Use case: CryoEM Single Particle Anlaysis

Data and Software used:

• Raw data from EMPIAR-10950 (Fujita et al., 2023)
• RELION-5 and ModelAngelo (Jamali et al., 2024)
• CryoSPARC (Punjani et al., 2017)
• Coot (Emsley et al., 2010)

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 to set up and then click on Browse Globus button on the 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.
• 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.