Software

List of programs we use to process data obtained from cryo-electron microscopes

  1. Ctffind – determination of CTF params (astigmatism defocus) for untilted micrographs.
  2. Ctftilt – same program, but for tilted images. Additional input parameters: PAve – pixel average, TiltA – expected tilt angle, TitlR – deviation of tilt angle.
  3. Signature – particle picking program.
  4. EMAN – 3DEM suit for single particle analysis.
  5. Chimera – visualization software with many EM formats support.
  6. ChimeraX – new generation of Chimera. Supports Python3, integrations with modern web-services.
  7. FReAlign – 3D reconstruction refinement program. In last versions of the program conversion to and from Imagic format is available. EMAN2 includes Frealign scripts, also.
  8. IMAGIC-5 – one more software package for 3DEM data analysis.
  9. DireX, Rosetta, Gorgon, Situs – software for 3DEM model validation and docking