Software Updates

Chimera

a highly extensible, interactive molecular graphics program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. It is often a tool of choice for rendering EM volumes.

DeepEMhancer

(Deep cryo-EM Map Enhancer) a python package designed to perform non-linear post-processing of cryo-EM maps for local sharpening, automatic masking and denoising. Systems using cuda 11+ should use the 20210511 version of deepEMhancer, and the modified models distributed in /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints/

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.

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.

IsoNet

(ISOtropic reconstructioN of Electron Tomography) trains deep convolutional neural networks to reconstruct meaningful contents in the missing wedge for electron tomography, and to increase signal-to-noise ratio, using the information learned from the original tomogram.

DeepEMhancer

(Deep cryo-EM Map Enhancer) a python package designed to perform non-linear post-processing of cryo-EM maps for local sharpening, automatic masking and denoising. Systems using cuda 11+ should use the 20210511 version of deepEMhancer, and the modified models distributed in /programs/share/deepemhancer/20210511/deepEMhancerModels/production_checkpoints/

R

a free software environment for statistical computing and graphics.

TomoSegMemTV

is a software package for segmenting membranes in tomograms. It is based on (1) a Gaussian-like model of membrane profile, (2) a local differential structure approach and (3) anisotropic propagation of the local structural information using the tensor voting algorithm.