Cheat sheet

In the following, I describe the steps that I typically do for processing a dataset. The links given in the form XDSGUI#Frame refer to the webpage wiki.uni-konstanz.de/xds/index.php/ , in this example wiki.uni-konstanz.de/xds/index.php/XDSGUI#Frame .

Action	why? what to look out for? what else to know?
1. open terminal and move the window to the left side of the screen. Optional (since this can be done in XDSGUI): cd to an existing XDS directory, or create a new (empty) directory (mkdir <name>). Type 'xdsgui' and move its window so that you still see the left half of the terminal window.	Keeping the terminal window in sight makes it possible to see some output of XDSGUI, e.g. error messages, or the pointless output.
2. click the 'Projects' tab and either choose an existing entry (if there is a list of previous projects) or browse to an existing XDS directory, or create a new (empty) directory	Note that the directory name appears in the title bar of the XDSGUI window!
3. click the 'Frame' tab and load a frame of your dataset. Click 'generate XDS.INP' - this reads the header of that frame, and counts the frames of the dataset. Use Zoom, Contrast and Brightness and move around the frame to evaluate the shape and separation of the reflections: are they smeared or sharp, tiny or broad, regular of broken, symmetric or asymmetric? Look at other frames as well!	Watch the green crosshair at ORGX, ORGY, the green circle around it (lower INCLUDE_RESOLUTION_RANGE), the red UNTRUSTED_RECTANGLEs at the module borders, and the blue TRUSTED_REGION appear.
4. mask the shaded regions of the detector: most likely the beamstop shadow, and the beamstop holder. There is a button on the upper right with three tools: UNTRUSTED_ELLIPSE, UNTRUSTED_RECTANGLE, UNTRUSTED_QUADRILATERAL	This step is important, do not skip it! Reason is in the XDSGUI paper (reference at the end). More technical explanation of the tools at XDSGUI#Frame
5. click the 'XDS.INP' tab and inspect its contents. For HDF5 data, make sure that the LIB= line points to the "Generic frame library" that appears in XDSGUI under 'Preferences' (macOS) or 'settings' (Linux). For a first XDS run, typically you would leave everything else at its defaults, except with broad reflections covering many pixels, set MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT to 6 instead of 3.	Depending on where you measured the HDF5 data, export the environment variable NEGGIA_PATH=/usr/local/lib64/dectris-neggia.so or DURIN_PATH=/usr/local/lib64/durin-plugin.so (the path must match YOUR computer; the paths given are just reasonable defaults). That should work for both XDSGUI and XDS.
6. click 'run XDS' and watch the adjacent tabs to the right flash yellow as they are being filled with text and graphics. Inspect the left (text) and right (graphics) sides of the tabs.	If XDS stops after the IDXREF step (with ERROR in IDXREF.LP), it most often happens because it could only index less than 50% of the spots. This may be due to ice rings that obviously cannot be indexed, or due to additional lattices. In most cases, this should just prompt you to think about the possible reasons. To continue, just set JOB=DEFPIX INTEGRATE CORRECT in the XDS.INP tab, and click 'run XDS'.
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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 .