https://blake.bcm.edu/emanwiki/ 2026-05-10T02:59:58+00:00 https://blake.bcm.edu/emanwiki/ https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2025-06-19T21:09:49+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:addingwizard&rev=1750367389&do=diff Adding a Wizard to projectmanager The projectmanager wizards are just JSON files specified in the spr.json or tomo.json files. To add a wizard to a program represented in the projectmanager workflow tree, just add in the the WIZARD key value pair. text/html 2025-06-19T03:01:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:advancedtutorials&rev=1750302064&do=diff AdvancedTutorials Archive of weekly EMAN2/Python discussion session This is an archive of a previous weekly discussion series we used to host on EMAN2. We have started archiving the meetings via YouTube: * July 15, 2022 - Using the new filter.helix processor to investigate objects with helical symmetry, some use of Jupyter EMAN2 plugins and e2filtertool.py. text/html 2025-07-04T19:43:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:angstep&rev=1751658186&do=diff Angular sampling, number of projections and resolution Note: If you are running e2refine_easy, you should not really need to worry about this parameter. It will be computed for you based on your project parameters. If you use speed=5, the angular sampling will be a bit finer than required based on the discussion below. If you lower speed to 1, angular sampling is increased roughly 2-fold (making the refinements take considerably longer). If you want to experiment with angular step, I suggest fi… text/html 2025-07-04T19:39:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:applicationpreferences&rev=1751657962&do=diff Application Preferences Preferences can be set for a variety of GUI features either locally within a project or globally for a user. These are stored in .eman2settings.json in the project or in ~/.eman2/eman2settings.json, and can be modified using e2procjson.py with the text/html 2025-06-19T18:42:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:appmetadata&rev=1750358568&do=diff This page is obsolete Global dictionaries/parameters 00image_counts database Every EMAN2DB directory will contain an image count cache database which will contain a number of parameters associated with each image in that directory, updated as necessary. text/html 2025-07-04T22:53:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:boxerfaq&rev=1751669588&do=diff NOTE that this is a wiki and if your question is not here then simply add it. An email will be sent to all people who are subscribed to this page letting them know that the page has been changed and your question will be answered. * How do I use e2boxer to automatically box many images (potentially hundreds) from the command line? text/html 2025-07-04T18:10:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:boxsize&rev=1751652630&do=diff Particle Box Size * For single particle analysis the particle box-size must be 1.5-2x the size of the largest axis of your particle. For subtomogram averaging, padding is largely handled internally, but the box should still have at least a 10-20% margin on the edge. This reduces the impact of edge effects on the reconstruction, and improves the smoothness of the FFT of the map, so Fourier interpolation is more accurate. If you are stuck with data which was boxed with an insufficient size, the text/html 2025-06-19T21:33:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:buildsystem&rev=1750368814&do=diff The information on this page is no longer entirely accurate. Builds are handled in the cloud via conda-forge, and standalone binaries are no longer distributed. Binary Distribution !GitHub webhooks are setup to send notifications to blake. Blake forwards those to three build machines. Currently, webhooks are being listened to only on Linux. Linux runs the server that drives the Jenkins jobs. text/html 2025-07-04T19:19:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:classesfiles&rev=1751656742&do=diff classes_xx files Produced by: e2classaverage.py This is a stack of images containing class-averages for each iteration. There should be a 1-1 correspondence of images in this file to images in the projections_xx file. Each image contains header information indicating which particles were used to create the average, and the number of particles in the average, as well as other details. text/html 2025-07-04T19:17:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:classmxfiles&rev=1751656661&do=diff Classification Matrix Image Files Produced by: e2classify.py There are now two types of classification matrix files, those for 2-D image stacks and those for 3-D volume stacks. More 'layers' are used in the 3-D case because there are more alignment parameters. text/html 2025-07-04T19:18:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:clsresultfiles&rev=1751656705&do=diff cls_results_xx files Produced by: e2classaverage.py These files have the same format as classify_xx files. They contain the final 2-D alignment information for each particle vs its classified reference projection. Information is present for particles even if they were excluded from the final class-averages. text/html 2025-07-04T19:48:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:concepts&rev=1751658523&do=diff EMAN2 Concepts and Conventions Box Size (Important) * Particle box-size - Impacts quality and speed of reconstructions! Data Storage * Supported image file formats and usage * How EMAN2 stores data in HDF5 files * Header information (key/value pairs) associated with a specific image * Information stored in text/html 2025-06-29T23:48:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:condabuildsystem&rev=1751240918&do=diff Under Construction EMAN2 is built with `conda-build` using binaries from <https://anaconda.org>, packaged into an installer with constructor as of v2.2. 