Re: [scipion-users] movie alignments

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

Hi Dmitry,

I can try to answer a couple of your questions:

I assume you are in release-1.1 branch (Scipion v1.1-beta (2017-04-21)
Balbino)?

1) I think it's a bad idea to use aligned movies as input for a second
alignment - the interpolation will cause you more problems and will not
improve any alignment. Also, motioncor2 cannot read input shifts for the
movies.

3) hm, can't seem to reproduce your error (neither in normal, no in
streaming mode). Is it failing in the middle of the run (not first few
movies)?

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 Sat, Apr 29, 2017 at 10:35 AM, Dmitry Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
> The issue is again with movie correction scripts.
>
> 1. Motioncorr2
> As input, I use the movie stacks (can I use corrected movies as an input
> to increase the quality - for example after xmipp3-correlation alignment or
> it will be repetition?) and get the error  -
>
> ProgrammingError: Incorrect number of bindings supplied. The current
> statement uses 32, and there are 22 supplied.
> (the git was updated)
>
> [image: Встроенное изображение 1]
>
> How can I fix that?
>
>
> 2. xmipp3 - correlation alignment / optical alignment
>
>
>
>
> 2.1 correlation alignment
>
> - from time to time the protocol stops. When I resubmit it continues
> working.
> But the question is why does that happen: problem with my dataset and/or
> bug?
>
>
> 2.2 optical alignment
>
> - if you may remember the problem was that it finished because of an error
> in 1 file.
>
> Is there already the solution for skipping the movies that causing the
> error?
>
> Alternatively, I removed that file (it looked fine in terms of frames and
> visibility - I can send it for the analysis) and have to rerun the
> xmipp3-correlation again. But there is no guarantee that the program will
> not stop on some other file.
>
>
>
> 3. grigoriefflab - Input - movie stacks
>
> stops in the beginning with error -
>
> Input stack filename
> 14274:   [Runs/022622_ProtUnblur/tmp/movie_000010/FoilHole_
> 26594251_Data_25564934_25564935_20160826_2014-21929.mrc] : 24
> 14275:
> 14276:    No Such File - please enter a valid filename
>
>
>
>
> [image: Встроенное изображение 2]
>
>
>
> Sincerely,
> Dmitry
>
>
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