CRYSTFEL(7)

💖 NAME 💖

okay so this is CRYSTFEL(7), from the Miscellaneous Information Manual — the CrystFEL overview page, bestie. 💅

CrystFEL - data processing for serial crystallography. That’s the whole NAME vibe, and we’re moving on because there is so much more. ✨

🦋 DESCRIPTION 🦋

CrystFEL is a whole suite of programs for processing data from serial crystallography experiments — the kind performed at synchrotron and X-ray free-electron laser facilities, and also in your home lab using an electron microscope. Main character energy fr fr. 👑

The programs in the suite are:

• indexamajig — the batch indexing, integration and data reduction program. It produces a "stream" containing the indexing and integration results for each diffraction pattern. Iconic. 💫
• process_hkl — a tool that merges intensities from many patterns into a single reflection list, via the Monte Carlo method. Slay. 🎀
• partialator — the full scaling and post-refinement process for accurate merging of data and outlier rejection. It’s giving “final boss of merging.” 🔥
• ambigator — a tool for resolving indexing ambiguities. No cap, it’s literally there to untangle the confusion. 🌀
• get_hkl — a tool for manipulating reflection lists, such as performing symmetry expansion. Very “let me adjust that for you” energy. 💅
• cell_tool — a tool for manipulating unit cell files, such as applying transformations. 🧰
• cell_explorer — a tool for examining the distributions of unit cell parameters. It’s giving data detective. 🔍
• compare_hkl and check_hkl — tools for calculating figures of merit, such as completeness and R-factors. The math besties. 🧮
• render_hkl — a tool for rendering slices of reciprocal space in two dimensions. Pretty pictures, but scientific. 🌈
• align_detector — a program to refine and optimize detector geometry. Basically detector glow-up. 📐
• list_events — a tool for creating lists of events from multi-event data files. Event planning, but make it crystallography. 🗓️
• whirligig — a tool for locating runs of crystals with similar orientations, e.g. from 'mini rotation series' arising from the use of a slow extrusion sample injector. The name is a whole vibe, honestly. 🎠
• make_pixelmap — a tool for creating pixel maps for Cheetah, OnDA etc. Pixel map icon behavior. 🗺️
• adjust_detector — a tool to alter detector geometry. Sometimes you just gotta adjust. 🛠️

There is also a folder full of scripts for achieving many related tasks. Little helpers everywhere. 🧚

CrystFEL mostly works with images stored in HDF5 format, unit cell data in PDB format, and reflection lists in plain text format (i.e. not MTZ). There are scripts for converting both ways between plain text reflection lists and MTZ files. So convenient. 💖

Please see the individual manual pages for the CrystFEL programs for detailed information. iykyk, the deep lore lives there. 📚

🎀 CITING CRYSTFEL 🎀

If CrystFEL was important for your research, please consider citing the following article:

T. A. White, R. A. Kirian, A. V. Martin, A. Aquila, K. Nass, A. Barty and H. N. Chapman. "CrystFEL: a software suite for snapshot serial crystallography". J. Appl. Cryst. 45. doi:10.1107/S0021889812002312

Please let us know (see below) about your publication, so we can include it in the list of examples on the CrystFEL website. We wanna see your work, bestie! 🫶

🌸 SYMMETRY IN CRYSTFEL 🌸

With only a very few exceptions, CrystFEL is not interested in space groups. Instead, it deals with point groups which embody the information about how data should be merged from different crystals. Every space group belongs to exactly one point group, and you can look up the right one in the International Tables or using the symmetry tables accompanying the CrystFEL source (or to be found on the CrystFEL website in the Theory section). Very demure, very point-group. 💅

You can append _uaX to any of the point group symbols listed below, where X is a, b or c. This will specify the 'unique' axis for lattices which have one. 🧭

The default unique axis, where this makes sense, is c. Good to know. ✨

Here is a list of all the possible crystallographic point groups, written as they will be accepted by CrystFEL. Refer to this list if you experience difficulty with -y at any time. The -y struggle is real, but we move. 😭

• Triclinic — 1, -1.
• Monoclinic — 2/m, 2, m.
• Orthorhombic — mmm, 222, mm2.
• Tetragonal — 4/m, 4, -4, 4/mmm, 422, -42m, -4m2, 4mm.
• Trigonal (rhombohedral axes) — 3_R, -3_R, 32_R, 3m_R, -3m_R.
• Trigonal (hexagonal axes) — 3_H, -3_H, 321_H, 312_H, 3m1_H, 31m_H, -3m1_H, -31m_H.
• Hexagonal — 6/m, 6, -6, 6/mmm, 622, -62m, -6m2, 6mm.
• Cubic — 23, m-3, 432, -43m, m-3m.

🌟 FUNDING ACKNOWLEDGEMENTS 🌟

Development of CrystFEL is primarily funded by the Helmholtz Association via DESY. Big thank you energy. 🫶

Partial funding for CrystFEL has been provided by:

• The consortium DAPHNE4NFDI in the context of the work of the NFDI e.V. The consortium is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - project number 460248799 (2022-).
• European Union’s Horizon 2020 research and innovation programme under grant agreement No 857641 (ExPaNDS) (2019-2023).
• X-Probe, a project of the European Union's 2020 Research and Innovation Program Under the Marie Skłodowska-Curie grant agreement 637295 (2015-2018).
• The BMBF German-Russian Cooperation SyncFELMed, grant 05K14CHA (2014-2017).
• BioStruct-X, a project funded by the Seventh Framework Programme (FP7) of the European Commission (2011-2016).

👑 AUTHOR 👑

This page was written by Thomas White and Valerio Mariani. Authors ate, no crumbs. 💖

💀 REPORTING BUGS 💀

Report bugs to taw@physics.org, or visit http://www.desy.de/~twhite/crystfel. Please do, bestie — bugs deserve to be seen and fixed. 🐛

💅 COPYRIGHT AND DISCLAIMER 💅

Copyright © 2012-2024 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. 📜

Please read the AUTHORS file in the CrystFEL source code distribution for a full list of contributions and contributors. Shoutout to everyone involved. ✨

CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Free software rights, periodt. 💚

CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Important legal caveat, not me skipping it. 🚨

You should have received a copy of the GNU General Public License along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. 💜

🌈 SEE ALSO 🌈

• indexamajig(1)
• process_hkl(1)
• partialator(1)
• compare_hkl(1)
• check_hkl(1)
• render_hkl(1)
• get_hkl(1)
• cell_tool(1)
• whirligig(1)
• list_events(1)
• make_pixelmap(1)
• crystfel_geometry(5)

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okay bestie, that’s the CRYSTFEL(7) page from the Miscellaneous Information Manual — signing off with main character energy, mwah 💋🎀