CryoEM Software
MATLAB
MATLAB combines a desktop environment tuned for iterative analysis and design processes with a programming language that expresses matrix and array mathematics directly. It includes the Live Editor for creating scripts that combine code, output, and formatted text in an executable notebook.
Available on: all workstations
Warp
Warp tightly couples cryo-em collection and data preprocessing to ensure the best data quality and efficient microscope usage. Warp is software that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Warp corrects micrographs for global and local motion, estimates the local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. The software further includes deep-learning-based models for accurate particle picking and image denoising. The output from Warp can be fed into established programs for particle classification and 3D-map refinement. Warp has an intuitive, streamlined user interface.
Available on: Warp for Linux - all workstations, Warp for Windows - the two Warp workstations in NHB 4.332
SBGrid
The SBGrid Consortium (operated out of Harvard University) provides a complete execution environment that includes a suite of over 400 pre-compiled structural biology applications pre-configured to run without any additional settings. Applications are invoked from the shell prompt; there is no need to set up additional variables, change your path environment, or install supporting applications. The environment is simply invoked by a simple source command and can be easily integrated into HPC job submission script templates.
Available on: all workstations
CryoSPARC
CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art HPC software solution for complete processing of single-particle cryo-electron microscopy (cryo-EM) data. CryoSPARC is useful for solving cryo-EM structures of membrane proteins, viruses, complexes, flexible molecules, small particles, phase plate data and negative stain data.
See: CryoSPARC