rich text” format in TextEdit when saving "generate_XDS.INP". It is solved by re-downloading the script, and changing format to Plain - everything is working now.

# on a Mac, you may find a stream of the following error messages in the console window: <code>Jan 31 14:35:17  xdsgui[20939] <Error>: Error: this application, or a library it uses, has passed an invalid numeric value (NaN, or not-a-number) to CoreGraphics API and this value is being ignored. Please fix this problem. Jan 31 14:35:17  xdsgui[20939] <Error>: If you want to see the backtrace, please set CG_NUMERICS_SHOW_BACKTRACE environmental variable.</code> This sounds terrible, but is actually harmless. Since it is a message from Qt (which XDSGUI uses for graphics), ''it does not compromise the XDS data processing in any way''. If it bothers you, just suppress the printout of these messages, by <code>xdsgui 2>&1 | egrep -v 'CoreGraphics|CG_NUMERICS'</code>

* The green INCLUDE_RESOLUTION and red semi-transparent EXCLUDE_RESOLUTION_RANGE circles in the Frame tab as well as all resolution values in the Frame and IDXREF tabs are calculated from values in XDS.INP (rather than from the refined values in XPARM.XDS, which XDS uses). For the (segmented) Pilatus 12M, the calculations in XDSGUI do not give the correct results - this is fixed in versions from Sep-2023 onwards.