Moving from EMAN1 to EMAN2

A choice of paths

EMAN2 can be used in many different ways:

• A high-level integrated workflow interface
• Stand-alone GUI tools (like EMAN1)
• Command-line programs (direct analogs to EMAN1)
• A Python library (a easy to learn scripting language)
• A C++ library

We strongly encourage most users to use the workflow interface, as this offers an integrated solution which:

• takes you step by step through the reconstruction process, with help along the way
• Stores all data in a logical organization of subdirectories, and keeps track of all details at each step of the process, so the final results can be archived, used to seed an EMDatabank/PDB submission, etc.
• shows you all of the complicated command line options in an organized fashion so you don't forget anything

However, it is also quite possible to use EMAN2 directly from the command-line very much like EMAN1.

We have separate guides depending on what you want to do:

• I don't want to read all this stuff, I just want to try my EMAN1 refinement in EMAN2 ! (Quickstart Guide)

• Overview of changes between EMAN1 and EMAN2 (read this first)

• I want to give the (old) workflow a try. (Note: the workflow is being replaced by e2projectmanager.py, but this portion of the documentation hasn't been updated yet)

• I prefer to use the command-line and stand alone GUI tools

• Forget this 'command-line' stuff, I want to write my own scripts !