Hi Sjors and all,

I averaged movie files by using the command line like the following: "relion_image_handler --i $input --o output --avg_bin 20" which generated movies including 3 sub-frame. Then I extracted particles from movie. However when I was trying to run movie processing, relion give me error like "

Expanding current model for movie frames... 

Experiment::expandToMovieFrames: ERROR: no movie frames selected. Check filenames of micrographs, movies and particle stacks!"

Actually, the other clue is I can't get particle subset by running make_movie_subset.csh either.

Any idea?

Thanks you all,

Yan

On Wed, May 20, 2015 at 1:56 PM, Sjors Scheres <[log in to unmask]> wrote:

Hi Giulia,
That's a good one! Perhaps the avg_movie_frames extraction option is buggy
together with the polishing... Haven't seen that one before. Anyone else
perhaps?
To answer your question: yes, it should do the same thing, but on the
micrographs. So it would indeed be a good way of finding such a bug.
HTH,
S

> Dear Sjors, does this (--avg_bin 10) do the same thing as if you used
> --avg_movie_frames 10 when extracting movie particles?
>
> I ask because Yan and I seem to have very similar problems at the
> polishing stage, i.e. the per-frame reconstructions look black, apart
> from those that have frame number n, where n is a multiple of the frame
> averaging bin factor (when imposed at the particle extraction stage).
> This error does not appear in my hands with tutorial or test data (i.e.
> less particles from same dataset) where no frame-averaging was applied.
>
> Using a different way to average frames would allow to see if the bug is
> in the relion frame-averaging procedure.
>
> Thanks
> Giulia
>
>
>
> On 20/05/2015 08:30, Sjors Scheres wrote:
>> Hi Yan,
>> You could run relion_image_handler on each movie. It's option --avg_bin
>> 10
>> HTH,
>> Sjors
>>
>>> Hi all,
>>>
>>> I hope you are all doing great.
>>>
>>> I am processing one data with 60-frames per movie. At first, movement
>>> was
>>> corrected by motion correction from Xueming Li. Before running movie
>>> processing in RELION, I would like to integrate 10 sub-frames into one
>>> sub-frame so that there are 6 sub-frames per movie instead of 60
>>> sub-frames
>>> in aid of memory. Is there any software or command could achieve this
>>> aim?
>>>
>>> Thanks for your help,
>>> Yan
>>>
>
> --
> Giulia Zanetti
> ISMB, Birkbeck College
> Malet St. London
> WC1E 7HX
> 02076316898
>

--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres