Software Updates

CTFFIND 4

a new version of ctffind (a program for finding CTFs of electron micrographs) that should run significantly faster than CTFFIND 3 and may give slightly improved results when processing data from detectors other than scanned photographic film.

SIMPLE

(Single-particle IMage Processing Linux Engine) does ab initio 3D reconstruction (programs cluster & origami), heterogeneity analysis (programs cluster, origami & cycler), and high-resolution refinement (programs align, reconstruct, automask & cycler).

Google Cloud SDK

tools and libraries for interacting with Google Cloud products and services.

CAVER Analyst

a software tool for the calculation, analysis, and real-time visualization of access tunnels and channels in static and dynamic protein structures with an intuitive GUI.

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.

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.

LightDock

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

Julia

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.

ChimeraX

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.

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.

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)