Re: [scipion-users] Going back to motioncorr to get movie-particles.

[Matthews-Palmer, T. <t.m...@im...>]

Hi Grigory,

Thanks a lot for the guidance. :-)
In order to run step 1 on the same import movies input, I need to fix the symlinks to point to the new location of the original data.
I imagine I can just replace the symlinks in Runs/xxxxProtImportMovies/extra/ with new, correct symlinks and Scipion should refer to those.
Here goes.

Thanks & best wishes,
Teige

On 21 Mar 2018, at 16:46, Gregory Sharov <sha...@GM...<mailto:sha...@GM...>> wrote:

Hi Teige,

the usual way to do this would be:

1) copy motioncor2 protocol and run it with save movies=yes
2) extract coordinates from you refined subset (apply shifts = no)
3) extract movie particles using inputs (1) and (2) with apply movie alignments=no
4) continue with relion movie refinement and polishing or whatever you would like to do :)

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267542<tel:+44%201223%20267542>
e-mail: gs...@mr...<mailto:gs...@mr...>

On Wed, Mar 21, 2018 at 4:02 PM, Matthews-Palmer, Teige <t.m...@im...<mailto:t.m...@im...>> wrote:
Dear Scipion-users,

I have a situation in Scipion where a dataset of movies was motion-corrected with motioncor2, but aligned movies were not saved (at the time, there was not storage space). Now the processing is at a late stage and I would like to attempt movie refinement & particle polishing, so aligned movie frames are necessary.

I cannot restart the motioncorr protocols because they are referenced from subsequent protocols.
I could run a new motioncorr protocol.
Does anyone know if I will be able to easily transfer co-ordinates and angles from a late-stage set of particles to these new movies to make movie-particles?
Will scipion - extract coordinates be able to extract the right co-ordinates from aligned movies? Is there something else I need to bear in mind to handle movie-particles in Scipion?

Thanks for any help,
All the best
Teige
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