I am sending along our conversion script which I use to go from SPARX to FREALIGN.  I believe it was originally written by Mike Cianfrocco and Gabe Lander.  The input is an alignment parameter file from SPARX, a ctf parameter file which is formatted like a frealign parameter file, and a black imagic stack. The CTF parameter file is generated by the current version of APPION.  The script is slightly broken such that I have to actually run it with python ("python EMAN2toFREALIGN.py"); I've not been able to diagnose why it won't run directly in the shell.  

Right now it outputs an "old" format frealign parameter file, but v9 seems to be able to handle it without a problem.

I've also attached some representative parameter files so you can tinker around with it (if you don't give it a stack it just generates parameter files).  

RE the stack generating portion: We generally used MRC format for frealign.  The script makes use of an "MRC" module which is a part of the Legionon / Appion package to do the conversion.

Let me know if you have any questions about it; I hope this is useful.

Cheers,
-Greg


Gregory M. Alushin, Ph.D.
Laboratory of Macromolecular Interactions
Cell Biology and Physiology Center, NHLBI