.. _tutorial:

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 <http://www.ebi.ac.uk/pdbe/emdb/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 <http://dx.doi.org/10.1016/j.jsb.2014.12.002>`_ publication on TMV for \
further details. The respective data sets acquired on direct electron detector cameras \
`K2 Summit <http://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10020>`_ \
and `Falcon II <http://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10021>`_ 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 :ref:`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. <http://dx.doi.org/10.3934/biophy.2015.2.219>`_

**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.

|tutorial2017.pdf| 

 .. |tutorial2017.pdf| image:: tutorial/tutorial.pdf
            :alt: Spring Tutorial 2017.pdf
            :target: _images/tutorial.pdf


.. _small_tmv_data_set:

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 <_download/TMV_Krios_FalconII_001.mrc>`_ | `TMV_Krios_FalconII_001.box <_download/TMV_Krios_FalconII_001.box>`_ |
+---+----------------------------------------------------------------------+----------------------------------------------------------------------+
| 2 | `TMV_Krios_FalconII_002.mrc <_download/TMV_Krios_FalconII_002.mrc>`_ | `TMV_Krios_FalconII_002.box <_download/TMV_Krios_FalconII_002.box>`_ |
+---+----------------------------------------------------------------------+----------------------------------------------------------------------+
| 3 | `TMV_Krios_FalconII_003.mrc <_download/TMV_Krios_FalconII_003.mrc>`_ | `TMV_Krios_FalconII_003.box <_download/TMV_Krios_FalconII_003.box>`_ |
+---+----------------------------------------------------------------------+----------------------------------------------------------------------+
| 4 | `TMV_Krios_FalconII_004.mrc <_download/TMV_Krios_FalconII_004.mrc>`_ | `TMV_Krios_FalconII_004.box <_download/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\ :sup:`-`\ /Angstrom\ :sup:`2` . 

+-----------------------+-------+
| Imaging Parameter     | Value |
+=======================+=======+
| Voltage (kV)          | 300   |
+-----------------------+-------+
| Cs (mm)               | 2.7   |
+-----------------------+-------+
| Pixel size (Angstrom) | 1.062 |
+-----------------------+-------+