Export particle coord as .box file

[Sean]

Hi all!

I have recently used e2spt_boxer.py by EMAN2 to pick particles in tomograms. How can I export the particles coord as .box files?

Best,

Sean

[Ludtke, Steven J.]

The traditional .box format actually came from EMAN1, and doesn't support 3-D coordinates. What purpose do you need them for? If following the EMAN2 pipeline, you never generate these files. If you need them for use with other software, there are a few ways of getting the coordinates.

In the boxer gui, there is a File menu with an option for saving particle coordinates, but this would have to be done one tomogram at a time. It produces a simple flat file with x/y/z coords for each particle one per line.

This command:

e2procjson.py --extractkey boxes_3d --allinfo

will extract all of the 3d coordinates from all tomograms into "jsoninfo.txt", but you'd have to parse it into whatever format you prefer.

If you can do a little python coding it's pretty trivial to get the info out programmatically in whatever format you like, but would need to know what the 3-D ".box" files look like...

Maybe Muyuan has some other standard script I'm not thinking of...

--------------------------------------------------------------------------------------

Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine

Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 

Deputy Director, Advanced Technical Cores                   and Molecular Biology

Academic Director, CryoEM Core

Co-Director CIBR Center

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[Sean]

Hi Steven,

Thanks for the fast reply! I want to use EMAN2 to pick particles form several tomograms to generate an initial template in RELION (have the script to convert .box to .star already) for template matching.

Best,

Sean