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link to paper rather than preprint #50

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May 20, 2024
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link to paper rather than preprint #50

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5 changes: 3 additions & 2 deletions docs/about.md
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# About the `matchmaps` algorithm

If you want to learn more about the idea behind `matchmaps`, along with some examples, please check out our new pre-print!
If you want to learn more about the idea behind `matchmaps`, along with some examples, please check out paper in the Journal of Applied Crystallography!

> [MatchMaps: Non-isomorphous difference maps for X-ray crystallography](https://www.biorxiv.org/content/10.1101/2023.09.01.555333v2)
> [MatchMaps: non-isomorphous difference maps for X-ray crystallography](https://journals.iucr.org/j/issues/2024/03/00/ei5112/index.html)

If you're looking for a user guide, you can find that [here](quickstart.md). But if you're looking for more details about how `matchmaps` works, read on!

## Abstract

Conformational change mediates the biological functions of macromolecules. Crystallographic measurements can map these changes with extraordinary sensitivity as a function of mutations, ligands, and time. A popular method for detecting structural differences between crystallographic datasets is the isomorphous difference map. Isomorphous difference maps combine the phases of a chosen reference state with the observed changes in structure factor amplitudes to yield a map of changes in electron density. Such maps are much more sensitive to conformational change than structure refinement is, and are unbiased in the sense that observed differences do not depend on refinement of the perturbed state. However, even modest changes in unit cell properties can render isomorphous difference maps useless. This is unnecessary. Here we describe a generalized procedure for calculating observed difference maps that retains the high sensitivity to conformational change and avoids structure refinement of the perturbed state. We have implemented this procedure in an open-source python package, MatchMaps, that can be run in any software environment supporting PHENIX and CCP4. Through examples, we show that MatchMaps "rescues" observed difference electron density maps for poorly-isomorphous crystals, corrects artifacts in nominally isomorphous difference maps, and extends to detecting differences across copies within the asymmetric unit, or across altogether different crystal forms.

## Algorithm overview
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