particles.star from relion export particles not compatible with pyem

[andreanans]

Hi,

I noticed that the star file written out by 'relion export particles' is incompatible with the pyem scripts. I have to pass the star file through relion_star_handler to produce a star file in the correct format.

We often run this command: csparc2star.py --copy-micrograph-coordinates particles.star particles_selected.cs final_particles.star

and get the following error:

File "pandas/_libs/parsers.pyx", line 545, in pandas._libs.parsers.TextReader.cinit pandas.errors.EmptyDataError: No columns to parse from file

I think it's something to do with the delimiter but I have no clue how to fix it other than running relion_star_handler and removing a column to reformat the file.

Any ideas?

[pconesa]

Hi @andreanans , if you are running Scipion 2.0, we have released a plugin to send jobs to cryosparc:

2D classification, ab-initio, and refinement (uniform and non-uniform)....

All of them import the particles into cryosparc so you can: 1.- use those methods and stay in scipion for further processing. 2.- If you want other jobs not yet implemented.....you can kick off one of them and you will have a workspace with the particles in cryosparc.

Probably we can add a "export to cs" to export particles, volumes ....as we are already doing now, but this is not done yet.

[delarosatrevin]

Pablo, in any case would be good to take a look a this incompatibility issue.

On Wed, Jul 17, 2019, 12:08 PM Pablo Conesa notifications@github.com wrote:

Hi @andreanans https://github.com/andreanans , if you are running Scipion 2.0, we have released a plugin to send jobs to cryosparc:

2D classification, ab-initio, and refinement (uniform and non-uniform)....

All of them import the particles into cryosparc so you can: 1.- use those methods and stay in scipion fot further processing. 2.- If you want other jobs not yet implemented.....you can kick off one of them and you will have a workspace with the particles in cryosparc.

Probably we can add a "export to cs" to export particles, volumes ....as we are already doing now, but this is not done yet.

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[andreanans]

Hi guys,

Thanks very much for the comments. I'll be sure to test the new plugin.

Just to clarify, we're having issues when going back to Scipion from cryosparc. As you probably know, some metadata is not preserved in those .cs files from cryosparc. If we want to generate a star file containing the original micrograph coordinates (for particle re-extraction) we must source our original star file from Scipion using the --copy-micrograph-coordinates flag. For some reason the scripts cannot read this star file unless I run it through relion_star_handler.

Another side note, in previous versions of scipion (1.1 or 1.2?) when you ran a particle extraction job it wrote out a star file automatically. This star file works fine with the script so I wonder if you could compare the two different files and see if the delimiter has changed somehow?

I hope this makes sense!!

[pconesa]

@delarosatrevin sure, I was just trying to give a workaround (if possible), but yes, something to look at.

@andreanans thanks for the tip....

I wish I could transfer this to scipion-em-relion repo.

[pconesa]

Added to relion repo.