SPARX

Announcing SPARX v2.0

We are pleased to announce a release of a new single particle package SPARX with EMAN2 as its essential dependency. Both components together with all other necessary dependencies are available through a single installation step:

http://sparx-em.org/sparxwiki/Installer

The software is introduced in:

• SPARX, a new environment for Cryo-EM image processing. Hohn, M., Tang, G., Goodyear, G., Baldwin, P. R., Huang, Z., Penczek, P. A., Yang, C., Glaeser, R. M., Adams, P. D., Ludtke, S. J., 2007. J. Struct. Biol. 157, 47-55.
• EMAN2: An extensible image processing suite for electron microscopy. Tang, G., Peng, L., Baldwin, P. R., Mann, D. S., Jiang, W., Rees, I., Ludtke, S. J., 2007. J. Struct. Biol. 157, 38-46.
• The Transform Class in SPARX and EMAN2. Baldwin, P. R., Penczek, P. A., 2007. J. Struct. Biol. 157, 250-261.

Main features include:
•       New generation of 2D and 3D alignment protocols.
•       Ab initio structure determination programs.
•       Resampling methods for investigation of structural heterogeneity (3D variance).
•       Advanced code for multivariate statistical analysis (PCA, Varimax),
•       New generation of interpolation methods relaxing the need for oversampling the data.
•       Wiki-based interactive documentation http://sparx-em.org/sparxwiki/
•       Extensive C++ library of general and EM-specific image operations with Python bindings, thus accessible to Python programmer. 
•       All structure determination applications written as user transparent Python scripts http://sparx-em.org/sparxwiki/HowToUseSparx
•       All major scripts parallelized for clusters of workstations using MPI.
•       The Transform Class supports all Eulerian angles conventions commonly used in EM, generates point-group symmetries, and provides definitions of asymmetric units.
•       Package reads/writes all commonly used file formats (SPIDER, Imagic, MRC,…) 
•       New HDF5 data format.  In addition to storing image data, the file headers store data processing information (orientation parameters) and can also store any other information provided by the user.
•       Run-through example of a structure determination project.

• SPARX is issued under a joint BSD/GNU license and is provided free of charge as a service to the scientific community.

• Pawel A. Penczek, UTH
• Steven Ludtke, Baylor College
• Robert M. Glaeser, LBL

02/04/2023

Contributors

Phil Baldwin, Julien Bert, Jia Fang, Grant Goodyear, Mike Hohn, Zhong Huang, Julio Kovacs, Steve Ludtke, Pawel Penczek, Grant Tang, Guozhi Tao, Chao Yang, Zhengfan Yang, Wei Zhang