Differences between revisions 77 and 108 (spanning 31 versions)

EMAN2 TUTORIALS

Beginners (introductory tutorials)

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.

Video tutorials and discussions

EMAN2 Video Tutorials

Written Tutorials

Single particle analysis (SPA) - 2D particles

2016 Summer Tutorial for EMAN2.12 June 2016 snapshots
- EMAN2-13_pre_Tutorial.pdf
- use Required data from 2015 tutorial
- EMAN2-13_pre_Heterogeneity.pdf
- see also: http://www.sciencedirect.com/science/article/pii/S0076687916300362
2015 Fall Tutorial for EMAN2.12
- EMAN2-12_Tutorial.pdf
- Required data - Bgal.zip
- EMAN2-12_Tutorial2_heterogeneity.pdf
- Required data - ribosome.zip
2015 Workshop Tutorials and Demo data - This includes updated tutorials on both high resolution single particle analysis and 2D/3D heterogeneity analysis along with sample data, freshly updated for the EMAN2.12 release. The workshop also included a number of other related topics also available on that page.
EMAN1 to EMAN2 Transition Guide - Also with useful quickstart guides for users of other software
Tilt Validation tutorial
Random Conical Tilt Tutorial
An experimental new particle picker (requires installation of additional libraries)

Single particle tomography (SPT) - 3D particles

BOTH the tutorial in .pdf format and the data needed for the tutorial in a .zip file are provided in the page linked below:

Single particle tomography

Using the Built-In Modules from Other Software

Out of date tutorials (provided for data access, etc.)

Tutorial from the 2014 Workshops in Shanghai, Brisbane and online - Based on EMAN2.1 beta4. Full single particle reconstruction tutorial
Single particle reconstruction tutorial from 2008 Workshop ( - Full tutorial on single particle reconstruction using the workflow (uses Workshop demo data DVD)
Tutorial from the 2011 EMAN2 workshop (Data on same page) - Based on EMAN2.01. Full single particle reconstruction tutorial
Tutorial from the 2012 Workshop in Singapore (Data on same page) - Based on EMAN2.06. Full single particle reconstruction tutorial
Tutorial from the 2013 Workshop in Beijing (Data on same page) - Based on EMAN2.1alpha. Full single particle reconstruction tutorial

Advanced (EMAN2 through the ''e2.py'' Python prompt)

* Generate and display an EMAN2 test image

* Rotate, translate, scale or mirror an image

* Add and multiply images, add and multiply by constants

* Convert a real/imaginary image into an amplitude/phase image and vice versa

* Iterate through the pixels of an image

* Make a projection of a 3D model, project through the asymmetric unit

* Change log level in EMAN2

-  ⇤ ← Revision 77 as of 2012-06-27 18:42:32 → 
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+   ← Revision 108 as of 2016-07-23 14:35:47 → ⇥
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+=== Video tutorials and discussions ===
  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]

=== Written Tutorials ===
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+Line 16:
+ * 2016 Summer Tutorial for EMAN2.12 June 2016 snapshots
  * [[attachment:EMAN2-13_pre_Tutorial.pdf||&do=get]]
  * use Required data from 2015 tutorial
  * [[attachment:EMAN2-13_pre_Heterogeneity.pdf||&do=get]]
  * see also: http://www.sciencedirect.com/science/article/pii/S0076687916300362
 * 2015 Fall Tutorial for EMAN2.12
  * [[attachment:EMAN2-12_Tutorial.pdf||&do=get]]
  * Required data - [[attachment:Bgal.zip||&do=get]]
  * [[attachment:EMAN2-12_Tutorial2_heterogeneity.pdf||&do=get]]
  * Required data - [[attachment:ribosome.zip||&do=get]]
 * [[Ws2015|2015 Workshop Tutorials and Demo data]] - This includes updated tutorials on both high resolution single particle analysis and 2D/3D heterogeneity analysis along with sample data, freshly updated for the EMAN2.12 release. The workshop also included a number of other related topics also available on that page.
-Line 13:
+Line 28:
- * [[Ws2011/Eman2|Tutorial from the 2011 EMAN2 workshop (Data on same page)]] - Based on EMAN2.01. Full single particle reconstruction tutorial
 * [[OxfordWs2012|Tilt Validation tutorial from the Oxford 2012 mini-workshop]] - Requires EMAN 2.05+
 * [[RctTutorial|Random Conical Tilt Tutorial]] - Requires EMAN 2.05+

Obsolete tutorials still provided for data access, etc.
 * Single particle reconstruction tutorial from 2008 Workshop ( - [[attachment:workflow_tutorial_2010_08_25.pdf|Full tutorial on single particle reconstruction using the workflow]] (uses [[http://blake.grid.bcm.edu/dl/data/workshop5.iso|Workshop demo data DVD]])
+ * [[OxfordWs2012|Tilt Validation tutorial]]
 * [[RctTutorial|Random Conical Tilt Tutorial]]
 * [[EMAN2/Programs/convnet_pickparticle|An experimental new particle picker]] (requires installation of additional libraries)
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+Line 33:
- * Single particle tomography USER'S GUIDE (updated on June 2012; under major refactoring do to extensive changes in e2spt capabilities; look for an extensively different version soon)
 [[attachment:e2spt_users_guide.pdf| e2spt_users_guide.pdf|&do=get]]
+BOTH the tutorial in .pdf format and the data needed for the tutorial in a .zip file are provided in the page linked below:
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+Line 35:
- * Data needed for the User's Guide up to 06/2012
 [[attachment:e2spt_data.zip| e2spt_data.zip|&do=get]]
+ * [[SPT/Spt|Single particle tomography]]
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+Line 37:
-==== 2D assessment of heterogeneity ====
 * [[attachment:population_dynamics_2009_11.pdf|Full tutorial on 2-D analysis for assessment of structural heterogeneity and population dynamics]] (under construction)
+==== Using the Built-In Modules from Other Software ====
 * [[EMAN2/Programs/e2refinetorelion2d/e2refinetorelion2dtutorial|2D Class Averaging with Relion]]
 * [[EMAN2/Programs/e2refinetorelion3d/e2refinetorelion3dtutorial|3D Refinement with Relion]]
 * [[EMAN2/Programs/e2refinetofrealign/e2refinetofrealigntutorial|3D Refinement with FreAlign]]
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+Line 42:
-==== Adding an e2program to the program manger workflow ====
 * [[EMAN2PMWorkflow|Modifying the EMAN2 projectmanager workflow]]
+=== Out of date tutorials (provided for data access, etc.) ===
 * [[Ws2014|Tutorial from the 2014 Workshops in Shanghai, Brisbane and online]] - Based on EMAN2.1 beta4. Full single particle reconstruction tutorial
 * Single particle reconstruction tutorial from 2008 Workshop ( - [[attachment:workflow_tutorial_2010_08_25.pdf|Full tutorial on single particle reconstruction using the workflow]] (uses [[http://blake.grid.bcm.edu/dl/data/workshop5.iso|Workshop demo data DVD]])
 * [[Ws2011/Eman2|Tutorial from the 2011 EMAN2 workshop (Data on same page)]] - Based on EMAN2.01. Full single particle reconstruction tutorial
 * [[Ws2012/EMAN2|Tutorial from the 2012 Workshop in Singapore (Data on same page)]] - Based on EMAN2.06. Full single particle reconstruction tutorial
 * [[Ws2013/EMAN2|Tutorial from the 2013 Workshop in Beijing (Data on same page)]] - Based on EMAN2.1alpha. Full single particle reconstruction tutorial