SPHIRE: semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data

Quick Links

SPHIRE (SPARX for High-Resolution Electron Microscopy) is an open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. It allows fast and reproducible structure determination from cryo-EM images.

References:

T.Moriya, M.Saur, M.Stabrin, F.Merino, H.Voicu, Z.Huang, P.A.Penczek, S.Raunser, C.Gatsogiannis
High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
J. Vis Exp., 2017, 123(21), p.55448; doi:10.3791/55448.

Documentation

SPHIRE Wiki page

Important Notes

Module Name: SPHIRE (see the modules page for more information)
Unusual environment variables set
- SPHIRE_HOME installation directory
- SPHIRE_BIN executable directory
- SPHIRE_TEST test scripts

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=16g --gres=gpu:v100:1
[user@@cn4471 ~]$ module load SPHIRE
[+] Loading SPHIRE  1.1

Run basic commands for the spire executable:

[user@cn4471 SPHIRE]sphire -h
Usage: sphire 
	The main SPHIRE GUI application. It is designed as the command generator for the SPHIRE single particle analysis pipeline.

Options:
  --version   show program's version number and exit
  -h, --help  show this help message and exit

[user@cn4471 SPHIRE]sphire
Python 2.7.14 | packaged by conda-forge | (default, Dec  9 2017, 16:18:43) 
Type "copyright", "credits" or "license" for more information.

IPython 5.8.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.
Welcome to the interactive SPARX-NoGUI Python interface, provided by ipython
   SPARX v4.0 (GITHUB: 2018-08-20 20:32)

 In [1]: import mpi

 In [2]: Util.version() 
   Source modification date: August 2018 release 

In [3]: quit 
[user@cn4471 SPHIRE]$ e2version.py 
EMAN 2.22 final (GITHUB: 2018-08-20 20:32 - commit: f4f3952 )
Your EMAN2 is running on: Linux-3.10.0-862.14.4.el7.x86_64-x86_64-with-centos-7.5.1804-Core 3.10.0-862.14.4.el7.x86_64
Your Python version is: 2.7.14

Copy test scripts to your current folder:

[user@@cn4471 ~]$ cp -r $SPHIRE_TEST/* .

Run a test:

[user@@cn4471 ~]$ ./test_cmp.py 
test_DotCmp (__main__.TestCmp)
test DotCmp ...................................... ... ok
test_FRCCmp (__main__.TestCmp)
test FRCCmp ...................................... ... ok
test_OptVarianceCmp (__main__.TestCmp)
test OptVarianceCmp .............................. ... ok
test_PhaseCmp (__main__.TestCmp)
test PhaseCmp .................................... ... ok
test_QuadMinDotCmp (__main__.TestCmp)
test QuadMinDotCmp ............................... ... ok
test_SqEuclideanCmp (__main__.TestCmp)
test SqEuclideanCmp .............................. ... ok
test_basic_cmp (__main__.TestCmp)
test basic cmp ................................... ... ok
test_variance (__main__.TestCmp)
test variance .................................... ... ok

----------------------------------------------------------------------
Ran 8 tests in 0.041s

OK
[user@cn4471 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$