Differences between revisions 71 and 156 (spanning 85 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

Short tutorials and info sheets

EMAN2/NegativeStain - special issues that impact processing negative stain single particle images
Information about images
Filtering and basic image processing
CTF Simulator

Single particle analysis (SPA) - 2D particles

Latest EMAN2.31 single particle tutorial PDF
- Tutorial Data Download
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.
- Practice data for 2-D variability analysis
Sample images to explore the GUI
- eman2_samples.zip
tutorial for the Neural network particle picker (requires CUDA for good performance)
These haven't been updated in a while, please ask if you have problems
- EMAN1 to EMAN2 Transition Guide - Also with useful quickstart guides for users of other software
- Tilt Validation tutorial
- Random Conical Tilt Tutorial

Tomography - tilt series through subtomogram averaging

Complete workflow for tomography and subtomogram averaging (subnanometer resolution, 2+ days, full workstation)
- 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 tomography workflow tutoria (small)
- Tomography Mini-tutorial Data Download
Automated Cellular Tomogram Annotation using Neural Networks
- Tomogram Annotation

Exchanging Data Between EMAN2 and Other Software

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

2019 May UTMB Workshop (full site with talks)
2019 January Tutorial for EMAN2.22
- EMAN2-22Tutorial.pdf (version 1)
  - Tutorial Data Download
2018 May Tutorial for EMAN2.21a
- EMAN2-21Tutorial.pdf (version 1)
  - Tutorial Data Download
2017 February Tutorial for EMAN2.2
- EMAN2-2Tutorial.pdf
  - Tutorial Data Download
2016 Summer Tutorial for EMAN2.12 June 2016 snapshots
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.
Single particle tomography - Tutorial for deprecated Single particle tomography (SPT) workflow.
Tutorial from the 2014 Workshops in Shanghai, Brisbane and online - Based on EMAN2.1 beta4. 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
Tutorial from the 2012 Workshop in Singapore (Data on same page) - Based on EMAN2.06. Full single particle reconstruction tutorial
Tutorial from the 2011 EMAN2 workshop (Data on same page) - Based on EMAN2.01. 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)

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-Deletions are marked like this.
+Additions are marked like this.
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-are planned but the tutorials have not yet been completed. If you have a request for a particular tutorial
+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
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+=== Video tutorials and discussions ===
  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]]

=== Written Tutorials ===

==== Short tutorials and info sheets ====
 * [[EMAN2/NegativeStain]] - special issues that impact processing negative stain single particle images
 * [[attachment:image_info.pdf|Information about images]]
 * [[attachment:image_proc.pdf|Filtering and basic image processing]]
 * [[attachment:ctf_sim.pdf|CTF Simulator]]
-Line 11:
+Line 22:
+ * [[attachment:EMAN2-31Tutorial.pdf|Latest EMAN2.31 single particle tutorial PDF]]
  * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * [[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.
  * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
 * 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)
 * These haven't been updated in a while, please ask if you have problems
  * [[EMAN2/Eman1Transition|EMAN1 to EMAN2 Transition Guide]] - Also with useful quickstart guides for users of other software
  * [[OxfordWs2012|Tilt Validation tutorial]]
  * [[RctTutorial|Random Conical Tilt Tutorial]]
-Line 12:
+Line 35:
- * [[EMAN2/Eman1Transition|EMAN1 to EMAN2 Transition Guide]]
 * The old SPR tutorial (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|The NEW tutorial from the 2011 EMAN2 workshop, compatible with EMAN 2.01 (Data on same page)]]
 * [[OxfordWs2012|The Tilt Validation tutorial from the Oxford 2012 EMAN2 workshop, compatible with EMAN Nightly Build (Data on same page)]]
 * [[attachment:rct_tutorial.pdf|Tutorial on using EMAN2 for Random Conical Tilt reconstructions|&do=get]]
+==== Tomography - tilt series through subtomogram averaging ====
-Line 18:
+Line 37:
+ * 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]]
 * Automated Cellular Tomogram Annotation using Neural Networks
  * [[EMAN2/Programs/tomoseg|Tomogram Annotation]]
-Line 19:
+Line 46:
-==== Single particle tomography (SPT) - 3D particles ====
 * NEW single particle tomography USERS' GUIDE.
 [[attachment:e2spt_users_guide.pdf| e2spt_users_guide.pdf|&do=get]]
+==== Exchanging Data Between EMAN2 and 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]]
-Line 23:
+Line 51:
-==== 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)

==== Adding an e2program to the program manger workflow ====
 * [[EMAN2PMWorkflow|Modifying the EMAN2 projectmanager workflow]]

== Advanced (EMAN2 through the ''e2.py'' Python prompt) ==
* [[EMAN2/Galleries/Testimages|Generate and display an EMAN2 test image]]

* [[EMAN2/Tutorials/RotateTranslate|Rotate, translate, scale or mirror an image]]

* [[EMAN2/Tutorials/AddAndMultiply|Add and multiply images, add and multiply by constants]]

* [[EMAN2/Tutorials/ri2ap|Convert a real/imaginary image into an amplitude/phase image and vice versa]]

* [[EMAN2/Tutorials/iter_pixels|Iterate through the pixels of an image]]

* [[EMAN2/Tutorials/make_a_projection|Make a projection of a 3D model, project through the asymmetric unit]]

{{attachment:2d_image_3dplot_2.png}}

* [[EMAN2LogLevel|Change log level in EMAN2]]
+=== Archive of Workshop Material (Lectures, specific tutorials, etc. ===
 * [[UTMBWorkshop2019|2019 May UTMB Workshop]] (full site with talks)
  * [[https://blake.bcm.edu/emanwiki/UTMBWorkshop2019?action=AttachFile&do=get&target=EMAN2-3Tutorial.pdf|Latest EMAN2.3 single particle tutorial PDF]]
  * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
  * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
 * 2019 January Tutorial for EMAN2.22
  * [[attachment:EMAN2-22Tutorial.pdf||&do=get]] (version 1)
   * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * 2018 May Tutorial for EMAN2.21a
  * [[attachment:EMAN2-21Tutorial.pdf||&do=get]] (version 1)
   * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * 2017 February Tutorial for EMAN2.2
  * [[attachment:EMAN2-2Tutorial.pdf||&do=get]]
   * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
 * 2016 Summer Tutorial for EMAN2.12 June 2016 snapshots
  * [[attachment:EMAN2-13_pre_Tutorial.pdf||&do=get]]
   * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
  * [[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.
 * [[SPT/Spt|Single particle tomography]] - Tutorial for deprecated Single particle tomography (SPT) workflow.
 * [[Ws2014|Tutorial from the 2014 Workshops in Shanghai, Brisbane and online]] - Based on EMAN2.1 beta4. 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
 * [[Ws2012/EMAN2|Tutorial from the 2012 Workshop in Singapore (Data on same page)]] - Based on EMAN2.06. Full single particle reconstruction tutorial
 * [[Ws2011/Eman2|Tutorial from the 2011 EMAN2 workshop (Data on same page)]] - Based on EMAN2.01. 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]])