Polish tomogram

[Reza Khayat]

Hi,

My particles are a bit easier to see and pick after tomograms are polished (i.e. I have more particles to select). Can I pick particles from these tomograms, or will the lack of updated "tlt_params" in the .json files be problematic? I'm referring to the e2spt_polishtomo.py routine not updating the .json file. 

Best wishes,
Reza

[Muyuan Chen]

Hi Reza,

You can pick particles in those tomograms. The polishtomo.py program does not affect the tilt series alignment parameters, but you can still take advantage of the previous alignment by running e2spt_gathermeta.py (with the last refinement you run e2spt_polishtomo) before refinement. 

There is also a new e2tomogram_refine.py that refines the tilt series alignment aiming to improve contrast. This one tlt_params, and does not require gathermeta. It improves results in most of my tests, but if your initial refinement is good (e.g. virus or ribosome), polishitomo may still work better.

Muyuan

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