py4sci

Tutorial

The following tutorial has been taught at the EMBO course in Heidelberg August 2012 and 2014 and updated to work with the latest version of Spring. A couple micrographs of Tobacco Mosaic Virus (downloadable from the EM Pilot Image Archive EMPIAR) are sufficient to compute a near-atomic resolution 3D structure of the virus on a portable computer (e.g. MacBookPro 2012). Please, refer to our latest J Struct Biol 189, 87–97 publication on TMV for further details. The respective data sets acquired on direct electron detector cameras K2 Summit and Falcon II are available for download. If you do not want to spend a lot of time fetching the raw data sets and need a quick data set sufficient for launching the tutorial, download 4 micrographs from a Small TMV data set below.

UPDATE Jul 27 2015 For the basic theory refer to our new review article: Sachse, C. (2015). Single-particle based helical reconstruction—how to make the most of real and Fourier space. AIMS Biophysics, 2(2), 219–244.

UPDATE Apr 17 2015 Tutorial includes a section on segment frame processing using SPRING.

UPDATE Dec 18 2017 We added tutorial instructions for automated helix tracing using SPRING.

Spring Tutorial 2017.pdf

Small TMV data set

Micrographs were recorded as 7-frame movies with a Falcon II DED mounted on the Titan Krios at EMBL Heidelberg. Shared examplary micrographs including corresponding box files:

1 TMV_Krios_FalconII_001.mrc TMV_Krios_FalconII_001.box
2 TMV_Krios_FalconII_002.mrc TMV_Krios_FalconII_002.box
3 TMV_Krios_FalconII_003.mrc TMV_Krios_FalconII_003.box
4 TMV_Krios_FalconII_004.mrc TMV_Krios_FalconII_004.box

The images are motion-corrected sums obtained with MOTIONCORR (Li X et al., Nature Methods 2013) and contain an accumulated dose of ~30 e-/Angstrom2 .

Imaging Parameter Value
Voltage (kV) 300
Cs (mm) 2.7
Pixel size (Angstrom) 1.062