Differences between revisions 172 and 180 (spanning 8 versions)
Revision 172 as of 2022-08-30 03:43:21
Size: 7146
Editor: SteveLudtke
Comment:
Revision 180 as of 2024-04-05 01:50:10
Size: 8234
Editor: MuyuanChen
Comment: re-organize gmm part
Deletions are marked like this. Additions are marked like this.
Line 5: Line 5:
 * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]] - These are a valuable supplement to the tutorials here, but are NOT a replacement
Line 7: Line 7:
== Written Tutorials == == Standard Tutorials ==
Line 18: Line 18:
 * [[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]]
Line 19: Line 22:
 * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * [[http://blake.bcm.edu/dl/tutorial_tomo_mini.zip|Tomography Mini-tutorial Data Download]]
Line 23: Line 24:
 * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW)  * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022)
Line 37: Line 38:
  * 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
Line 39: Line 39:
 * [[EMAN2/e2gmm|3-D variability analysis using GMM (Gaussian Mixture Model) and deep learning]] (requires CUDA, still under active development)
Line 47: Line 46:
  * [[EMAN2/e2TomoSmall|EMAN2 tomography workflow tutorial]]   * [[EMAN2/e2TomoSmall|Tomography and Subtomogram Averaging Tutorial]]
Line 53: Line 52:
  * [[EMAN2/e2tomo_more|Advanced Subtomo]]
 * Preview tutorial for the new version of integrated subtomogram averaging (under development)
  * [[EMAN2/e2tomo_new|New 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.

=== 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.

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)