Software Updates

vlion

a slightly vectorized (AVX & SSE instructions) version of the original RELION 1.4 code by Dmitry Tegunov of the Max Planck Institute.

Toronto Single Particle Cryo-EM Software Tool Collection

a collection of software tools for computational analysis of cryo-EM images developed by John Rubinstein/U Toronto

SPARX

(single particle analysis for resolution extension) an image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. It includes a graphical user interface that provides a complete graphical programming environment.

Situs

a program package for modeling of atomic resolution structures into low-resolution density maps. The software supports both rigid-body and flexible docking using a variety of fitting strategies.

NumPy

contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities.

NumPy is installed as a module within Python.

Xmipp

(X-Window-based Microscopy Image Processing Package) a suite of image processing programs primarily aimed at single-particle 3D electron microscopy.

pytz

cross platform time zone library that brings the Olson tz database into Python and allows accurate and cross platform timezone calculations using Python 2.4 or higher. It also solves the issue of ambiguous times at the end of daylight saving time, which you can read more about in the Python Library Reference (datetime.tzinfo).

IPython

Biopython

a set of tools for biological computation written in Python by an international team of developers.

CCPNMR ChemBuild

a graphical tool to construct chemical compound definitions for NMR, created to handle concepts like protonation variants and magnetic equivalence that are required for NMR resonance assignment. Several different chemical file formats are supported, including PDB, .mol and .mol2, but ChemBuild is special in its ability read and write CCPN chemical component XML files, which store NMR-aware information.