Reconstruct volume from previous alignment

[Jacob Croft]

Hello,

I was wondering if it is possible to reconstruct a final volume from a set of particle alignment parameters without re-running the alignment?  I'm using EMAN2 for subtomogram averaging, and would like to reconstruct the final volume of a subtilt refinement with a different mask than I used during the original alignment.  I see now there is the "maskalign" option which would have allowed me to specify a different mask for the final volume than for alignment from the beginning, but is there a way to do this after the fact?

Thank you,

Jacob Croft

Lee Lab

University of Washington

[MuyuanChen]

You can run the same command that the refinement program use to produce the maps. You should be able to find the command in the file “.eman2log”. If you are using e2spt_refine.py, look for the last command of “e2spt_average.py”. If you are doing subtilt refinement, look for “e2make3dpar”, for the new pipeline of e2spt_refine_new.py, look for the last command of “e2spa_make3d” in the file. Either way, the last command before e2refine_postprocess should work. You may also be able to use the threed_even_unmasked.hdf in the folder, which corresponds to the threed_xx_even.hdf file of the last iteration. It is filtered but not masked. 

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[Jacob Croft]

Hi Muyuan,

Thanks for the response.  Should the ".eman2log" file show up in the same directory as the results of the subtilt refinement (subtlt_xx)?  I don't see the file in there.

This was run on eman/2.31 by the way, if that clears anything up regarding why the file is missing.

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[Muyuan Chen]

It is a hidden file in the main project folder. You can just run something like “grep make3d .eman2log” in Linux terminal to find commands.

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[Jacob Croft]

Ahh, got it.  Thank you!

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[Ludtke, Steven J.]

If you are doing anything with tomography or subtomogram averaging, you should be using EMAN2.91 or newer, not 2.31. There were very significant changes and improvements made between those versions.

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

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Jacob Croft]

Hi Steven,

Thank you for letting me know.  I'll make sure to use 2.91 from now on.

best,

Jake

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