International Workshop of Advanced Image Processing of Cryo-Electron Microscopy
Institute of Biophysics, Chinese Academy of Sciences, Beijing
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.
WARNING for ',' countries
There is a known bug in Qt which can cause some issues on machines in countries where the decimal separator is a comma rather than a period. This has been discussed on the mailing list. If you are having difficulties viewing some images in any of the graphical tools, you may need to set these environment variables as a workaround:
- LC_CTYPE="en_US.utf8"
- LC_ALL=en_US.utf8
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)
- After installing, test your installation by running:
- download the sample data (you only need one of these two files):
- (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:
to uncompress this file on linux/mac: tar xvjf workshop-beijing-complete.tbz
While not absolutely required, having UCSF Chimera installed as well can be useful ( http://www.cgl.ucsf.edu/chimera/download.html )