meteor-maps 0.2.5

denoise crystallographic difference maps

METEOR

Map Enhancement Tools for Ephemeral Occupancy Refinement

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.

First, meteor needs a python3.11 environment. We're working hard to extend this to as many versions as possible. To be sure things work, we recommend installing conda and creating a fresh environment,

conda create --name meteor python==3.11 --yes
conda activate meteor

Then install meteor using pip

pip install meteor-maps

Once installed, you will have two command-line scripts. Ask for more info using -h:

meteor.diffmap -h
meteor.phaseboost -h

these scripts 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.