---
title: "Use case: CryoEM Single Particle Anlaysis"
url: "https://help.dectris.cloud/en/article/use-case-cryoem-single-particle-anlaysis"
language: "en"
last_updated: "2025-06-23T11:20:02.147Z"
---

# Use case: CryoEM Single Particle Anlaysis

This use case covers single particle analysis of cryoEM data from raw movies to atomic model using a combination of RELION and CryoSPARC.

[Embedded content](https://www.youtube.com/embed/h4Tj_aT6fEc)

## Data and Software used:

-   Raw data from [EMPIAR-10950](https://www.ebi.ac.uk/empiar/EMPIAR-10950/) ([Fujita et al., 2023](https://doi.org/10.1038/s41598-023-29396-0))
-   [RELION-5](https://relion.readthedocs.io/en/release-5.0/) and ModelAngelo ([Jamali et al., 2024](https://doi.org/10.1038/s41586-024-07215-4))
-   [CryoSPARC](https://cryosparc.com/) ([Punjani et al., 2017](https://doi.org/10.1038/nmeth.4169))
-   [Coot](https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/) ([Emsley et al., 2010](http://journals.iucr.org/d/issues/2010/04/00/ba5144/ba5144.pdf))

### DECTRIS CLOUD environments

-   Globus Data Transfer v0
-   CryoSPARC v1
-   RELION-5.0 v0
-   CCP4 & XDS & PyMOL GUI v1

## Data upload:

-   Create a new project and start a session using the Globus environment
-   Follow the instructions of the [help page](https://help.dectris.cloud/en/article/upload-via-globus) to set up and then click on `Browse Globus` button on the [EMPIAR-10950](https://www.ebi.ac.uk/empiar/EMPIAR-10950/) dataset page within the Session.
-   Download the dataset to `/dectris_data/path_to_your_project/raw/`.
-   After the download is completed, check if the files are present via the DECTRIS CLOUD data browser.

## Processing steps:

-   Generate the gain reference from the raw movies by running the  `Calculate Gain Reference` **public job template** on the raw folder of your project. This job does not require a GPU.
-   Create a **Session** using the `CryoSPARC` **Environment**. Make sure the node has at least 1 GPU.
-   Follow the standard CryoSPARC workflow. You can find a general tutorial [here](https://guide.cryosparc.com/processing-data/get-started-with-cryosparc-introductory-tutorial).
-   Download the final map and copy it to a `/dectris_data/path_to_your_project/` subfolder.
-   To build the atomic model automatically, run the `ModelAngelo` **public job template** using the final map as input. This job requires a GPU.
-   Create a new **Session** using the `CCP4 & XDS & PyMOL GUI` **Environment**, open a terminal and run `coot`, load your map and model to inspect the result.