1. conda is the package manager. 2. <https://anaconda.org> is the online repository of binaries. 3. conda-build is the tool to build from source. 4. constructor is the tool to package eman2 and dependency binaries into a single installer file. text/html 2025-07-06T18:56:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:cprogquickstart&rev=1751828199&do=diff * What is EMAN2's coding style? * How to add a new processor in EMAN2? * What about the unit test in EMAN2? * How to use assertion in EMAN2? * How to use Exception handling in EMAN2? * How to use log in EMAN2? * How to handle large-file (>2G) IO? * How to handle image data byte-order? * How to Wrap my C++ class/function to Python? * Use float numbers explicitly in EMAN2. text/html 2025-07-04T19:45:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:ctfmodel&rev=1751658354&do=diff The CTF Model(s) used in EMAN2 This page describes CTF correction from a programmer's perspective. There is a theory page describing the theoretical underpinnings of the CTF correction method. --- UNDER CONSTRUCTION Like other aspects of EMAN2, the CTF model infrastructure is extensible, though less so than the Processors, Reconstructors, etc. At present, there are 2 types of CTF instances in EMAN2: EMAN1Ctf and EMAN2Ctf. The EMAN1Ctf is provided for backwards compatibility, so if particles … text/html 2025-07-05T23:05:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:databasewarning&rev=1751756758&do=diff In early versions of EMAN2, files were stored using BDB databases. There were a number of problems this database system could cause in specific situations, and this page originally held a warning about how/when to use BDB. The BDB system was deprecated in the early 2010s, and removed entirely ~2020, so we no longer include this warning. text/html 2025-07-05T23:07:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:datastorage&rev=1751756839&do=diff Image Data files in EMAN2 Virtually all cryo-EM file formats are supported as well as some good generic formats. The default format used in EMAN2 processing is HDF5, which supports stacks of 2-D and 3-D images as well as arbitrary header information for each image in the file. If you convert an image to a format like MRC, you will lose any metadata not compatible with that format. text/html 2025-06-19T03:23:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:directorystructure&rev=1750303427&do=diff Folder Arrangement in EMAN2.2 projects Detailed description of files You will find a detailed description of the contents of many files produced by refinements and other programs here: Output file descriptions and details Overall project folder arrangement When using e2projectmanager.py and following canonical EMAN2 procedures, your data will be contained within a text/html 2026-04-07T19:12:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2gmm&rev=1775589168&do=diff THIS PAGE IS UNDER CONSTRUCTION * TODO - indicates incomplete tutorial sections * THE e2gmm program is under active development. STRONGLY encourage using an EMAN2 snapshot or source version dated 12/2022 or later. Even with a current version you may notice some small differences in the display, etc. text/html 2025-06-19T01:27:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2gmmoriginal&rev=1750296446&do=diff Structural variability analysis with Gaussian mixture model Available in EMAN release after 10/01/2020. Still under development. For details of the method, refer to Chen2021. Updates: * After 03/22/2021, a new GUI program, e2gmm_analysis is added to visualize the motion trajectory of the Gaussian model after training. text/html 2025-06-19T01:37:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2gmm_model&rev=1750297043&do=diff Gaussian mixture model based atomic model refinement (2024) Refine atomic models to better fit into a given map, and get better PDB validation score. For detailed method (and to cite), see Preprint here. Dataset In this tutorial, we use TRPV1 as an example. Starting from a relatively old PDB model (PDB: text/html 2025-06-19T01:35:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2gmm_refine&rev=1750296937&do=diff Particle orientation refinement using GMM representation * Most programs are available in EMAN2 builds after 2023-03, but some are still under continuous development. Newer versions are typically better. * The tutorial is only tested on Linux with Nvidia GPU and CUDA. text/html 2025-07-04T22:53:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2make3dfaq&rev=1751669637&do=diff Q: Does e2make3d.py work on tomographic stacks? A: Yes, it is now possible to directly reconstruct aligned stacks (.ali) files from imod using the corresponding .tlt file. In fact, the Fourier reconstruction algorithm