Crystallographic data processing & analysis
A user-friendly interface for XDS. From the images to a merged data set and Table 1, all in one place in your browser. Learn as you process. Free and open source.
Version 0.7.0b (beta) · All versions · GPL-3.0 · DOI
One real data set, followed through the pipeline. Keep scrolling.
| Bravais | Qual. | a | b | c |
|---|---|---|---|---|
| aP | 0.0 | 77.3 | 77.4 | 161.1 |
| mC | 1.9 | 119.4 | 98.3 | 161.1 |
| oC ★ | 5.4 | 98.3 | 119.4 | 161.1 |
| Axis | Expected | Detected |
|---|---|---|
| a (h00) | none | ✓ none |
| b (0k0) | none | ✓ none |
| c (00l) | 2₁ | ✓ 2₁ |
Values in parentheses are for the highest-resolution shell.
1XYCORR · INIT
Point CrystalPilot at your images. It writes XDS.INP from the image header, and AutoPilot imports the one written at the beamline when it matches. Eiger HDF5, CBF and IMG frames open in the built-in viewer.
In this simulation, point at a spot to read its indices and resolution. Move the detector and the rings follow.
2COLSPOT
Run the pipeline step by step, to IDXREF, Integrate & Correct, or all at once, with a live log. The XDS.INP keywords are laid out as fields, and the optional ones have a switch to make them active or commented, so SPOT_RANGE is one field away.
3IDXREF
The spots go into reciprocal space, and the lattice shows up. CrystalPilot pulls the outcome out of IDXREF.LP with the key values colour-coded: indexed fraction, spot and spindle deviations, refined beam centre and distance, and the Bravais table with the suggested lattice.
Look down c*. Only every other point is there: h + k is even, the C-centring.
4DEFPIX · XPLAN · INTEGRATE · CORRECT
The whole of CORRECT.LP is there to review, while the key values are pulled out and graphed, with a Matthews calculator, ISa, ice-ring analysis and the systematic absences. Screw axes are compared with the space group, and AutoPilot sets them from the absences.
In the 0kl plane the other columns have every l. The column at k = 0 has only even l: a 2₁ axis along c.
5XSCALE
The common cut-off criteria are marked directly on the statistics table and the graph, and each one goes into XSCALE.INP in one click. The Cutoff Preference sets which one the XSCALE autofill takes. AutoPilot has its own setting.
Click a criterion under the graph. These are the real shells of this data set.
6XDSCONV · Statistics
Table 1 is built from the processing statistics, with the outer shell in parentheses. Copy it as TSV or LaTeX, or export a .csv. XDSCONV prepares the merged data for refinement and phasing: an MTZ when CCP4 is installed, or SHELX and XtalView formats.
The moving pictures are calculated in your browser from the cell, space group and detector geometry of this data set (EIGER 16M, C222₁, 1800 frames at 0.2°). The crystal orientation is made up, and the spot intensities are made up around its real I/σ per shell. The numbers in the panels and tables, and the screenshots, come from its actual processing.
A short tour, and videos from CrystalPilot's own manual.
The highlights: input filled in for you, processing, key metrics, analysis tools, the frame viewer, work modes and Table 1.
Read the code, report a problem or ask for a feature on GitHub. Free to use, study, change and share under the GNU GPL.
Four levels set how much of the program you see. A higher level only adds, it never removes anything.
CrystalPilot does not replace XDS. It writes the input, runs XDS, XSCALE and XDSCONV, and reads what they report. XDS.INP stays a plain file, and the whole of every LP file is there to read.
Change a field here and the line changes. The editor in the program has the same fields and switches.
CrystalPilot is in beta. If something goes wrong, click ⚠ Report a problem at the top of the interface, or open an issue on GitHub.
Version 0.7.0b (beta)
XDS has no Windows version, so CrystalPilot runs inside WSL2. The one-click installer sets that up for you, and you never need a Linux terminal. Windows may warn you the first time: click More info, then Run anyway.
Download installerRuns natively with the macOS build of XDS. Unpack the package and double-click mac/Install CrystalPilot.command (the first time: right-click, Open). Needs Python 3.7 or newer.
Download packageInstall it with a desktop entry and a crystalpilot command. Or take the single Python file, no installation: copy it into your XDS folder and run it.
Download packageFirst download from their authors: XDS, DECTRIS neggia for Eiger data, and optionally CCP4 for POINTLESS, AIMLESS and the MTZ export. XDS and CCP4 are free for academic use.
Step-by-step instructions are in the README. Installers and a complete package for all systems are on the releases page.
Please cite it together with the programs it runs. With gratitude to Wolfgang Kabsch for XDS; Greta Assmann, Wolfgang Brehm and Kay Diederichs for XDSCC12; Phil Evans for POINTLESS, and Phil Evans and Garib Murshudov for AIMLESS; CCP4 for the CCP4 suite; Marcin Wojdyr for gemmi; and DECTRIS for neggia. References
CrystalPilot