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Protocols and methods

  • Notes about 3DEM software
  1. Ctffind - determination of CTF params (astigmatism defocus) for untilted micrographs. Input parameters of ctffind3.com: here. For an optimal correlation of ctfpfit and power spectrum one should correct params ResMin and ResMax.
  2. Ctftilt - the same program but for tilted images. Additional inptut params PAve - pixel average, TiltA - expected tilt angle, TitlR - deviation of tilt angle.
  3. Signature - particle picking program. Comprehensive manual is still available here, also you can look at introductory presentation and and article here.
  4. EMAN - 3DEM suit for single particle analysis. Web site as well the program are under active development and are available here. Last new tutorial can be downloaded here. PowerPoint Presentation about EMAN2 is over here.
  5. Chimera - visualization software with many EM formats support. Plenty of manuals are here. New easy and interesting tutorials can be downloaded from here and there.
  6. FReAlign - 3D reconstruction refinement program. In last versions of the program convertion to and from Imagic format is available. EMAN2 includes Frealign scripts also, tutorial can be found here. Working scripts can be found in folder "examples". Full list of params is shown here. Forum about frealign is located here. Also here is an article devoted to Frealign program. Web-cast from workshop in 2006 can be downloaded here (245Mb, mid quality). Podcast can be found here.
  7. IMAGIC-5 - one more software package for 3DEM data analysis. Official manual is available here. Quick tutorial from N.Grigorieff lab is over here.
  8. Software for 3DEM model validation and docking: DireX (tutorial), Rosetta (tutorial), Gorgon, Situs.
  • Protocols
    1. O.S. Sokolova, A.G. Bogdanov, A.V. Grizel. "Electron microscopy of nanoobjects". Part 1. Download PDF
    2. TEM FEI Tecnai G12 Spirit TWIN notes for negative-stained specimens. Download DOC
    3. Schedule for TEM and SEM for the 1th quarter, 2013. Download DOC