eman2
Overview
EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. It performs single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, and also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing very large data sets (>100,000 particle) very efficiently
Note that EMAN2 is the successor to EMAN1 (which is not available on the iCSF).
Version 2.11 of EMAN2 is installed on the iCSF.
MPI support is provided by the PyDusa v1.15. This has required a custom build of the CSF OpenMPI 1.6 gcc installation.
Restrictions on use
The software is free to use to all iCSF users. However all users make themselves aware of the citation requirements requested by the authors.
Set up procedure
To access the software you must first load one of the following modulefiles:
- For serial / multi-threaded batch jobs and interactive usage:
module load apps/binapps/eman/2.11
- For small, multi-process jobs
module load apps/binapps/eman/2.11-mpi
The above modulefiles will automatically load any dependent modulefiles (e.g., mpi).
Running the application
Serial execution
A number of EMAN2 tools can be run interactively, including e2projectmanager.py, e2display.py and an interacive python shell e2.py (for advanced users). For example,
e2projectmanager.py # # Could also be e2display.py or e2.py for an interactive python shell.
Parallel execution
It is worth checking with top whether anything else is running on the same iCSF node as you before you launch a parallel job. The example below uses 4 cores/threads
e2appname.py --parallel=thread:4 args
#
# replace with the required EMAN2 tool (e.g., e2boxer.py)
# (not all e2 programs support parallel execution)
Only single node jobs are possible on iCSF.
Further info
Updates
None.