Classic Papers (Indexing)

Education Diffraction
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This topic is meant for sharing and discussing classic papers about the indexing problem in crystallography. The scope includes both rotation method and stills, monochromatic and Laue. I’ll start us off with some of my favorite resources.

  • Chapter 5 of Biomolecular Crystallography by Bernhard Rupp is a classic introduction to diffraction geometry
  • The DIALS conventions webpage is a useful reference
  • The Rossmann Fourier autoindexing algorithm in MOSFLM describes the FFT1D indexing algorithm applicable to rotation method and stills.
  • Integration, scaling, space-group assignment and post-refinement section 2.7 describes the rotation-method indexer in XDS.
  • DIALS uses a 3-D Fourier transform which was originally suggested in 1986 but had to wait for computers with more memory. Read about the history here
  • The XGandalf paper describes a popular indexing algorithm for serial crystallography data based on optimization.
  • PinkIndexer is a robust but somewhat expensive algorithm which can index both monochromatic and Laue stills. The paper has a very clear geometric interpretation of the indexing problem.
  • The small cell indexing algorithm from DIALS/CCTBX is a good choice for serial crystallography data of small molecules and peptides.
  • The TORO indexer is a newcomer which boasts GPU acceleration for fast feedback during serial crystallography experiments.

I’m sure I’m forgetting many important contributions, but hopefully others can help fill in the gaps!

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These, from 1986, have just been made available online. They are an important part of the history of MX data processing software:

Phases I and II: Proceedings of the EEC Cooperative Workshop on Position-Sensitive Detector Software (Phases I & II) | Zenodo
Phase III: Proceedings of the EEC Cooperative Workshop on Position-Sensitive Detector Software (Phase III) | Zenodo

A particular highlight is the first proposal of FFT-based indexing of diffraction patterns (Phase 3, Contribution 4).

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Thank you, @taw! I was looking for these but I couldn’t find a source. :clap: