export Assets and import in Relion

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rddey80
export Assets and import in Relion

Dear Members,

I exported an asset in relion format from cisTEM and it created a stack file and a star file. Can someone tell step by step how I can use these two files to run 2D classification in Relion? I tried, but it did not work for me. What I did in Relion, is as follows:

1. Imported motion corrected mrc files, that created micrographs.star file

2. used particle extraction as attached screenshot

where to use the stack file?

Thanks for your time,

raj

timgrant
Hi Raj,

Hi Raj,

You should be able to straight to the 2D classification job line in Relion, select the star file that you exported from cisTEM, setup your parameters and run.

Cheers!

Tim

rddey80
export Assets and import in Relion

Hi Tim,

Mant thanks for your reply. I tried and got an error as follows:

Error:

cannot read file*-stack it does not exist

File: /usr/local/src/relion/src/image.h line: 157

Any idea?

Thanks,

Raj

timgrant
Did you move the stack after

Did you move the stack after you exported it?

Cheers,

Tim

rddey80
Hi Tim,

Hi Tim,

No, I did not move. Both star and stack files are located at the same place where cisTEM exported. Please see below:

[rdey@phoebe cistem]$ pwd
/ddn/TarkD/prex2/cistem
[rdey@phoebe cistem]$ ls

micrographs-neg  micrographs-pp  prex2-225k-stack  prex2-225k-star.star  prex2-neg  prex2-pp
[rdey@phoebe cistem]$ cd ../relion/

[rdey@phoebe relion]$  

I ran Relion 2D Classification here browsing the *.star file in the input gui and got the following error

ERROR:
Cannot read file prex2-225k-stack It does not exist
File: /usr/local/src/relion/src/image.h line: 157

Thanks,

Raj

timgrant
Hi Rak,

Hi Raj,

It is strange it does not have an extension, it should have the .mrcs extension.  Can you try to export it again with the filename prex2-225k-stack.mrcs

Thanks,

Tim

rddey80
Hi Tim,

Hi Tim,

Thanks. It is now running.

Best regards,

Raj

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