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Overview

Synthetic occupancy model Synthetic map estimate

What is OccuPy

The primary purpose of OccuPy is to estimate the local scale of cryo-EM maps.

What does the 'local scale' mean? In simple terms, think of it as the range of pixels values. In well-resolved regions, contrast is high, and we expect very bright and very dark pixels. If that region has decreased resolution or occupancy, we expect decreased contrast and a narrower range of pixel values. The limit is solvent, which has Gaussian distribution. OccuPy was built to estimate this 'scale', to quantify relative contrast degradation. This means that it can estimate the relative resolution, or occupancy. OccuPy also uses this scale as a tool for map modification.


In essence, OccuPy locates the region that exhibits the highest range of pixel values, and utilizes this to place all other regions on a nominal scale between 0 and 1. This very useful:


Disclaimer

SPA or STA, but no single tomo

OccuPy is only applicable to reconstructions produced by ensemble averaging, like SPA and STA.
That is, it is incompatible with analysis of a single tomogram.

This is not postprocessing

OccuPy does not sharpen maps. It tries not to.

No number for your abstract

OccuPy will not provide an absolute local resolution in Å, only a relative local resolution.

Why estimate local scale?

The local scale contains information about both resolution and occupancy. With this in mind, OccuPy is designed to estimate the local scale

  • extremely fast
  • without half-sets
  • without GPUs
  • without masks

The reason for this is that it is intended to be compatible with the expectation maximization (fast) maximum likelihood classifiers (no half-sets) based on prior alignments (no GPUs), and be compatible with unbiased discovery of macromolecular heterogeneity and/or components (no masks). In this context, it will provide ways to weight data and/or provide a displacement vector to emphasize macromolecular resolution and/or occupancy during gradient descent. Basically, it needs to be fast enough to run repeatedly without delaying processing, and simple enough to use that it needs no input other than a cryo-EM map.

The gist

OccuPy is currently implemented as a GUI and command-line tool using open-source python libraries, to facilitate visualization of partial occupancy and the relative resolution of cryo-EM reconstructions by e.g implementing map modification as spatial filtering based on the estimated partial occupancy of local map components. This is intended to create maps that emulate reconstruction expected if the input (image) data was more homogenous at lower or higher occupancy.