Exporting box coordinates in EMAN2

[Joel Meyerson]

Hi,
I picked particles within the EMAN2 project manager and would like to export the box coordinates. I don't find an answer in the EMAN2 documentation though perhaps I'm not looking deeply enough. Can someone advise on how to do this?
Thanks as always,
Joel

[Joel Meyerson]

Since posting the message I've poked around on the EMAN2 group and found a way to easily extract the particles.

From within the project directory:
e2bdb.py --dump bdb:e2boxercache#boxes > boxes.txt

If there is a better way that would still be helpful to hear.
Thanks,
Joel

[Ludtke Steven]

Hi Joel. Most of the programs at least have decent parameter-level documentation. From e2boxer.py --help 

  --write_dbbox         Write coordinate file (eman1 dbbox) files

This is also available in the gui in the 'generate output' tool, as the "write_ddbox" checkbox. This will write EMAN1-style '.box' files.

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[Witchukorn Phuthong]

As a followup, are the precision of coordinates fixed to 0.5 pixel? Is there a way to make this number smaller, say 0.1 pixel?

Thanks,

Champ

[Steven Ludtke]

Actually, box locations are limited to whole pixels. However, since the values are stored as a center position with a box size (to make resizing easier) you can sometimes see 0.5 values. I'm not quite sure where you are expecting sub-pixel particle picking accuracy to come from here... particle picking is often +- 5 or more pixels. Final translational alignments of the particles with respect to references are where true centering occurs. Since the particles are noisy, there really isn't any good way to accurately center most particles (other than spherical viruses) without having references...

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Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

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[Witchukorn Phuthong]

Thank you for your reply. My goal at this point is to get coordinates of the swarm-boxed particles out (may be as Joel's). With my minimal knowledge of python, I don't know where to insert the --write_dbbox and how to get x,y coordinates from the bdb file. I have been sometimes successful in doing that with e2bdb.py --dump bdb:e2boxercache#boxes > boxes.txt typed directly in terminal after interactive boxing, writing output using interactive boxing window, and generating e2box output. I found that the underlined step is needed for this command. However, today I did the exact same thing, but boxes.txt doesn't show the coordinate. 

I attach the terminal output with some highlight here as well.

I can't figure out if the wrong order that I did, how I manually select particles, how I use only swarm to select particles, how I use both to select particles or it's the bug that blocking me to obtain the coordinate in txt. I got only blank boxes.txt with the message:.#####  boxes Can you tell me what happens to e2workflow? Is there any other simple way to get coordinates in text file out?

Thanks again.

Champ

[Witchukorn Phuthong]

Somehow, after restarting the computer, it just works.

-Champ

[Steven Ludtke]

:^)