Thursday PM Practical
EMEN2 is a comprehensive database and electronic notebook with a primary focus on TEM data. More generally it is a broad-purpose object oriented database which can be applied to a wide range of different problems.
If you are using the EMAN2 binaries, the simplest way to install EMEN2 is to install it into that Python environment, as it already has several of the dependencies installed.
You will need to use the "easy_install" script provided by that environment. On Linux, if you installed EMAN2 in your home directory, it will be "...." On Mac OS X, it will be the system default "easy_install" script.
First, install the remaining EMEN2 dependencies:
sudo easy_install mako sudo easy_install twisted sudo easy_install Markdown
Then install EMEN2 itself:
sudo easy_install emen2
If you are not using one of our EMAN2 binaries, you will need to take care of installing Berkeley DB, bsddb3, and Matplotlib (optional) yourself. If you want to take advantage of some cryo-EM specific features, such as viewing MRC/DM3 images in your web browser, it is easiest if EMEN2 and EMAN2 can be loaded into the same Python environment.
You can import the current database schema from NCMI and initialize a simple database with the command:
python -m emen2.db.clone -h $HOME/test_db -- --defs
This will prompt you to supply a root password for the database, and an administrator email for notifications and password recovery.
You can start the EMEN2 web server:
python -m emen2.web.server -h $HOME/test_db
...and connect with your web browser at http://localhost:8080