Software Updates

ORCA

an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.

PyEM

a set of Python modules and command-line utilities for electron microscopy of biological samples.

Molecular Nodes

a tool that enables quick import and visualisation of structural biology data inside of Blender.

XDS

(X-ray Detector Software) a software tool for processing single-crystal monochromatic diffraction data recorded by the rotation method.

IMP

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

PyTOM

a tool that unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.

DENSS

(DENsity from Solution Scattering) an algorithm used for calculating ab initio electron density maps directly from solution scattering data.

PyMOL

a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

Ringer

a program to detect molecular motions by automatic electron density sampling.

ChimeraX

a tool of the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

PyMOL

a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

Schrodinger

a suite of tools for drug discovery. The Schrodinger suite runs on Linux and Mac workstations, but due to its size, it is not included in our default installation.

pyRMSD

a python package that offers RMSD calculations on large sets of structures, especially large pairwise RMSD matrices through multiple algorithmic implementations.

GROMACS

a versatile package that performs molecular dynamics of proteins, lipids and nucleic acids.

PyTME

a software for template matching on tomographic electron microscopy data.

Spire

a graphical user interface for executing SPIDER batch files and other programs, Spire offers a way to manage and organize the many output files created by SPIDER during reconstruction projects.

CCP4

(Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries used for macromolecular structure determination by X-ray crystallography.

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.

ALBULA

a fast and easy-to-use program that allows optimal visualization of PILATUS and EIGER data, and ALBULA API, a Python programming interface for displaying images and performing operations and calculations. The API enables you to easily integrate the viewer functionality into your beamline infrastructure or experimental setup. Consists of the standalone program ALBULA VIEWER.

Amber

a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community.

Foldtree

a snakemake workflow for making and benchmarking structure based trees using Foldseek.

Python

a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.

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.

DeepETPicker

a deep learning based open-source software with a friendly user interface to pick 3D particles rapidly and accurately from cryo-electron tomograms.

ChimeraX

a tool of the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. Compared to Chimera, ChimeraX has improved graphics (e.g. interactive ambient shadows); faster handling of large structures (millions of atoms); and a more modern, single-window user interface.

BUSTER

a software system containing crystallographic structure refinement using Bayesian statistical methods (BUSTER), ligand fitting (rhofit) and a fully automated pipeline (Pipedream) to drive a structure based fragment/ligand screening pathway.