diff --git a/README.md b/README.md index b387b91..de839cf 100644 --- a/README.md +++ b/README.md @@ -6,4 +6,43 @@ Map Enhancement Tools for Ephemeral Occupancy Refinement [![Mypy](https://github.com/alisiafadini/meteor/actions/workflows/mypy.yml/badge.svg)](https://github.com/your_username/your_repo/actions/workflows/mypy.yml) [![Ruff](https://github.com/alisiafadini/meteor/actions/workflows/lint.yml/badge.svg)](https://github.com/your_username/your_repo/actions/workflows/lint.yml) [![codecov](https://codecov.io/gh/alisiafadini/meteor/graph/badge.svg?token=NCYMP06MNS)](https://codecov.io/gh/alisiafadini/meteor) -Set of tools for crystallographic electron density maps containing low ligand/species populations. + +`meteor` is a tool for computing crystallographic difference maps. + +`meteor` specializes the robust identification of weak signals arising from minor but scientifically interesting populations, such as bound ligands or changes that occur in time-resolved experiments. That said, if you need an difference map, `meteor` can do it! + + +## quickstart + +❗ `meteor` is currently **in beta**. We re-wrote everything recently, moving from a research code to something that can be robustly used as a tool. If you are willing to put up with a few sharp edges, it would be great if you give it a spin and then send us feedback: on how easy/not it was to use and what kinds of scientific results you obtain. + +Finally: a word of caution. Expect changes in the coming weeks as we stress test the code. You might want to consider this before publishing any results with `meteor` until we exit `beta`. + +``` +TODO: installation instructions +``` + +Once installed, you will have two command-line scripts. Ask for more info using `-h`: +``` +meteor.diffmap -h +meteor.tvphase -h +``` +which compute denoised difference maps using the constant-phase approximation _vs._ iterative phase retrieval, respectively. + + +## philosophy: better science through automation + +`meteor` aims to: + +1. maximize signal to noise +2. be objective and reproducible (minimize user choice & bias) +3. be easy to use + +Aim 1 is met using structure factor amplitude weighting (e.g. k-weighting, existing art) and TV denoising (new in the context of crystallography). Aims 2 and 3 are met through automatically setting parameters using negentropy maximization. For all the details, see our paper (coming soon to a preprint server near you). + + +## isomorphous data, please + +METEOR is only for isomorphous difference maps, meaning the lattices/symmetries of the `native` and `derivative` datasets are comparable. If you need to compare non-isomorphous lattices, check out [matchmaps](https://github.com/rs-station/matchmaps). + +