used in EMAN2 has produced substantially better results than either back-projection or SIRT in a number of cases. text/html 2025-07-04T18:14:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2tomo&rev=1751652893&do=diff EMAN2 Tomography Workflow Tutorial * This tutorial is best suited for EMAN2 built after 09/27/2018. Not everything described in the tutorial was functioning yet in the 2.22 release. * The pixel size in the header of the files are incorrect as provided by EMPIAR. The correct Apix value (2.62) should be specified when importing the images. text/html 2025-08-05T11:06:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2tomosmall&rev=1754391981&do=diff EMAN2 Tomography and Subtomogram/Subtilt Averaging Workflow Tutorial Important note: Throughout the tutorial you will see a split between (small) and (large) instructions. The (small) tutorial is designed for laptops or basic desktops and can achieve ~12 Å resolution in a time compatible with live tutorial sessions. The (large) tutorial really requires a proper tomography workstation, but can achieve subnanometer resolution. Do not intermix (small) and (large) options below! text/html 2025-08-05T02:17:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2tomo_more&rev=1754360245&do=diff Extra functions for EMAN2 tomography * This page describes extra functionalities of EMAN2 tomography workflow. This tutorial is frequently updated, so it is better to have EMAN2 version as new as possible. Generate tilt series from micrographs text/html 2025-08-05T00:22:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2tomo_new&rev=1754353341&do=diff This is for the new subtomogram-subtilt refinement pipeline that is available in Github and continuous build after EMAN2.91 (03/09/2021). Both the pipeline and the tutorial are still under construction. Backward compatibility of the results is not guaranteed text/html 2025-06-19T01:19:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2tomo_p22&rev=1750295955&do=diff Advance tutorial of EMAN2 tomography workflow This tutorial uses a CryoET dataset of P22 bacteriophage infecting cells, which is kindly provided by Jun Liu from Yale. The dataset contains 4 tilt series and can be downloaded here. This tutorial contains advanced topics of the SPT workflow, such as focused refinement and classification, symmetry breaking, and analysis of continuous motion. For new users, it is recommended to start with a simple text/html 2026-03-20T17:45:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e3make3d_point&rev=1774028720&do=diff Preview of e3make3d_point for better 3-D reconstructions THE METHOD DESCRIBED ON THIS PAGE IS NOT YET PUBLISHED, IT IS PROVIDED TO GIVE PEOPLE THE OPPORTUNITY TO TRY IT OUT AS WE MAKE FINAL IMPROVEMENTS If you have any difficulties (or successes) with this method, please let us know, and feel free to ask questions (sludtke@bcm.edu). text/html 2025-06-19T19:51:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman1to2translation&rev=1750362697&do=diff This is a mapping of EMAN1 EMData methods to EMAN2 so old scripts can be updated. EMAN EMAN2 .calcCCF .calc_ccf .copy .copy .doFFT .do_fft or .do_fft_inplace .EMData .EMData .gimmeFFT Not necessary, no FFT caching .Mean .get_attr(“mean”) or .get_attr_dict() text/html 2025-06-19T01:43:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman1transition&rev=1750297425&do=diff Moving from EMAN1 to EMAN2 A choice of paths EMAN2 can be used in many different ways: * A high-level integrated workflow interface * Stand-alone GUI tools (like EMAN1) * Command-line programs (direct analogs to EMAN1) * A Python library (a easy to learn scripting language) text/html 2025-07-04T22:07:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman1transition_commandline&rev=1751666832&do=diff WARNING: This page was written in the early days of EMAN2 and some of its concepts are no longer accurate. For example, the BDB database system was retired over a decade ago in favor of HDF and LST files. There are still some useful things here, but take them with a grain of salt. text/html 2025-07-04T20:14:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman1transition_eman1v2&rev=1751660071&do=diff WARNING: This page was written in the early days of EMAN2 and some of its concepts are no longer accurate. For example, the BDB database system was retired over a decade ago in favor of HDF and LST files. There are still some useful things here, but take them with a grain of salt. text/html 2025-07-04T22:08:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman1transition_python&rev=1751666905&do=diff WARNING: This page was written in the early days of EMAN2 and some of its concepts are no longer accurate. For example, the BDB database system was retired over a decade ago in favor of HDF and LST files. There are still some useful things here, but take them with a grain of salt. text/html 2025-07-04T20:06:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman1transition_quickstart&rev=1751659619&do=diff Porting an EMAN1 refinement project to EMAN2.3 Note : This page contains a simplified version of the EMAN2.1 tutorial, and assumes you are familiar with EMAN1. The full tutorials provide a much better way of learning EMAN2. This page will get you started if you just want to rapidly switch a project from EMAN1. If you find