https://blake.bcm.edu/emanwiki/ 2026-05-10T07:07:16+00:00 https://blake.bcm.edu/emanwiki/ https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2025-07-06T16:27:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2classaverage&rev=1751819276&do=diff usage: e2classaverage.py <output> [options] This program produces iterative class-averages, one of the secrets to EMAN's rapid convergence. Normal usage is to provide a stack of particle images and a classification matrix file defining class membership. Members of each class are then iteratively aligned to each other and averaged together with (optional) CTF correction. It is also possible to use this program on all of the images in a single stack. positional arguments: positionalar… text/html 2025-07-06T16:27:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2classify&rev=1751819226&do=diff usage: e2classify.py <simMatrixIn> <classMatrixOut> [options] This program analyzes a similarity matrix as produced by e2simmx.py and produces a classification matrix mapping class membership for each particle, which can in-turn be used with e2classaverage.py. Takes a similarity matrix that has been created between reprojections-input (col) and particles-input (row) stacks of 2-D images. Typically these have been created via e2simmx such as e2simmx.py proj.hed part.hed simMatrix.hed --sa… text/html 2025-06-19T03:40:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2display&rev=1750304422&do=diff EMAN2 File Browser 2D Display 2D Stack Display 3D Image Display Euler Tool e2display The main interface for browsing and viewing images, volumes, 2D & 3D plots, ... See the above subitems for more details. To display a specific file: e2display.py <filename> or simply open the generic browser, which will let you explore files and metadata and visualize: text/html 2025-07-06T15:59:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2initialmodel&rev=1751817577&do=diff Note: you may wish to consider using the alternative e2initialmodel_sgd.py program which works with raw particle images, and often does a better job. This program will take a set of class-averages/projections and build a set of 3-D models suitable for use as initial models in single particle reconstruction. The set is theoretically sorted in order of quality (best one is numbered 1), though it's best to look at the other answers as well. text/html 2025-07-06T15:44:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2project3d&rev=1751816651&do=diff This is a work in progress e2project3d.py <35%><<TableOfContents>> Add your related questions to e2project3d FAQ. A desciption of how EMAN demarcates the asymmetric unit is presented here Description This program creates projections distributed quasi-uniformly over the asymmetric unit. text/html 2025-07-06T03:01:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2projectmanager&rev=1751770869&do=diff e2ProjectManager The e2projectmanager is a GUI project manager system for EMAN2, which guides the user through a series of steps to achieve either a single particle reconstruction or an sub tomogram average depending on the mode e2projectmanager is being used. This text/html 2025-07-06T16:24:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2simmx&rev=1751819052&do=diff usage: prog [options] <c input> <r input> <output> Computes a similarity matrix between c-input (col - projections) and r-input (row - particles) stacks of 2-D images. Images may optionally be aligned before comparison. Output is a matrix stored as an image with similarity value pairs. When used for classification, c input is the references and r input are the particles. More information on the output file can be found in the Wiki. positional arguments: positionalargs options: -h, --he… text/html 2025-07-06T16:06:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2simmx2stage&rev=1751817982&do=diff e2simmx2stage FAQ e2simmx2stage <35%><<TableOfContents>> This program computes a similarity matrix similar to e2simmx, but in this case, the matrix is sparse to make the computation faster. The populated regions will correspond to the best similarity values. text/html 2025-06-14T21:05:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2tomoseg&rev=1749935102&do=diff Tomogram Annotation/Segmentation Availability: EMAN2.2+, or daily build after 2016-10 This is the tutorial for a Convolutional neural network(CNN) based semi-automated cellular tomogram annotation protocol. If you are using this in a publication, please cite: M. Chen et al. (2017). Convolutional Neural Networks for Automated Annotation of Cellular Cryo-Electron Tomograms. Nature Methods, text/html 2025-07-06T15:40:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e2workflow&rev=1751816425&do=diff Note that this program is deprecated. Please use e2projectmanager instead. e2workflow EMAN2 uses a project management Workflow system to guide users through a series of steps embodying specific tasks, for example, single particle reconstruction. The user creates and empty directory, and runs: text/html 2026-03-20T05:21:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs:e3make3d_point&rev=1773984069&do=diff e3make3d_point.py