exporting subtomos from EMAN to relion

[Mohsen Kazemi]

Dear all,

Happy NY with best wishes. 

I am going to use the subtomos in EMAN to do another averaging in relion and comparing the results. Wondering if it is possible to export coordinate and alignment information from EMAN?

Wbw,

Mohsen

 

[Steve Ludtke]

Unfortunately, it can be quite challenging to move tomographic information from one package to another. Certainly it is straightforward to extract the 3-D particles from EMAN2 if you like (use e2proc3d.py on .hdf or .lst files to convert to .mrc), or you can extract the aligned per-particle subtilt series if you like (e2proc2d.py in a similar way). You can also get access to the 3-D alignment information for each particle if you like, and can get these in MRC convention, but you would then need to refactor all of this data/metadata into whatever form you need for your followup testing (these are in the particle_parms JSON files. While you certainly get also get the coordinates for the particles within the tomograms (info/*json files), those are only valid within the context of EMAN2's overall tomographic reconstruction. If you were to redo the tomogram, then there box locations wouldn't be in the right place anymore...

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[Mohsen Kazemi]

Thanks for the quick reply... I will certainly follow your advice.

Cheers,

Mohsen