emmer 0.1.2

A python toolkit for the cryo-EM developer

EMmer

This is a python package to collect important functions related to cryo EM data processing. Broadly, EMmer tools are divided based on the input data type: either a coordinate file (PDB) or a map data (as a numpy array). They are structured as follows:

Structuring

• emmer

  • ndimage

    • filter (Low-pass, high-pass, band-pass filters and FSC filters)
    • mask (Compute FDR confidence masks and atomic model masks)
    • radial_profile (Compute radial profile from a map, estimate bfactors from radial profile)
    • fsc (compute FSC between two maps)
    • contour (compute properties of a contour at a given threshold like surface area, volume, number of segments)
    • sharpen (modify maps by rescaling the amplitudes)
    • general tools:
      • average half maps
      • compute real space correlation
      • estimate center of mass of a map
      • I/O operations
      • Trim map between residues

  • pdb

    • SSE (Secondary Structure Estimation using DSSP algorithm)
    • convert (to convert PDB to map)
    • General tools:
      • perturb PDB
      • Compute RMSD between two PDB
      • Get bfactors of all atoms
      • Set bfactors of all atoms to a uniform value
      • Neighbor analysis (estimate number of neighbors at a given position)

Installation

You can install using pip

pip install emmer

Recommended python version: > 3.6

Usage

You can load modules inside your python script like this:

1. Convert PDB to map

from emmer.pdb.convert.convert_pdb_to_map import convert_pdb_to_map
simulated_map = convert_pdb_to_map(input_pdb="/path/to/pdb.pdb", apix=1.1, size=(256,256,256)) # Returns a numpy.ndarray of shape: (256,256,256)

2. Compute FSC curve from two halfmaps

from emmer.ndimage.fsc.calculate_fsc_curve import calculate_fsc_curve
fsc_curve = calculate_fsc_curve(halfmap1, halfmap2)

3. Compute real space correlation between map and model

from emmer.pdb.convert.convert_pdb_to_map import convert_pdb_to_map
from emmer.ndimage.compute_real_space_correlation import compute_real_space_correlation as rsc
simulated_map = convert_pdb_to_map(input_pdb="/path/to/pdb.pdb", apix=1.1, size=(256,256,256))
emmap_path = "/path/to/emmap.mrc"
real_space_correlation = rsc(simulated_map, emmap_path)  # Input can either be a path to a map or a numpy.ndarray of shape:(N,N,N) 

Conventions

Some suggestions:

• emmap density data is named "emmap"
• Pixel size is named 'apix'
• Distances are measured in Angstrom.

Etymology

Refers to a person doing EM: an EM-mer

Is also a bucket in Dutch... "Een emmer is een waterdicht vat dat aan een hengsel gedragen en meestal gebruikt wordt voor het vervoer van vloeistoffen."

It is also a type of wheat.

Acronym for: Electron Microscopy Mightier (than) Ex Rays

Feature requests

WRITE THEM HERE