Cheat sheet
In the following, I describe the steps that I typically do in my processing workflow. The links given in the form XDSGUI#Frame refer to the webpage https://wiki.uni-konstanz.de/xds/index.php/ (in this example https://wiki.uni-konstanz.de/xds/index.php/XDSGUI#Frame ). I assume that the programs have been properly installed - see . Troubleshooting hints are at Problems.
| Action | why? what to look out for? what else to know? | ||
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1. open a terminal and move the window to the left side of the screen. If you work with HDF5 data, type Type |
Keeping the terminal window to the left of the XDSGUI window makes it possible to see some screen output of XDSGUI, e.g. error messages, or the pointless output. For HDF5 data from DIAMOND, use export DURIN_PATH=/usr/local/lib64/durin-plugin.soinstead (of course with the correct path).
Optionally, before typing |
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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
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If XDS's files already exist in the XDS directory, their content is shown in the tabs of XDSGUI. Note that the XDS directory name appears in the title bar of the XDSGUI window! | ||
3. click the Frame tab and load a frame of your dataset (for HDF5, load xxx_master.h5). 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 or broken, symmetric or asymmetric? Look at other frames as well!
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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. The corresponding keyword=parameter lines in XDS.INP have the same colour code.
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| 4. mask the shaded regions of the detector: at least 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 . Wrongly positioned UNTRUSTED areas can be removed by deleting their lines in XDS.INP .
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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.
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| 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 .