Re: [scipion-users] Export particles from cryosparc

[Dmitry S. <Sem...@gm...>]

 <>Dear Grigory,

 

The files are in mrc format.

 

Please, let me try to explain more plan:

 I have a project in cryosparc. There I have cryosparc selected 2D classes. I want to export the particles of those classes into SCIPION.

 So I I pressed Export (fig 1) and the program(cryosparc) created the folder with mrc  + other files (fig 2;3). I looked into J48 and found many *.mrc files of the particles. But it is not 1 mrc = 1 particle. It seems to be a mrc stuck - so I have several files inside 1 *.mrc  (fig 4) (you can also notice that they all have different sizes) 

 So I need to export them somehow in SCIPION

 For that, I used the SCIPION export - images protocol where for the files to add I put *.mrc. But the protocol seems to be added only 1 mrc as 1 picture and instead of having 46392 particles I have ~600 particles.

 (Also the geometry seems not preserved).

 

So my question how to export the particles from cryosparc into SCIPION correctly?

 

 Thank you!





 https://disk.yandex.com/d/Fv3Q1lpwEzSisg


 Sincerely,

Dmitry




> On 17. May 2021, at 18:12, Grigory Sharov <sha...@gm...> wrote:
> 
> Hi Dmitry,
> 
> mrc stacks should have "mrcs" extension. Is this the problem you are getting?
> 
> 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 267228 <tel:+44%201223%20267228>
> e-mail: gs...@mr... <mailto:gs...@mr...>
> 
> 
> On Mon, May 17, 2021 at 4:49 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote:
>  <>Dear colleagues,
> 
>  I would like to export the particles from cryosparc to SCIPION.
> 
>  How to do that?
> 
>  
>  
> 
> 
> What I tried:
> 
>  
> 1.     In cryosparc I pressed Export – to export the particles I am interested in.
> 
> 2.     In the folder Export – I found many mrc stacks with particles in each.
> 
> 3.     I tried to export them to SCIPION using Export particles but instead of reading each stack and combine them in the 1 dataset I received 1 particle / per each mrc stack.
> 
>  
> Any ideas?
> 
>  
> Thank you
> 
>  Sincerely,
> 
> Dmitry
> 
>  
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