Pyem consists of a suite of applications for cryo-EM. Chief among these applications is csparc2star, a utility to convert .cs (cryoSPARC) files to .star (RELION) files. Converting from .star to .cs is fairly straightforward, however the inverse is true from .cs to .star. It’s not abnormal to experience frustrations with this application. The following guide was written and tested for cryoSPARC v4 to RELION 5. According to personal communications, CryoSPARC updates can institute changes to the file format that require later iterations of pyem. Some advice before beginning:

  1. Try to ensure you have the latest version of pyem
  2. Examine what the file format looks like in RELION first. The RELION .star format is easily opened and manipulated using a text editor.
  3. Try to extract particles in cryoSPARC first. For example, if the particles from a NU-Refinement (i.e. NU-Refinement Job 101) are desired for further processing in RELION, extract those particles unbinned. (NUR 101→Extract Particles Job 102). This can get rid of unnecessary information that complicates downstream processing in RELION.

Procedure

This has been tested using Pyem v, RELION v. 5.0, and cryoSPARC v. 4.4.1.

  1. Export the desired job in cryoSPARC. Copy the files to the RELION workstation.

csparc2star 1.png

  1. There are two files we require. The first is a passthrough_particles.cs and a particles.cs. Find them, and move them to the workstation with RELION. If you are dealing with a NU-Refinement job first look at the final volume. It should have a volume_003 or 004. The particles you are desirous of converting would correspond to the final volume number (i.e. particles_004.cs). The files required for proceeding forward in this example are highlighted.

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  1. Run csparc2star in the following format with inverty and strip-uid flags. Strip UID is required to remove unnecessary file information imported from cryosparc. It will take a few seconds to run.
csparc2star.py particles.cs passthrough_particles.cs newfilename.star --inverty --strip-uid

terminal 1.png

  1. Open the new file in a text editor. There are some modifications that need to be performed. In this example, we can see that the file looks like a .star file but there are elements that will prevent RELION from being able to understand what’s here.

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  1. We will first remove the file path, J2/motioncorrected and replace it with