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XDSGUI: Difference between revisions
→Frame: mention HKL indices display
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XDSGUI gives access to George Sheldrick's SHELXC, SHELXD and SHELXE programs, via the [[XDSGUI#SHELX|SHELX]] tab, and to Isabel Uson's ARCIMBOLDO programs, via the [[XDSGUI#ARCIMBOLDO|ARCIMBOLDO]] tab. | XDSGUI gives access to George Sheldrick's SHELXC, SHELXD and SHELXE programs, via the [[XDSGUI#SHELX|SHELX]] tab, and to Isabel Uson's ARCIMBOLDO programs, via the [[XDSGUI#ARCIMBOLDO|ARCIMBOLDO]] tab. | ||
The XDSGUI paper (Brehm, Triviño, Krahn, Usón and Diederichs (2023) XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO. J. Appl. Cryst. 56) is open access at https://doi.org/10.1107/S1600576723007057 . | |||
== How to use XDSGUI == | == How to use XDSGUI == | ||
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=== Technical aspects of XDSGUI usage === | === Technical aspects of XDSGUI usage === | ||
* the simple editor operating in the tabs understands ctrl-X (cut), ctrl-c (copy), ctrl-v (paste), ctrl-z (undo) and ctrl-Z (redo) | * 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. | ||
* with SHIFT+(left-mouse-click) in the "Frame" tab one can set the direct beam impact position. | |||
* flexibility of operation: all commands in the [[XDSGUI#TOOLS|TOOLS]] tab may be modified by the user, simply by modifying the (bash) code in the text field below the button. The user-changed command is automagically and permanently stored in ~/.xds-gui . The user may also change what is written on a button, by editing ~/.xds-gui. It should be obvious what to change. | * flexibility of operation: all commands in the [[XDSGUI#TOOLS|TOOLS]] tab may be modified by the user, simply by modifying the (bash) code in the text field below the button. The user-changed command is automagically and permanently stored in ~/.xds-gui . The user may also change what is written on a button, by editing ~/.xds-gui. It should be obvious what to change. | ||
* Menu / Settings is used for specifying: In "Paths" the "generic library" (e.g. /usr/local/lib64/dectris-neggia.so) for reading HDF5 files and for binaries (xds_par, xscale_par, shelxc/d/e, ...), in "Appearance" (font size and default plot height), and in "User Buttons" the names for user defined tool buttons. The Settings menu can be opened on the Mac by clicking upper-left on "xdsgui", then "Preferences ...", or pressing the "Command" (⌘) key and the "," key. Changed settings are automatically stored in ~/.xdsgui . | * Menu / Settings is used for specifying: In "Paths" the "generic library" (e.g. /usr/local/lib64/dectris-neggia.so) for reading HDF5 files and for binaries (xds_par, xscale_par, shelxc/d/e, ...), in "Appearance" (font size and default plot height), and in "User Buttons" the names for user defined tool buttons. The Settings menu can be opened on the Mac by clicking upper-left on "xdsgui", then "Preferences ...", or pressing the "Command" (⌘) key and the "," key. Changed settings are automatically stored in ~/.xdsgui . | ||
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=== Frame === | === 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 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 | 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. After XDS has indexed spots, they can be visualized with the *predictions* button. Prediction display can be toggled off and on to refresh predictions from an updated XPARM.XDS, and with refined BEAM_DIVERGENCE from INTEGRATE. | ||
When predictions are displayed, the corresponding HKL indices will be displayed in the pixel value panel. HKL indices depend on the current spacegroup, which is also displayed, and will be P1 if SPACE_GROUP_NUMBER is not defined in XDS.INP. | |||
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 placed in the XDS.INP tab. Step-by-step: | 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 placed in the XDS.INP tab. Step-by-step: | ||
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=== [[IDXREF]] === | === [[IDXREF]] === | ||
detailed explanation of output: see [[IDXREF.LP]]. | detailed explanation of output: see [[IDXREF.LP]]. | ||
The right side of the tab shows the indexed (black) and not-indexed (red) reflections of [ | The right side of the tab shows the indexed (black) and not-indexed (red) reflections of [https://xds.mr.mpg.de/html_doc/xds_files.html#SPOT.XDS SPOT.XDS]. | ||
=== DEFPIX === | === DEFPIX === | ||
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The XDSGUI paper Brehm, Triviño, Krahn, Usón and Diederichs (2023) XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO. J. Appl. Cryst. 56, is open access at https://doi.org/10.1107/S1600576723007057 | The XDSGUI paper Brehm, Triviño, Krahn, Usón and Diederichs (2023) XDSGUI: a graphical user interface for XDS, SHELX and ARCIMBOLDO. J. Appl. Cryst. 56, is open access at https://doi.org/10.1107/S1600576723007057 | ||
Version 2023-11-21 fixes a bug (predictions were only available if XDS.INP was older than XPARM.XDS). To update XPARM.XDS, run JOB=IDXREF or "cp GXPARM.XDS XPARM.XDS" in the Tools tab. Please note that hkl values in predictions are based on the spacegroup in XPARM.XDS, not on the spacegroup in XDS.INP . | |||
Version 2023-12-29 now displays CBF files written at PETRA-III BLs. | |||
== See also == | == See also == | ||