Import/export functionality

nextPYP supports importing and exporting single-particle and tomography Sessions or Projects, as well as Relion 4.0 or Relion 5.0 projects.

Import Sessions

Importing a nextPYP session

  • Create a new project in nextPYP or navigate to an existing one

  • Click on Import Data and select Single-particle (from Session)

  • Start typing the name of a single-particle session in the Session field

  • Select the name of session you want to import from the list of available sessions

  • Click Save and a new Single Particle (from Session) block will appear on the project page

  • Click on Import Data and select Tomography (from Session)

  • Start typing the name of a tomography session in the Session field

  • Select the name of the session you want to import from the list of available sessions

  • Click Save and a new Tomography (from Session) block will appear on the project page

  • Click Run followed by Start Run for 1 block to launch the import process

  • Once the run finishes, click inside the block to inspect the results

Import Projects

Importing a nextPYP project

  • Create a new project in nextPYP or navigate to an existing one

  • Click on Import Data and select Single-particle (from Project). A new Single Particle (from Project) block will appear on the page

  • Select the Path to existing CLI project by clicking on the icon and navigating to the location of the project you want to import

  • Click Save

  • Click on Import Data and select Tomography (from Project). A new Tomography (from Project) block will appear on the page

  • Select the Path to existing CLI project by clicking on the icon and navigating to the location of the tomography project you want to import

  • Click Save

  • Click Run followed by Start Run for 1 block to launch the import process

  • Once the run finishes, click inside the block to inspect the results

Import (from *.star)

Single-particle

Importing a single-particle project from *.star files

  • Create or navigate to an existing project in nextPYP

  • Click on Import Data and select Single-particle (from Star)

  • Go to the Import parameters tab:

    • Set the Relion project path by clicking on the icon and browsing to the corresponding directory

    • Set the location of the 3D refinement file (*.star) by clicking on the icon and browsing to the corresponding file

    • (optional) Set the location of the Motion file (*.star) by clicking on the icon and browsing to the corresponding file

    • Go to the Raw data tab:

    • Set the Location of the raw data by clicking on the icon and browsing to the corresponding directory

    • Click on the Microscope parameters tab

    • Set Pixel size (A)

    • Set Acceleration voltage (kV)

    • (optional) Set parameters in other tabs as needed

  • Click Save and a new Single Particle (from star) block will appear on the project page

  • Click Run followed by Start Run for 1 block to launch the import process

  • Once the run finishes, click inside the Single Particle (from star) block to inspect the results

Tomography

Importing a tomography project from *.star files

  • Create or navigate to an existing project in nextPYP

  • Click on Import Data and select Tomography (from Star)

  • Go to the Import parameters tab:

    • Set the Relion project path by clicking on the icon and browsing to the corresponding directory

    • Set the location of the Tomograms file (*.star) by clicking on the icon and browsing to the corresponding file

    • Set the location of the 3D refinement file (*.star) by clicking on the icon and browsing to the corresponding file

    • Select the Relion version used to generate the star file (4.0 or 5.0)

    • Go to the Raw data tab:

    • Set the Location of the raw data by clicking on the icon and browsing to the corresponding directory

    • Click on the Microscope parameters tab

    • Set Pixel size (A)

    • Set Acceleration voltage (kV)

    • Set Tilt-axis angle (degrees)

    • (optional) Set parameters in other tabs as needed

  • Click Save and a new Tomography (from star) block will appear on the project page

  • Click Run followed by Start Run for 1 block to launch the import process

  • Once the run finishes, click inside the Tomography (from star) block to inspect the results

Export (to *.star)

Exporting refinements to *.star files

  • Go to an existing refinement block, click on the menu icon , and select the Edit option

  • Check Show advanced options

  • Go to the Reconstruction tab:

    • Check Export metadata (*.star)

  • Click Save

  • Click Run followed by Start Run for 1 block

Note

This will perform a single round of refinement and export the resulting metadata to a .star file. To prevent additional refinement from being executed, ensure that all refinement options are unchecked in the Refinement tab before running the block

If you wish to export results from the Reference-based refinement, Ab-initio reconstruction, or Calculate reconstruction blocks, you have two options:

  • Re-run the original block after enabling the Export metadata (*.star) option

  • Alternatively, create and run a new 3D refinement block downstream, making sure to check the Export metadata (*.star) option and uncheck all refinement settings in the Refinement tab

Once the job ends, the results will appear in the specified folder and will be ready to import into other packages. For a tomography project, for example, you can use the Relion’s Import Coordinates procedure to import the data