Re: [scipion-users] The relion bayesian polishing gives an error

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

Hi Dmitry,

the answers are below:

1) Relion polishing training output file is a simple txt file with 3
parameters. These 3 numbers you have to put into scipion protocol for
polishing.
2) Yes, it should work. Motioncor-produced global frame shifts should work
in Relion within Scipion. Let us know if it doesn't.

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 Fri, Jul 26, 2019 at 7:03 PM Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear Grigory,
>
> Sorry but  think I made a mistake for the input files - instead of save
> particles from the relion-3d refinement as an input for both -ctf
> refinement & polishing I used just the extracted particles.
> That explains why the software didn't have required tables.
>
> Small question -
> when I do the bayesian polishing there are 2 options - a) training and
> then b) polishing itself.
>
> In relion (separately) it is possible to use the output file from a)
> --opt_params to run b)
>
> But in Scipion i can not find in b) where to insert this file and b)
> starts itself (without using the results from a)
>
> Could you please tell me how to use the opt_parameter file?
>
> Another question - can I use motion cor results (not the relion motion
> cor) for the "input movies" input?
>
> Thank you!
>
> Have a great weekend
>
> Sincerely,
> Dmitry
>
>
> On July 25, 2019 16:47:51 Gregory Sharov <sha...@gm...> wrote:
>
>> Hi Dimitry,
>>
>> Could you please open an issue on github.com :
>> https://github.com/scipion-em/scipion-em-relion/issues
>>
>> On Thu, Jul 25, 2019, 14:28 Dmitry Semchonok <sem...@gm...> wrote:
>>
>>> Dear colleagues,
>>>
>>> The *relion bayesian polishing* gives an error
>>>
>>> ERROR:
>>> 00034:   Runs/007845_ProtRelionBayesianPolishing/input_particles.star
>>> does not contain all of the required columns (rlnOriginX, rlnOriginY,
>>> rlnAngleRot, rlnAngleTilt, rlnAnglePsi and rlnRandomSubset)
>>>
>>>
>>> Could you please fix that?
>>>
>>>
>>>
>>> Sincerely,
>>> Dmitry
>>>
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