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The Aaron Klug Centre for Imaging and Analysis

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Processing software

After collecting the images and the movies from the microscopes, you will need to process the data.

  • relion - refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data
    • invoke from command line as relion installed at /opt/relion/bin/relion
  • coot - model building, refinement, and validation of macromolecular structures.
    • installed as part of ccp4 at /opt/ccp4-7.0/bin/coot - invoke as coot from command line
  • chimera - interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments
    • invoke as chimera - installed at /usr/local/bin/chimera
  • chimerax - molecular visualization program
    • Isolde - chimerax plugin for building high quality macromolecular models into low to medium resolution experimental maps
    • invode as chimerax - install isolde from toolbox. Installed from package ucsf-chimerax.
  • CCP4 - integrated suite of programs that allows researchers to determine macromolecular structures by X-ray crystallography, includes coot
  • Phenix - automated determination of molecular structures using X-ray crystallography and other methods
    • Invoke from the command line - phenix - installed at /opt/phenix-1.18.1-3865/build/bin/phenix

For remote access to the computers, I recommend VNC for graphical access. For command line access, use ssh, and for long-running sessions, screen.