Install and Setup
Please review the detailed system requirements and install instructions available here. If you are currently running v0, you can seamlessly install and run v2 alongside, as they use different port numbers. These cover workstation and cluster installs, file configuration and how to update cryoSPARC v2 when new versions become available. For assistance, please refer to the cryoSPARC discussion forum or send us an email at email@example.com.
We recommend starting off with the T20S Tutorial to become familiar with cryoSPARC v2. The tutorial takes you from raw movies through to a refined structure, using a small set of 20 movies.
Process Your Cryo-EM Data
The Documentation section of this website is a live reference for all things cryoSPARC v2 and is continuously updated with new information and links.
The Basics: Consult this section for a quick walk-through of everything you need to know about processing data in cryoSPARC v2, including:
- How to organize projects and workspaces
- Navigation, keyboard shortcuts and the tree view
- How to connect inputs and queue jobs and modify parameters
- Killing, deleting, coning, moving and linking jobs
- How to use the Resource Manager
- How to set up automated workflows that run on their own
Jobs and Parameters: The Guide to Jobs and Common Parameters contains comprehensive information on all job types in cryoSPARC v2, with detailed information on:
- What these jobs do, and when to use them
- Inputs and outputs
- Commonly adjusted parameters
- Common next steps
- Tutorials: Find in-depth tutorials covering various aspects of processing data in cryoSPARC. We are always working to add more.
- Blog: On the blog, you can find data processing case studies, information on new features and fixes, new papers published, and cryo-EM related news.
- Discussion Forum: Contribute to and learn from a vibrant community of cryoSPARC users who may have similar questions on the discussion forum.
- Stay in the know: You can sign up for our newsletter to receive updates on new features and data processing tips.
- Contact Us: Issues or feedback? Drop us a line at firstname.lastname@example.org, we would love to hear from you!
A manuscript describing new methods in cryoSPARC v2 is in preparation. In the interim, please cite the following papers as appropriate:
- For general cryoSPARC use, please cite the original cryoSPARC paper: Punjani, A., Rubinstein, J.L., Fleet, D.J. & Brubaker, M.A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nature Methods 14, 290-296 (2017).
- For motion correction tools in v2, please cite the original alignparts paper in the interim: Rubinstein, J.L. & Brubaker, M.A. Alignment of cryo-EM movies of individual particles by optimization of image translations. Journal of Structural Biology 192 (2), 188-195 (2015).
- For CTFFIND, wrapped into cryoSPARC, please cite: Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Journal of Structural Biology 192 (2), 216-221 (2015).
- For ResLog analysis, please cite: Stagg, S.M., Noble, A.J., Spilman, M. & Chapman, M.S. ResLog plots as an empirical metric of the quality of cryo-EM reconstructions. Journal of Structural Biology 185 (3), 418-426 (2014).
- For 3DFSC, please cite: Tan, Y.Z., Baldwin, P.R., Davis, J.H., Williamson, J.R., Potter, C.S., Carragher, B. & Lyumkis, D. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nature Methods 14, 793-796 (2017).
For more information on these job types in cryoSPARC v2, please locate them in the Guide to Jobs and Common Parameters.