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

[Gregory S. <sha...@gm...>]

Hi,

yes, updating symlinks in extra folder should work. Or you could copy the
import movie protocol specifying new location (it also create symlinks ;).
Unless you have changed filenames when moving the data, it should also work.

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 <+44%201223%20267542>
e-mail: gs...@mr...

On Wed, Mar 21, 2018 at 5:01 PM, Matthews-Palmer, Teige <
t.m...@im...> wrote:

> 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...> 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 <+44%201223%20267542>
> e-mail: gs...@mr...
>
> On Wed, Mar 21, 2018 at 4:02 PM, Matthews-Palmer, Teige <
> 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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>
>