Software Updates

TranSPHIRE

a software package for fully automated processing of cryo-EM data sets during data acquisition. TranSPHIRE transfers data from the microscope, automatically applies the common pre-processing steps, picks particles, performs 2D clustering and 3D refinement parallel to image recording. Importantly, TranSPHIRE introduces a machine learning-based feedback loop to re-train its internally used picking model to adapt to any given data set live during processing. This elegant approach enables TranSPHIRE to process data more effectively, producing high-quality particle stacks. TranSPHIRE collects and displays all microscope settings and metrics generated by its individual tools in order to allow users to quickly evaluate data during acquisition. TranSPHIRE can run on a single work station and also includes the automated processing of filaments.

GROMACS

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

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.

Coot

(Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. This application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.

jq

is a lightweight and flexible command-line JSON processor.

TranSPHIRE

a software package for fully automated processing of cryo-EM data sets during data acquisition. TranSPHIRE transfers data from the microscope, automatically applies the common pre-processing steps, picks particles, performs 2D clustering and 3D refinement parallel to image recording. Importantly, TranSPHIRE introduces a machine learning-based feedback loop to re-train its internally used picking model to adapt to any given data set live during processing. This elegant approach enables TranSPHIRE to process data more effectively, producing high-quality particle stacks. TranSPHIRE collects and displays all microscope settings and metrics generated by its individual tools in order to allow users to quickly evaluate data during acquisition. TranSPHIRE can run on a single work station and also includes the automated processing of filaments.

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.

XIA2

an expert system for automated reduction of X-Ray diffraction data from macromolecular crystals, making use of existing software (CCP4, XDS, Phenix, CCTBX.) XIA2 is now included with DIALS.

ResMap

(Resolution Map) a Python (NumPy/SciPy) application with a Tkinter GUI. It is an easy to use software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM). ResMap has a both a GUI (window) and a command line interface.

R

a free software environment for statistical computing and graphics.

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.

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.

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).

KLTPicker

KLT (Karhunen Loeve Transform) picker is a fully automatic EM particle picker and requires only the approximated particle size as an input . It is especially designed to handle low SNR micrographs. It is based on learning a set of optimal templates through the use of multi-variate statistical analysis via the Karhunen Loeve Transform. DOI: 10.1016/j.jsb.2020.107473

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.

DOCK

a molecular docking application used to a) predict binding modes of small molecule-protein complexes; b) search databases of ligands for compounds that inhibit enzyme activity, bind a particular protein, bind nucleic acid targets; c) examine possible binding orientations of protein-protein and protein-DNA complexes; d) help guide synthetic efforts by examining small molecules that are computationally derivatized. Dock is offered in the SBGrid collection in two iterations, Dock 3 and Dock 6.

Illustrate

Illustrate is a small Fortran program for creating non-photorealistic illustrations of molecules, with cartoony colors and outlines, and soft ambient shadows. I originally developed it during postdoctoral training in the laboratory of Arthur J. Olson at the Scripps Research Institute, and have tinkered with it ever since. I have used it to create materials for my books and for PDB-101, the outreach portal of the RCSB Protein Data Bank, most notably, for the “Molecule of the Month.”

Xplor-NIH

a package for biomolecular structure determination from experimental NMR data combined with known geometric data. Xplor–NIH was derived from XPLOR version 3.851 and contains all of the functionality therein in addition to numerous new features designed to render a highly flexible architecture and foster the rapid and easy development of new functionality.

XIA2

an expert system for automated reduction of X-Ray diffraction data from macromolecular crystals, making use of existing software (CCP4, XDS, Phenix, CCTBX.) XIA2 is now included with DIALS.

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.

Global Phasing Suite

combined installation of autoPROC, BUSTER, and SHARP available to Global Phasing consortium members.