SPIND

SPIND (sparse-pattern indexing) is an auto-indexing algorithm for sparse snapshot diffraction patterns that requires the positions of only five Bragg peaks in a single pattern and known unit-cell parameters.

SPIND was developed primarily by Chufeng Li (Zatsepin lab) and Xuanxuan Li (Haiguang Liu's lab). It is written in Python and the source code is publicly available under the GNU General Public License from https://github.com/LiuLab-CSRC/SPIND and a manual can be found here: https://liulab-csrc.github.io/SPIND/

If you use SPIND, please cite: Chufeng Li, Xuanxuan Li, Richard Kirian, John Spence, Haiguang Liu and Nadia Zatsepin. SPIND: a reference-based auto-indexing algorithm for sparse serial crystallography data. IUCrJ 6 (1), 2019. https://doi.org/10.1107/S2052252518014951

The capability of SPIND is demonstrated for the orientation determination of sparse diffraction patterns (containing very few Bragg peaks) using simulated data from microcrystals of a small inorganic molecule, I3C (known as the magic triangle) or 5-amino-2,4,6-triiodoisophthalic acid monohydrate [1], which is challenging for commonly used Fourier-transform based indexing algorithms. SPIND, integrated with CrystFEL [2], is also shown to improve the indexing rate and quality of merged serial femtosecond crystallography data from two membrane proteins, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH₂ [3] and the NTQ chloride-pumping rhodopsin [4]. We demonstrate the suitability of SPIND for indexing sparse inorganic crystal data with small unit cells, and for improving the quality of serial femtosecond protein crystallography data, potentially significantly reducing the amount of sample and beam time required by making better use of limited data sets.

(1) Beck & Sheldrick (2008), Acta Cryst. E64, o1286.

(2) White et al. (2012), J. Appl. Cryst. 45, 335–341.

(3) White, Barty et al., (2016). Sci. Data, 3, 160057, and Fenalti, Zatsepin et al., (2015) Nat. Struct. Mol. Biol. 22, 265–268.

(4) Yun et al. (2018). J. Bio. Chem. http://www.jbc.org/content/early/2018/11/19/jbc.RA118.004038.short