International Workshop of Advanced Image Processing of Cryo-Electron Microscopy

Institute of Biophysics, Chinese Academy of Sciences, Beijing

I apologize for the late posting of the EMAN2 material. The struggle to get EMAN2.1alpha completed before the workshop pushed us closer to the deadline than we normally like. Everything is now complete and tested. In theory we should be able to go from raw micrographs to a subnanometer resolution structure of GroEL with clear alpha-helices during the

Update:

• 2013/07/04 11:00pm - The raw data download has now been posted. The tutorial PDF is in final editing. The data is a 1.3 GB download

• 2013/07/04 10:00pm - A new copy of the Linux binaries for EMAN2.1alpha1 was posted today due to problems with the fonts and a couple of other minor issues. The website still shows the date as 7/2, but the binaries have been changed (Linux only).

• 2013/07/02 6:00 pm - EMAN2.1 alpha1 is now available for download. Please report any problems you encounter. Data and tutorial files will follow over the next couple of days.

These tutorial materials are for the workshop hosted by the Chinese Academy of Sciences in Beijing in July 2013. Each day of the workshop is devoted to a different software package. The material on this page is the training material for EMAN2.

We will be using EMAN2.1alpha1, the first testing release of EMAN2.1, for this tutorial session. While this version is not yet completely stable, and not every feature will work, there are several important reasons to use it instead of EMAN 2.07:

• The BDB mechanism used by older EMAN2 versions has been retired. This means that projects are structured somewhat differently than earlier versions. If we used EMAN2.07 then in the next few months you would have to upgrade everything you've done to work with the new version.
• The HDF (image) and JSON (text metadata) files used instead of BDB are MUCH easier to manage and work with, which will mean we can spend more time on advanced image processing and less time dealing with the basics.
• The new e2refine-easy command means there are far fewer parameters you have to learn about to do reconstructions in EMAN2, and again, will allow us to focus on more advanced topics. It also integrates gold-standard resolution estimates, so is at least 2x faster than EMAN 2.07.

Downloads

Workshop participants who will be using their own laptop computers should at least install EMAN2 before the workshop. Probably a good idea to preinstall the data as well :

• install EMAN 2.1alpha (no earlier versions will work properly with the new tutorial)

  • After installing, test your installation by running:
    • e2version.py
    • e2speedtest.py
    • e2display.py (with no arguments this will open a browser and you can display any cryo-EM image)
• download the sample data (you only need one of these two files):

  • workshop_beijing.tgz

  • workshop_beijing.zip

• download the tutorial (not yet available)
• (optional) download the completed refinement directory. If you follow the tutorial, you will basically reproduce this, so you really only need this if you get stuck. It's a rather large download:

  • workshop_beijing_complete.tbz

  • to uncompress this file on linux/mac: tar xvjf workshop_beijing_complete.tbz