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dtegunov / vlion

Vectorized (AVX & SSE) version of RELION
GNU General Public License v2.0
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Analyzing phase shifted data #2

Open mcianfrocco opened 8 years ago

mcianfrocco commented 8 years ago

Hi @dtegunov -

Just to confirm with you, in order to analyze phase shifted data with your program, all we need to do is include _rlnPhaseShift in the star file of micrographs when extracting particles in degrees?

Is there anything else that I'm missing?

Thanks!

mcianfrocco commented 8 years ago

And should we include --use_custom_ctf at the command line ?

dtegunov commented 8 years ago

Sorry, totally missed this one. Due to how Relion <2.0 reads CTF information when extracting particles, the phase shift information needs to be included in each ctffind3 log file, as outlined in the original CCPEM message about vlion. The particle extraction won't read that information from .star files. Relion 2.0 (which is now public!) can read it directly from .star, and has been tested to work fine with phase shifts.

--use_custom_ctf will ignore all CTF parameters, and use a precalculated image instead, like in tomography mode.