Differences between revisions 157 and 178 (spanning 21 versions)
⇤ ← Revision 157 as of 2020-01-09 05:19:08 →
Size: 6330
Editor: SteveLudtke
Comment:
← Revision 178 as of 2024-01-22 14:54:47 → ⇥
Size: 7876
Editor: SteveLudtke
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
= 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 .''
Line 3: Line 4:
== 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
Line 5: Line 7:
''Please note that we are continuously developing and updating the tutorials. Items that are greyed out
are planned but the tutorials have not yet been completed. 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.
Line 9: Line 11:
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:
Line 10: Line 13:
=== Video tutorials and discussions ===
  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]		  * http://blake.bcm.edu/dl/eman2_tutorials_all.zip
Line 13: Line 15:
=== Written Tutorials === Alternatively, these individual data downloads cover the following standard workshop tutorial sequence:
Line 15: Line 17:
==== 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]]		  * [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]]
 * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
 * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * [[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)]]
Line 19: Line 23:
==== Short tutorials and info sheets ==== === Short tutorials and info sheets ===
 * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022)
Line 25: Line 30:
==== Single particle analysis (SPA) - 2D particles ====
 * [[attachment:EMAN2-31Tutorial.pdf|Latest EMAN2.31 single particle tutorial PDF]]		 === Single particle analysis (SPA) - 2D particles ===
 * [[attachment:EMAN2_GUITutorial.pdf|Quick Introduction to the EMAN2 GUI]] (Start here if you have never used EMAN2!)
  * [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]]
 * [[attachment:EMAN2_SingleParticleTutorial.pdf|Single particle analysis tutorial]]
Line 28: Line 35:
 * [[attachment:EMAN2-31FlexibilityTutorial.pdf|2-D variability tutorial]]
  * WARNING - there seems to be a bug in EMAN2.31 so the realign and rerefine buttons do not complete properly. Skip that step in the tutorial.		  * [[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)
 * [[attachment:EMAN2_FlexibilityTutorial.pdf|2-D variability analysis tutorial]]
Line 31: Line 39:
 * Sample images to explore the GUI
  * [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]]
 * [[EMAN2/Programs/convnet_pickparticle|tutorial for the Neural network particle picker]] (requires CUDA for good performance)
Line 39: Line 44:
==== 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 tutoria (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]]
Line 49: Line 51:
 * 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.
Line 50: Line 56:
==== Exchanging Data Between EMAN2 and Other Software ==== === 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_refine|GMM-based orientation refinement]] - Improve resolution for flexible samples.
 * [[EMAN2/e2gmmOriginal|Original GMM tutorial accompanying the paper]]

=== Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions) ===
Line 55: Line 67:
=== 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 - 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)