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eman2:tutorials [2025/06/14 17:23] – created steveludtkeeman2:tutorials [2025/06/24 01:20] (current) – [Archive of Workshop Material (Lectures, specific tutorials, etc.] steveludtke
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 ===== Video tutorials and discussions ===== ===== Video tutorials and discussions =====
-  * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]] - These are a valuable supplement to the tutorials here, but are NOT a replacement+  * [[EMAN2:VideoTutorials|EMAN2 Video Tutorials]] - These are a valuable supplement to the tutorials here, but are NOT a replacement
  
 ===== Standard Tutorials ===== ===== Standard Tutorials =====
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 ==== Short tutorials and info sheets ==== ==== Short tutorials and info sheets ====
-  * [[EMAN2/Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022) +  * [[EMAN2:Jupyter]] - Using EMAN2 widgets from JupyterLab notebooks! (NEW - 2022) 
-  * [[EMAN2/NegativeStain]] - special issues that impact processing negative stain single particle images +  * [[EMAN2:NegativeStain]] - special issues that impact processing negative stain single particle images 
-  * [[attachment:image_info.pdf|Information about images]] +  * [[http://blake.bcm.edu/dl/EMAN2/image_info.pdf|Information about images]] 
-  * [[attachment:image_proc.pdf|Filtering and basic image processing]] +  * [[http://blake.bcm.edu/dl/EMAN2/image_proc.pdf|Filtering and basic image processing]] 
-  * [[attachment:ctf_sim.pdf|CTF Simulator]]+  * [[http://blake.bcm.edu/dl/EMAN2/ctf_sim.pdf|CTF Simulator]]
  
 ==== Single particle analysis (SPA) - 2D particles ==== ==== 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/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]]     * [[http://blake.bcm.edu/dl/eman2_samples.zip|eman2_samples.zip]]
-  * [[attachment:EMAN2_SingleParticleTutorial.pdf|Single particle analysis tutorial]]+  * [[http://blake.bcm.edu/dl/EMAN2/EMAN2_SingleParticleTutorial.pdf|Single particle analysis tutorial]]
     * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]     * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
-  * [[attachment:EMAN2_boxer_tutorial_2021_04.pdf|Particle picking tutorial (basic tutorial only)]] +  * [[http://blake.bcm.edu/dl/EMAN2/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) +  * [[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]]+  * [[http://blake.bcm.edu/dl/EMAN2/EMAN2_FlexibilityTutorial.pdf|2-D variability analysis tutorial]]
     * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]     * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
   * These haven't been updated in a while, please ask if you have problems   * 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+    * [[EMAN2:Eman1Transition|EMAN1 to EMAN2 Transition Guide]] - Also with useful quickstart guides for users of other software
     * [[OxfordWs2012|Tilt Validation tutorial]]     * [[OxfordWs2012|Tilt Validation tutorial]]
     * [[RctTutorial|Random Conical Tilt Tutorial]]     * [[RctTutorial|Random Conical Tilt Tutorial]]
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 ==== Tomography - tilt series through subtomogram averaging ==== ==== 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))   * 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]]+    * [[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_small.zip|Small Data Download]]
     * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Data Download]]     * [[http://blake.bcm.edu/dl/tutorial_tomo_large.zip|Large Data Download]]
   * Automated Cellular Tomogram Annotation using Neural Networks   * Automated Cellular Tomogram Annotation using Neural Networks
-    * [[EMAN2/Programs/tomoseg|Tomogram Annotation]]+    * [[EMAN2:Programs:e2tomoseg|Tomogram Annotation]]
   * More advanced topics for subtomogram averaging   * More advanced topics for subtomogram averaging
-    * [[EMAN2/e2tomo_p22|Advanced SPT methods]] - Latest (2023) workflow for in situ SPT. +    * [[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: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.+    * [[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 ==== ==== 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.    * 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: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]]+    * [[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]].   * 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 +    * [[EMAN2:e2gmm_refine|GMM-based orientation refinement]] for SPA 
-    * [[EMAN2/e2tomo_p22#GMM-based_refinement|A brief tutorial]] on GMM based orientation refinement for SPT +    * [[EMAN2:e2tomo_p22#GMM-based_refinement|A brief tutorial]] on GMM based orientation refinement for SPT 
-  * [[EMAN2/e2gmm_model|Atomic model refinement]] - both single model and continuous movement. +  * [[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) ==== ==== Exchanging Data Between EMAN2 and Other Software (a bit outdated, untested with newer Relion versions) ====
-  * [[EMAN2/Programs/e2refinetorelion2d/e2refinetorelion2dtutorial|2D Class Averaging with Relion]] +  * [[EMAN2:Programs:e2refinetorelion2d:tutorial|2D Class Averaging with Relion]] 
-  * [[EMAN2/Programs/e2refinetorelion3d/e2refinetorelion3dtutorial|3D Refinement with Relion]] +  * [[EMAN2:Programs:e2refinetorelion3d:tutorial|3D Refinement with Relion]] 
-  * [[EMAN2/Programs/e2refinetofrealign/e2refinetofrealigntutorial|3D Refinement with FreAlign]]+  * [[EMAN2:Programs:e2refinetofrealign:tutorial|3D Refinement with FreAlign]]
  
