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| == Using e2.py == * [:EMAN2/Concepts/Display:Display a test image] * [:EMAN2/Concepts/RotateTranslate:Rotate and Translate an image] |
= 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.'' ==== Single particle analysis (SPA) - 2D particles ==== * [[EMAN2/Eman1Transition|EMAN1 to EMAN2 Transition Guide]] - Also with useful quickstart guides for users of other software * [[Ws2013/EMAN2|Tutorial from the 2013 Workshop in Beijing (Data on same page)]] - Based on EMAN2.1alpha. 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+ ==== 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: * [[SPT/Spt|Single particle tomography]] - Requires EMAN 2.05+ ==== 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 manager workflow ==== * [[EMAN2PMWorkflow|Modifying the EMAN2 projectmanager workflow]] ==== 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]] * [[EMAN2/Programs/e2refinetoxmippsom/e2refinetoxmippsomtutorial|2D Class Averaging with XMIPP -- Self-Organizing Maps]] * [[EMAN2/Programs/e2refinetoxmipphac/e2refinetoxmipphactutorial|2D Class Averaging with XMIPP -- Hierarchical Ascendent Classification]] === Out of date tutorials (provided for data access, etc.)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]]) * [[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 == 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]] |
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.
Single particle analysis (SPA) - 2D particles
EMAN1 to EMAN2 Transition Guide - Also with useful quickstart guides for users of other software
Tutorial from the 2013 Workshop in Beijing (Data on same page) - Based on EMAN2.1alpha. Full single particle reconstruction tutorial
Tilt Validation tutorial from the Oxford 2012 mini-workshop - Requires EMAN 2.05+
Random Conical Tilt Tutorial - Requires EMAN 2.05+
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 - Requires EMAN 2.05+
2D assessment of heterogeneity
Full tutorial on 2-D analysis for assessment of structural heterogeneity and population dynamics (under construction)
Adding an e2program to the program manager workflow
Using the Built-In Modules from Other Software
Out of date tutorials (provided for data access, etc.)
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
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
