Convert .cs file to star in 2D selection job

Import and Export
1

I use the csparc2star.py to convert the selected 2D class particle to star file. The command is show as below

csparc2star.py /mnt/DATA1/cryosparc_database/project/Wei/P4/J54/particles_selected.cs --passthrough /mnt/DATA1/cryosparc_database/project/Wei/P4/J54/passthrough_particles_selected.cs ./J54.star

However is show the error

csparc2star.py: error: unrecognized arguments: --passthrough
2

Hi Robin - the latest version of csparc2star.py does not take the passthrough flag. You can just add the passthrough cs file, if needed, as an additional cs file without this flag, e.g:

csparc2star.py my_particles.cs pasthrough_particles.cs output.star

3

@olibclarke
Thank you Oli, I try it as the command

csparc2star.py /mnt/DATA1/cryosparc_database/project/Wei/P4/J54/particles_selected.cs /mnt/DATA1/cryosparc_database/project/Wei/P4/J54/passthrough_particles_selected.cs ./J54.star

and found the error

Columns must be same length as key
A passthrough file may be required (check inside the cryoSPARC 2+ job directory)

it looks like the particle number is different in two cs file.
however the the job folder there is only two passthroug cs file, passthrough_particles_excluded.cs passthrough_particles_selected.cs. It looks strange.

4

Ignore the “passthrough may be required” message - it is a generic error message persisting from an older version of the script as I understand it (@DanielAsarnow is this right?).

But yes, it seems like these two files are not compatible - I’ve run into this as well with certain job types. which job types were they from? Does running csparc2star.py just on the particles_selected.cs work?

Cheers
Oli

5

It is a 2D select job, and I try to run the csparc2star.py just on the particles_selected.cs and is works and get the list of particle name.

6

Yes - I haven’t had any luck using csparc2star.py on the output of a select2D job either, I get the same error.

Oli

7

Hi, I have particles which were extracted in Relion and imported in cryoSPARC. When I tried to export .cs file from Select2D job to .star using the following command:

csparc2star.py particles_selected.cs passthrough_particles_selected.cs from_sparc2D.star

but got following error:
csparc2star.py: error: unrecognized arguments: from_sparc2D.star

Thank you for any suggestions.
Yixin

8

@yxlui 1) use --loglevel debug and post the entire stacktrace. 2) Make sure you have Python 3 and the latest master branch of pyem with all dependencies, and that csparc2star.py --help prints all options successfully.