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= EMAN2 TUTORIALS = = 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 .''
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== Beginners (introductory tutorials) == == Video tutorials and discussions ==
 * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]] - These are a valuable supplement to the tutorials here, but are NOT a replacement
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''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.''		 == Standard Tutorials ==
=== Tutorial Data Downloads ===
The actual tutorials are in the sections below, this section contains the various test data sets.
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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:
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=== Video tutorials and discussions ===
  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]		  * http://blake.bcm.edu/dl/eman2_tutorials_all.zip
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=== Written Tutorials === Alternatively, these individual data downloads cover the following standard workshop tutorial sequence:
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==== Tutorial Data ====
 * 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:
 * [[http://blake.bcm.edu/dl/eman2_tutorials_all.zip]]
 * This covers the following standard workshop tutorial sequence:
  * [[attachment:EMAN2_GUITutorial.pdf|Quick Introduction to the EMAN2 GUI]] (30 min)
  * [[attachment:EMAN2_FlexibilityTutorial.pdf|2-D variability analysis tutorial]] (30 min)
  * [[attachment:EMAN2_SingleParticleTutorial.pdf|Single particle analysis tutorial]] (1-4 hr plus some waiting)
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]] (1-4 hr plus some waiting)		  * [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]]
 * [[http://blake.bcm.edu/dl/tutorial_tomo_small.zip|Small Tomography Tutorial (for low end machines/laptops)]]
 * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Tomography Tutorial (for standard workstations)]]
 * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Single Particle Tutorial Data]]
 * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
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==== Short tutorials and info sheets ==== === Short tutorials and info sheets ===
 * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022)
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==== Single particle analysis (SPA) - 2D particles ==== === Single particle analysis (SPA) - 2D particles ===
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 * [[attachment:EMAN2_boxer_tutorial_2021_04.pdf|Particle picking tutorial (basic tutorial only)]]
 * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance)
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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. It will be fixed in the next release.
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 * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance)
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==== Tomography - tilt series through subtomogram averaging ====

 * Complete workflow for tomography and subtomogram averaging (subnanometer resolution, 2+ days, full workstation)
  * [[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). Note that the large version of the tutorial above is updated regularly. If you have issues with this tutorial check the corresponding section in the full tutorial above.
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial (small)]]
  * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Mini-tutorial Data Download]]		 === Tomography - tilt series through subtomogram averaging ===
 * Complete workflow for tomography and subtomogram averaging (includes both small version (laptop ~12 Å) and large version (subnanometer on workstation))
  * [[EMAN2/e2TomoSmall|Tomography and Subtomogram Averaging 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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 * More advanced topics for subtomogram averaging
  * [[EMAN2/e2tomo_p22|Advanced SPT methods]] - Latest (2023) workflow for in situ SPT.
  * [[EMAN2/TomoSymmetry|Working with pseudosymmetric particles]] - Improving resolution and exploring variability in symmetric particles
  * [[EMAN2/e2tomo_more| Miscellaneous tools]] - Various SPT tools that may not be included in the main workflows.
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==== Exchanging Data Between EMAN2 and Other Software ==== === Gaussian Mixture Model - for SPA and SPT data ===
 * Heterogeneity analysis - 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/e2gmmOriginal|Original GMM tutorial accompanying the 2021 paper]]
 * Orientation refinement - Improve resolution for flexible structures. For detailed methods, see the [[https://www.nature.com/articles/s41592-023-02082-9| 2024 paper]].
  * [[EMAN2/e2gmm_refine|GMM-based orientation refinement]] for SPA
  * [[A brief EMAN2/e2tomo_p22#GMM-based_refinement| tutorial]] on GMM based orientation refinement for SPT
 * [[EMAN2/e2gmm_model|Atomic model refinement]] - both single model and continuous movement.

=== Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions) ===
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=== Archive of Workshop Material (Lectures, specific tutorials, etc. === == Archive of Workshop Material (Lectures, specific tutorials, etc. ==

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 - for SPA and SPT data

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)