CryoSPARC Guide
CryoSPARC Guide
CryoSPARC Guide
This Guide contains detailed information on installing, configuring and using cryoSPARC v0.2.47 to 0.6.5. For detailed documentation, installation instructions and a tutorial for cryoSPARC v2.0+, please visit our new documentation page at cryosparc.com/docs. We highly recommend upgrading to v2.0 to take advantage of the full pipeline for processing single particle cryo-EM data, as well as powerful new workflow features.

Example Dataset

To verify performance, please first run cryoSPARC using the TRPV1 dataset:

Setup

  1. Download the TRPV1 dataset by running the following command from the same machine where you downloaded cryoSPARC:

    cryosparc fetchexamples

  2. Create the dataset in cryoSPARC:

    1. Click on the ‘Experiments’ page, then click ‘Configure’ and ‘Add New File Set’.
    2. Name the Dataset ‘TRPV1’ by clicking on ‘New Dataset’ and modifying the text.
    3. For Meta Data File, click ‘Browse Bulk Files’. From the dropdown menu, click on on the ‘example_datasets’ folder and select the .star file.
    4. For Image Data File, click click ‘Browse Bulk Files’. From the dropdown menu, click on on the ‘example_datasets’ folder and select the .mrc file.
    5. In this example, the .star file does not contain a pixel size and therefore must be entered. Scroll down to the (microscope) ‘Parameters’ section and manually enter the Pixel Size as 1.2156.

  3. Click ‘Visualize’ and ‘Launch’ to have cryoSPARC load and display the data.

Ab-initio Reconstruction

Perform a one-class Ab-Initio Reconstruction:

  1. Click on the ‘Datasets’ page and select the TRPV1 dataset.
  2. Click on the ‘Experiments’ page, then click ‘New Experiment’. Verify that the number of Ab-initio Classes (below the list of experiments) is set to the default value of 1.
  3. Select ‘Ab-initio’ from the list.
  4. Click on ‘Launch’ on the left-hand sidebar, then click ‘Enqueue’ to commence the experiment.
  5. View/download the results in real-time from the ‘Launch’ section or from the ‘Experiments’ page. The status indicator will show as green with a checkmark to indicate the experiment is complete.
  6. You can download the final result structure from the ‘Experiments’ page by clicking on the double chevron on the bottom left-hand corner of the image projection.

Homogeneous Refinement

Perform a Homogenous Refinement on the result of the Ab-Initio Reconstruction:

  1. Once the Ab-Initio Reconstruction is complete, click on the “Experiments” page and view the experiment that you created in the previous section. You will see a single image projection displaying the single structure that was reconstructed in the ab-initio experiment.
  2. Click once on the ‘Structure’ button below the image projection from the ab-initio reconstruction. This selects the single result structure from the previous experiment.
  3. Click on ‘New Experiment’ and then select ‘Refinement’ from the list.
  4. Click on ‘Launch’ on the left-hand sidebar, then click ‘Enqueue’ to commence the experiment.
  5. View/download the results in real-time from the ‘Launch’ section or from the ‘Experiments’ page. The status indicator will show as green with a checkmark to indicate the experiment is complete.
  6. You can download the final result structure from the ‘Experiments’ page by clicking on the double chevron on the bottom left-hand corner of the image projection.