 ===== Archive of Workshop Material (Lectures, specific tutorials, etc. ===== ===== Archive of Workshop Material (Lectures, specific tutorials, etc. =====
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     * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]     * [[http://blake.bcm.edu/dl/fassub.tgz|Practice data for 2-D variability analysis]]
   * 2019 January Tutorial for EMAN2.22   * 2019 January Tutorial for EMAN2.22
-    * [[attachment:EMAN2-22Tutorial.pdf||&do=get]] (version 1)+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-22Tutorial.pdf|PDF] (version 1)
       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
   * 2018 May Tutorial for EMAN2.21a   * 2018 May Tutorial for EMAN2.21a
-    * [[attachment:EMAN2-21Tutorial.pdf||&do=get]] (version 1)+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-21Tutorial.pdf|PDF]] (version 1)
       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
   * 2017 February Tutorial for EMAN2.2   * 2017 February Tutorial for EMAN2.2
-    * [[attachment:EMAN2-2Tutorial.pdf||&do=get]]+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-2Tutorial.pdf|PDF]]
       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
   * 2016 Summer Tutorial for EMAN2.12 June 2016 snapshots   * 2016 Summer Tutorial for EMAN2.12 June 2016 snapshots
-    * [[attachment:EMAN2-13_pre_Tutorial.pdf||&do=get]]+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-13_pre_Tutorial.pdf|PDF]]
       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]       * [[http://blake.bcm.edu/dl/workshop_2016_bgal.zip|Tutorial Data Download]]
-    * [[attachment:EMAN2-13_pre_Heterogeneity.pdf||&do=get]]+    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-13_pre_Heterogeneity.pdf|PDF]]
     * see also: http://www.sciencedirect.com/science/article/pii/S0076687916300362     * see also: http://www.sciencedirect.com/science/article/pii/S0076687916300362
   * 2015 Fall Tutorial for EMAN2.12   * 2015 Fall Tutorial for EMAN2.12
-    * [[attachment:EMAN2-12_Tutorial.pdf||&do=get]] +    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-12_Tutorial.pdf|PDF]] 
-    * Required data - [[attachment:Bgal.zip||&do=get]] +    * Required data - [[http://blake.bcm.edu/dl/EMAN2/Bgal.zip]] 
-    * [[attachment:EMAN2-12_Tutorial2_heterogeneity.pdf||&do=get]] +    * [[http://blake.bcm.edu/dl/EMAN2/EMAN2-12_Tutorial2_heterogeneity.pdf|PDF]] 
-    * Required data - [[attachment:ribosome.zip||&do=get]]+    * Required data - [[http://blake.bcm.edu/dl/EMAN2/ribosome.zip]]
   * [[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.   * [[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.   * [[SPT/Spt|Single particle tomography]] - Tutorial for deprecated Single particle tomography (SPT) workflow.
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   * [[Ws2012/EMAN2|Tutorial from the 2012 Workshop in Singapore (Data on same page)]] - Based on EMAN2.06. 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   * [[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]])+  * Single particle reconstruction tutorial from 2008 Workshop ( - [[http://blake.bcm.edu/dl/EMAN2/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]]) 
eman2/tutorials.1749921834.txt.gz · Last modified: by steveludtke