This page contains an EMAN2 reconstruction tilt validation tutorial using real data.


In this tutorial, we will validate the Ip3R structure or the PRD1 Virus(your choice): You MUST use the EMAN2 nightly build for this tutorial. In the future, we will put out EMAN2.1, which will be sufficient for EM validation. Follow this link to download the EMAN2 Nightly build:


installation instructions are provided at the download site. Please make sure you download the correct version for your computer. There are a number of possibilities. If you have any difficulty figuring out which version to download, or installation difficulties, contact gtang@bcm.edu.

Required Data Files

The data is provided as a compressed tar archive. Please download this file and unpack it into your workshop folder. This file includes demoistration data sets for PRD1 and Ip3R AND reconstructions we will validate:

Untar using (the directoriues Ip3R and PRD1 will appear):

tar -zxvf eman2_oxford2012_validation.tgz

Once you have installed the software and data, you can test the installation by :

  1. Run 'e2speedtest.py'.
    • If it will not run properly, check the installation tips page. Something didn't work right.

    • If it runs properly it will give you a 'speedtest score'. This is a relative indicator of how long it will take to perform refinements on a single core (CPU) on your computer. You can roughly multiply this by the number of cores to get a proper relative estimate. A fast, current generation Intel processor gives a score of ~4400. With 12 cores on a machine (even more will be possible soon), this gives an aggregate score for a single fast workstation of ~50,000. The workstations we will use at the workshop are several years old, and have speedtest scores of ~2000, with 2 cores. A good laptop will give a score of ~3000-3500 and have 2 cores.

If any of these tests fail, and the installation FAQ doesn't help, please contact sludtke@bcm.edu so he can assist you.

Tutorial PDF

The link below is a PDF tutorial for reconstruction validation. Please note that the tutorial below refers to BDB: files, which are no longer used in EMAN2. JSON files are used instead for most purposes, and images are stored in HDF format. At some point we need to update the tutorial...

Tutorial on using EMAN2 for Tilt Validation using projectmanager GUI

OxfordWs2012 (last edited 2019-02-21 13:37:00 by SteveLudtke)