using warp-reconstructed tomograms for subTOM

[Nikolai Darge]

Dear all,

I have been using MissAlignment to align my tomograms and I would like to extract and pre-align particles at low resolution with subTOM. I read that warp-reconstructed tomograms are supposed to be ctf-corrected, however they have much higher contrast compared to corrected tomograms from IMOD. 

Are these tomograms suitable for subtomogram averaging? Or if not is there a way to get subTOM compatible subtomograms?

Thank you and best,

Nikolai

[Mathew McLaren]

Hi Nikolai,

The Warp-reconstructed tomograms should be CTF-corrected and will be suitable for STA going forward although I haven't used subTOM so I'm not sure what it needs. I'm curious, after running MissAlignment, did you rerun the WarpTools ts_ctf on your data? The CTF information needs to be restored to the XML files after MissAlignment runs so if you haven't done this then the contrast may be higher than you expect.

Cheers,

Mat

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