[3dem] Micrographs manual sorting relion3

[Julien Bous]

Dear all,


Thank you all very much for your nice suggestions.

I tried to sort it with the motion estimation as suggested mazdak 
radjainia and it work quite well in my case so I'll gofor this solution.

Another sugestion was to do it in scipion and it looks really 
convenient, as well as the FOCUS software.

Thank you very much for all your answers.

Cheers,

Julien


Le 23/11/2018 à 11:57, Henning Stahlberg a écrit :
> Dear Julien,
>
> You could try FOCUS for this, see
> https://www.youtube.com/watch?v=fKees50shgY&list=PLteVxMX-rlQspNczCoWrLyamWHgrhTMGv&index=6
>
> Henning.
>
> Henning Stahlberg, PhD
> Prof. for Structural Biology, C-CINA, Biozentrum, University of Basel
> Mattenstrasse 26 | D-BSSE | WRO-1058 | CH-4058 Basel | Switzerland
> http://c-cina.org | Tel. +41-61-387 32 62
>
>
>
>
> Dear Julien,
>
> You can use Scipion to do that.
> When running movie alignment (motioncor2, unblur, xmipp3, etc) you can 
> active an option
> to generate a thumbnail and then after CTF estimation (gctf, ctffind4, 
> etc) you will have a GUI (see
> figure below) where you can sort by any column (estimated resoltion, 
> quality fit, defocus, etc)
> and select/deselect micrographs and create a new subset. You can also 
> change to a view to see
> a gallery of all thumbnails (real space micrograph) or a gallery of 
> all PSDs images, this also helps
> to screen the micrographs quickly in some cases. If you don't want to 
> continue processing
> inside Scipion, you could easily export micrographs + CTF (protocol 
> 'relion - export ctf') and then
> proceed in Relion.
>
> Please let me know if you want to give it a try and have any further 
> questions.
>
> Kind regards,
> Jose Miguel
>
>
>
> image.png



>
>
> On Thu, Nov 22, 2018 at 6:18 PM Julien Bous 
> <julien.bous at etu.umontpellier.fr 
> <mailto:julien.bous at etu.umontpellier.fr>> wrote:
>
>     Dear All,
>
>     I wish to realise a sorting of my realigned micrographs in
>     Relion3, in
>     order to get rid of broken ice area. I wanted to do it in the subset
>     selection mode but I was not able to set a lowpass filter in this
>     mode
>     and it was challenging to asses the micrographs quality. I thougt
>     to do
>     it in the manual picking mode or manually, with eman , but in this
>     way I
>     can just display the micrographs one by one and it'll be very time
>     consuming. Therefore if anyone  knows how to realise this task
>     effectively I'll be glad to know your opinion.
>
>     Cheers,
>
>     Julien
>
>
>
>
>> On 22 Nov 2018, at 18:18, Julien Bous 
>> <julien.bous at etu.umontpellier.fr 
>> <mailto:julien.bous at etu.umontpellier.fr>> wrote:
>>
>> Dear All,
>>
>> I wish to realise a sorting of my realigned micrographs in Relion3, 
>> in order to get rid of broken ice area. I wanted to do it in the 
>> subset selection mode but I was not able to set a lowpass filter in 
>> this mode and it was challenging to asses the micrographs quality. I 
>> thougt to do it in the manual picking mode or manually, with eman , 
>> but in this way I can just display the micrographs one by one and 
>> it'll be very time consuming. Therefore if anyone  knows how to 
>> realise this task effectively I'll be glad to know your opinion.
>>
>> Cheers,
>>
>> Julien
>>
>> _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu <mailto:3dem at ncmir.ucsd.edu>
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>

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