matchmaps Documentation

Welcome to the docs for matchmaps, a python package for aligning and subtracting non-isomorphous crystallographic datasets. Do you have a pair of datasets for which an isomorphous difference maps doesn’t quite work due to changes in your unit cell dimensions? If so, this is the package for you.

The quickstart guide contains installation instructions and sample usage of the basic matchmaps utility, along with other useful tips.

If you’d like to learn more about matchmaps, you can find our exploration of the package here. For even more information, and see the package in action, please check out our pre-print!

This software is part of the Reciprocal Space Station family of open-source crystallography software and was conceived in Doeke Hekstra’s Lab at Harvard by Dennis Brookner

The matchmaps functions in brief

matchmaps consists of three command-line utilities. A walkthrough of the core utility can be found here, and all options for all three utilites are documented here. All three utilities produce a real-space difference map and require a single starting model for phasing, but differ in the types of reflection data they require. Briefly:

  • matchmaps takes in two mtzs containing similar data and which are nearly isomorphous and computes an unbiased real-space difference map between them

  • matchmaps.mr takes in two mtzs containing similar data but which are in different spacegroups (or the same spacegroup but different crystal packing) and computes an unbiased real-space difference map between them.

  • matchmaps.ncs takes in a single mtz and computes an internal difference map across a defined non-crystallographic symmetry present in the data.