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 * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]] - These are a valuable supplement to the tutorials here, but are NOT a replacement
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== Written Tutorials == == Standard Tutorials ==
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 * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW)  * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022)
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  * WARNING - there seems to be a bug in EMAN2.31 so the realign and rerefine buttons do not work properly. Skip that step in the tutorial
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 * [[EMAN2/e2gmm|3-D variability analysis using GMM (Gaussian Mixture Model) and deep learning]] (requires CUDA, still under active development)
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 * Complete workflow for tomography and subtomogram averaging (subnanometer resolution, 2+ days, full workstation) - The small tutorial below is more up to date as of Feb 22
  * [[EMAN2/e2tomo|EMAN2 tomography workflow tutorial (large)]]
  * Data link is in the tutorial text
 * Small version of workflow for tomography and subtomogram averaging (~15 A, 1 day, possible on a laptop).
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]]
  * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Mini-tutorial Data Download]]		  * Complete workflow for tomography and subtomogram averaging (includes both small version (laptop ~12 Å) and large version (subnanometer on workstation))
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial]]
  * [[http://blake.bcm.edu/dl/tutorial_tomo_small.zip|Small Data Download]]
  * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Data Download]]
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=== Gaussian Mixture Model - Variability analysis both for SPA and SPT data ===
Strongly suggest reading [[https://www.nature.com/articles/s41592-021-01220-5|the paper]] (PMC8363932). While there have been some very significant improvements, it lays a foundation. This project has also bifurcated, as explained in the first tutorial below.
 * [[EMAN2/e2gmm|GMM GUI Tutorial - supports both SPA and SPT projects] - suggest starting here for most users
 * [[EMAN2/e2gmm|Original GMM tutorial accompanying the paper]]

EMAN2 Introductory Tutorials

Please note that we are continuously developing and updating the tutorials. Most tutorials include the necessary data. If you have a request for a particular tutorial please feel free to email sludtke@bcm.edu .

Video tutorials and discussions

  • EMAN2 Video Tutorials - These are a valuable supplement to the tutorials here, but are NOT a replacement

Standard Tutorials

Tutorial Data Downloads

The actual tutorials are in the sections below, this section contains the various test data sets.

Individual tutorial data downloads are available below, but for convenience, we have combined the data for the GUI introduction, single particle analysis tutorial, single particle 2-D dynamics tutorial and small tomography tutorial into a single download:

Alternatively, these individual data downloads cover the following standard workshop tutorial sequence:

Short tutorials and info sheets

Single particle analysis (SPA) - 2D particles

Tomography - tilt series through subtomogram averaging

Gaussian Mixture Model - Variability analysis both for SPA and SPT data

Strongly suggest reading the paper (PMC8363932). While there have been some very significant improvements, it lays a foundation. This project has also bifurcated, as explained in the first tutorial below.

Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions)

Archive of Workshop Material (Lectures, specific tutorials, etc.

EMAN2/Tutorials (last edited 2024-04-05 01:51:27 by MuyuanChen)