Software Updates

PyMOL (Schrodinger)

PyMOL from Schrodinger

CCP-EM

(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.

PyMOL (Schrodinger)

PyMOL from Schrodinger

py4xs

a python package for processing x-ray scattering data, first developed at the X9 beamline at NSLS, but revised multiple times and now n use at the LiX beamline at NSLS-II.

TomoAlign

programs for cryo-tomography tilt-series alignment and subsequent tomographic reconstruction that take into consideration beam-induced sample motion, modeled by means of polynomial surfaces. TomoAlign comprises: 1) tomoalign, for alignment, to determine the basic parameters of the images (rotation, magnification, tilt) along with the polynomial coefficients that model the motion; 2) tomorec to calculate the tomogram from the tilt-series and takes into account the motion estimated during the alignment; 3) auxiliary programs to analyze, transform, or scale the motion parameters.

IMP

(Integrative Modeling Platform) designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.

LIGPLOT

a program for automatically plotting protein-ligand interactions.

MotionCor2

a multi-GPU program that corrects beam-induced sample motion on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level across the whole frame, suitable for both single-particle and tomographic images.

RELION

(REgularised LIkelihood OptimisatioN) a stand-alone computer program for Maximum A Posteriori (MAP) refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.

PDB_REDO

refines any structural model you are working on, by optimising REFMAC refinement and by partial model rebuilding. The process is fully automated so you only need to provide an initial structure model and your reflection data.

Spring

(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.

PHENIX

(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.