XDSGUI: Difference between revisions

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It graphically displays the ASCII and [http://www.bernstein-plus-sons.com/software/CBF 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, in a simple, user-modifiable and user-extensible way.

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 also gives access to structure solution, through George Sheldrick's SHELXC, SHELXD and SHELXE programs via the [[XDSGUI#SHELX|SHELX]] tab, and to Isabel Uson's [https://ibmb.csic.es/en/department-of-structural-and-molecular-biology/crystallographic-methods/ 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 .

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* The third item ("Optimizing data quality") offers commands that manipulate [[XDS.INP]] in several ways. Please note: the popup "XDS.INP has been changed externally" is emitted by the Qt system and cannot be switched off. It appears if one of the scripts changes XDS.INP while it is opened by XDSGUI (which is always the case) . Thus, one should simply press the "Reload" button. The user-definable command may be used e.g. for <pre>echo RELRAD=7 ! default is 5 >x; grep -v BEAM_DIVERGENCE XDS.INP >>x; cat x > XDS.INP; rm x</pre> This provides more pixels to the background estimation (for another INTEGRATE), and is useful for weakly exposed data sets which have mostly pixels with zero counts.

* The last item ("Further analyses") offers useful commands. "determine spacegroup with pointless" runs [[pointless]] against the XDS_ASCII.HKL file. The button "show spots in reciprocal space" runs [[spot2pdb]] to show you the reflections of SPOT.XDS in reciprocal space, with coot. You see the reflections that could be indexed in IDXREF in yellow, the not-indexed ones in pink, the rotation axis in blue and the origin as a blue cross. Ice rings and additional lattices can be easily identified - see [[spot2pdb]] for examples!

* The last item ("Further analyses") offers useful commands. "determine spacegroup with pointless" runs [[pointless]] against the XDS_ASCII.HKL file. The button "show spots in reciprocal space" runs [[spot2pdb]] to show you the reflections of SPOT.XDS in reciprocal space, with coot. You see the reflections that could be indexed in IDXREF in yellow, the not-indexed ones in pink, the rotation axis in blue and the origin as a blue cross. Ice rings and additional lattices can be easily identified - see [[spot2pdb]] for examples! Reason for possible failure: the spot2pdb program expects SPOT.XDS to have 7 columns, as IDXREF attaches 3 columns with indices to the 4 columns that COLSPOT wrote. So you cannot visualize SPOT.XDS from COLSPOT - it has to be written by IDXREF.

* Useful scripts for user tools are shared in [[XDSGUI User tools]]

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Version 2023-12-29 now displays CBF files written at PETRA-III BLs.

Version 2024-11-04: Made tool categories and all button descriptions customizable. Prediction tool has note about customization. Add line-break to INTEGRATE graph for missing data regions. Works on Wayland. Bug fixes. (Juno Krahn)

Version 2025-05-15: Fix bug that SHELXC could not work with long paths (77 characters) to XDS_ASCII.HKL.

== See also ==

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 It graphically displays the ASCII and [http://www.bernstein-plus-sons.com/software/CBF 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, in a simple, user-modifiable and user-extensible way.
-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 also gives access to structure solution, through George Sheldrick's SHELXC, SHELXD and SHELXE programs via the [[XDSGUI#SHELX|SHELX]] tab, and to Isabel Uson's [https://ibmb.csic.es/en/department-of-structural-and-molecular-biology/crystallographic-methods/ 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 .
@@ Line 99: / Line 99: @@
 * The third item ("Optimizing data quality") offers commands that manipulate [[XDS.INP]] in several ways. Please note: the popup "XDS.INP has been changed externally" is emitted by the Qt system and cannot be switched off. It appears if one of the scripts changes XDS.INP while it is opened by XDSGUI (which is always the case) . Thus, one should simply press the "Reload" button. The user-definable command may be used e.g. for <pre>echo RELRAD=7 ! default is 5 >x; grep -v BEAM_DIVERGENCE XDS.INP >>x; cat x > XDS.INP; rm x</pre> This provides more pixels to the background estimation (for another INTEGRATE), and is useful for weakly exposed data sets which have mostly pixels with zero counts.
-* The last item ("Further analyses") offers useful commands. "determine spacegroup with pointless" runs [[pointless]] against the XDS_ASCII.HKL file. The button "show spots in reciprocal space" runs [[spot2pdb]] to show you the reflections of SPOT.XDS in reciprocal space, with coot. You see the reflections that could be indexed in IDXREF in yellow, the not-indexed ones in pink, the rotation axis in blue and the origin as a blue cross. Ice rings and additional lattices can be easily identified - see [[spot2pdb]] for examples!
+* The last item ("Further analyses") offers useful commands. "determine spacegroup with pointless" runs [[pointless]] against the XDS_ASCII.HKL file. The button "show spots in reciprocal space" runs [[spot2pdb]] to show you the reflections of SPOT.XDS in reciprocal space, with coot. You see the reflections that could be indexed in IDXREF in yellow, the not-indexed ones in pink, the rotation axis in blue and the origin as a blue cross. Ice rings and additional lattices can be easily identified - see [[spot2pdb]] for examples! Reason for possible failure: the spot2pdb program expects SPOT.XDS to have 7 columns, as IDXREF attaches 3 columns with indices to the 4 columns that COLSPOT wrote. So you cannot visualize SPOT.XDS from COLSPOT - it has to be written by IDXREF.
 * Useful scripts for user tools are shared in [[XDSGUI User tools]]
@@ Line 195: / Line 195: @@
 Version 2023-12-29 now displays CBF files written at PETRA-III BLs.
+Version 2024-11-04: Made tool categories and all button descriptions customizable. Prediction tool has note about customization. Add line-break to INTEGRATE graph for missing data regions. Works on Wayland. Bug fixes. (Juno Krahn)
+Version 2025-05-15: Fix bug that SHELXC could not work with long paths (77 characters) to XDS_ASCII.HKL.
 == See also ==