Particle location missing

Cryo-EM Data Processing
1

Hi,
I have imported particles without connecting them to micographs.
I have done some data processing/ classification jobs using the particles, and am trying to remove duplicates before I merge particles from different classification jobs. However, the remove duplicate job fails saying:

" 'Non-optional inputs from the following input groups and their slots are not connected: ’ + missing_inputs + ‘. Please connect all required inputs.’
AssertionError: Non-optional inputs from the following input groups and their slots are not connected: particles.location. Please connect all required inputs."

I think this is because the particle location is missing, as it says ‘empty’ for particle location in the inputs. Is there a way to get the particle location for the particles that have already been processed? I’ve tried “Re-assign particles” to get the missing particle location but it fails with the same error. I’m hoping I don’t have to import particles again with connected particles and perform all of the classifications jobs again…

Thank you in advance for the help!

2

You have to connect the micrographs to import the coordinates.

You also need coordinates to reassign - otherwise there’s no point.

You can export your subclassified imported particles and use --copy-micrograph-coordinates with the original .star file to get the coordinates, and then import the result - but this time connect the micrographs. That way will definitely work, without rerunning the classifications.

3

Hi,
Thank you for the reply.
I’m little bit lost with exporting the particles and using --copy-micrograph-coordinates with the orignal. star file…

  1. By exporting particles, do you mean I should export the refinement job of the particles?
  2. what do you mean by “original .star file”? Should I convert the “particles.cs” file from the refinement job of the subclassified particles to a “.star” file, and is this what you mean by the ‘original .star’ file? If so, why do i need to export the job?
4

“–copy-micrograph-coordinates” is a parameter of csparc2star.py (an util of pyem for exporting particles to relion from cryosparc ). your can do:

csparc2star.py cryosparc_xxx.cs cryosparc_xxx.star --strip-uid --copy-micrograph-coordinates xxx.star

Note that: the xxx.star is the star file from relion job which you imported into cryosparc, eg: Extract/job325/particles.star

Then re-import this new star file"cryosparc_xxx.star" with connection blob to micrographs. If still get errors, you can try to re-extract particles in relion, then import into cryosparc with connection blob to mics.

5

Thank you for the help!
I always get the following error when I try the --copy- micrograph

/programs/x86_64-linux/pyem/20220131/pyem_extlib/pyem-20220131-lksb/pyem/star.py:539: FutureWarning: Columnar iteration over characters will be deprecated in future releases.
df[UCSF.IMAGE_INDEX], df[UCSF.IMAGE_PATH] = \

Did anyone have the same issue?

6

It’s not an error (just a warning). The output will be fine.

Also - years old versions of pyem from sbgrid are not guaranteed to work.