ACCRE Cryosparc Instance

CryoSPARC on ACCRE Cluster

This guide outlines the process for setting up and managing CryoSPARC accounts on the ACCRE cluster at Vanderbilt University and provides an introductory tutorial for processing data in CryoSPARC.

Getting Started with CryoSPARC

CryoSPARC is a comprehensive software package for processing cryo-electron microscopy data. It enables users to perform a wide range of data processing tasks, including motion correction, CTF estimation, particle picking, classification, and high-resolution refinement.

Prerequisites

Before you can start using CryoSPARC on the ACCRE cluster, ensure you have:

• An ACCRE cluster account.
• Requested access to CryoSPARC through the PI Dashboard.
• Basic familiarity with Linux commands and the SLURM job scheduling system.

Requesting a CryoSPARC Account

1. Visit the PI Dashboard to submit a CryoSPARC account request.
2. Once your request is approved, a CryoSPARC administrator will create your account using your provided email address.
3. You will receive a registration token via email. Use this token to complete your account setup at CryoSPARC by setting your password.

First Steps in CryoSPARC

Once your account is set up, log in to CryoSPARC to begin processing cryo-EM data. The following steps will guide you through creating a project and importing data.

Creating a New Project

1. Log into the CryoSPARC web interface.
2. Click on the "New Project" button.
3. Enter a project name and description, then click "Create".

Importing Data

Refer to the introductory tutorial for detailed steps on importing your data. A brief overview is provided below:

1. In your project, click "New Job".
2. Select "Import Movies" from the job selection panel.
3. Configure the job parameters, including the path to your data.
4. Click "Queue" to start the job.

Processing Data in CryoSPARC

Following data import, you can proceed with motion correction, CTF estimation, and further data processing steps as outlined in the CryoSPARC introductory tutorial. Each step involves creating a new job, selecting the appropriate job type, and configuring parameters specific to your data and analysis goals.

Monitoring Job Progress

Monitor the progress of your jobs directly from the CryoSPARC interface. The job status is updated in real-time, allowing you to see completed tasks and review results as soon as they are available.

Conclusion

This guide provides a starting point for using CryoSPARC on the ACCRE cluster. For comprehensive documentation on using CryoSPARC, including advanced processing techniques and troubleshooting, visit the CryoSPARC Guide.

This document is intended to assist users of Vanderbilt University's ACCRE cluster in setting up and starting with CryoSPARC and has been developed by the Center for Applied AI in Protein Dynamics.