Software Updates

schrodinger_suite

A Schrodinger installation that does not include the SBGrid license, otherwise same as schrodinger.

PEET

(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

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.

R

a free software environment for statistical computing and graphics.

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.

MAFFT

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

nmrglue

a python module for reading, writing, and interacting with the spectral data stored in a number of common NMR data formats.

CCPNMR

a series of programs for macromolecular NMR spectroscopy integrated with the CCP data model, inspired partly by the program ANSIG (Per Kraulis) and partly by the program Sparky (T.D.Goddard and D.G.Kneller, UCSF).

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.

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.

LightDock

LightDock is a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm.

Julia

The Julia programming language is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.

schrodinger_suite

A Schrodinger installation that does not include the SBGrid license, otherwise same as schrodinger.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

ChimeraX

a next-generation molecular visualization program, 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. ChimeraX will have documented programming interfaces and an easy-to-use “Tool Shed” web repository of extensions.

SBGrid Installer

a graphical installation client used to install the SBGrid software collection on Apple OSX computers running MacOSX v10.13 - 10.15. Users can cherrypick a subset of applications for installation on their laptops or desktops. Software updates are highlighted, but users trigger the software update manually at their convenience.

CHAP

(The Channel Annotation Package) a tool for the functional annotation of novel ion channel structures that provides information on the biophysical properties of the ion permeation pathway by utilising molecular dynamics simulations.

cryoDRGN

a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

LigPlot+

a graphical front-end to the LIGPLOT (protein-ligand interactions) and DIMPLOT (protein-protein, domain-domain interactions) programs. The plots generated by these programs can be interactively edited on screen, superposed and printed.

DIALS

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.

R

a free software environment for statistical computing and graphics.

TVIPS tools

for the conversion of microED data collected on TVIPS TemCam-F416, Thermo Fisher CetaD, and Thermo Fisher Falcon III to SMV crystallographic format (*.img)