yourself asking 'but what does THAT mean' when you read this, you're reading the wrong page! text/html 2025-07-04T22:06:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman1transition_workflow&rev=1751666781&do=diff WARNING: This page was written in the early days of EMAN2 and some of its concepts are no longer accurate. For example, the BDB database system was retired over a decade ago in favor of HDF and LST files. There are still some useful things here, but take them with a grain of salt. text/html 2025-07-04T19:12:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman2datastorage&rev=1751656330&do=diff Image Data files in EMAN2 Virtually all cryo-EM file formats are supported as well as some good generic formats. The default format used in EMAN2 processing is HDF5, which supports stacks of 2-D and 3-D images as well as arbitrary header information for each image in the file. If you convert an image to a format like MRC, you will lose any metadata not compatible with that format. text/html 2025-07-04T19:30:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman2hdf&rev=1751657439&do=diff This page has moved text/html 2025-07-04T19:38:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman2infometadata&rev=1751657885&do=diff This page has moved text/html 2025-07-04T17:30:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman2jsstorage&rev=1751650231&do=diff JSON Files (BDB Replacement) JSON files replace the much despised BDB database mechanism for storing metadata in EMAN2. These files offer a number of advantages over BDB, but there are also a few tradeoffs. Advantages: * Human-readable, and human-editable. text/html 2025-07-04T16:51:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman2loglevel&rev=1751647866&do=diff How to change log level to print out more message at run time? . EMAN2's log has four levels: ERROR_LOG, WARNING_LOG, DEBUG_LOG, VARIABLE_LOG. . By default, only the error log will be printed out. . This log level can be changed at runtime at Python level. . What user need to do to change log level: . text/html 2025-07-04T22:54:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman2makingvolumes&rev=1751669681&do=diff Q: Is there a way to construct a volume (3-D) EMData object from a bunch of 2-D images ? A: Yes, EMData objects can be 1, 2 or 3-D. Effectively the data is stored as a single array of floats with x varying first, y second, z third. If nz=ny=1 then the image is 1-D, etc. Most 3-D data in cryo-EM comes from volumetric reconstructions from projections rather than slice data as in a lot of optical microscopy. Nonetheless, constructing a volume from a stack of slices can be done in a wide range of… text/html 2025-07-04T19:35:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman2metadata&rev=1751657750&do=diff This page has metadata text/html 2025-07-04T17:43:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman2otherfiles&rev=1751651033&do=diff Other Miscellaneous Files While EMAN2 prefers HDF and JSON files for most tasks, there are a few other formats which are supported and used in specific contexts. .lst files LST files and LSTX files originated in EMAN1. They are text files containing a list of image filenames and numbers, which EMAN2 will treat as if they contained actual images. These files follow the following format: text/html 2025-07-06T02:44:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman2transforminpython&rev=1751769898&do=diff This page has moved text/html 2025-06-14T22:15:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:eman22release&rev=1749939345&do=diff EMAN2 Release Notes Changes in 2.99.x include * Major changes and improvements to e2gmm * New EMAN3 pipeline being prototyped, including e3make3d_gauss and incorporation of Gaussian reconstruction into e2spa and e2spt refinement programs. With Pawel Penczek's retirement, SPHIRE and SPARX are no longer actively developed or maintained text/html 2025-06-19T21:31:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:factoriesinpython&rev=1750368679&do=diff The methods devised on this page are rarely used. The individual modular classes (Processors, Reconstructors, etc.) have mechanisms for using them already. This is for unusual/advanced use-cases. An abstract factory class is used to define an infrastructure for modular code. What does this mean ? Say you have a situation where you have a set of filters that you might want to apply to an image. In traditional C++ code, you would make a class or method for each filter, and would then have to har… text/html 2025-07-06T03:03:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq&rev=1751771014&do=diff Our Google Group is now the primary place for ongoing EMAN2 discussions. Note that the group has a searchable message archive. General: * What paper should I cite if I use EMAN2 for a reconstruction Installation * What sort of computer should I buy ? BDB Issues (obsolete. BDB no longer used in EMAN2.1) * We use NFS-mounted directories, how can I safely use EMAN2 with it's BDB system * How can I convert these funny 'bdb' files into something I can use in Chimera or other software ?… text/html 2025-07-04T22:46:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_automask&rev=1751669171&do=diff Q: How do I pick the correct parameters for automasking during refinement or using the mask.auto3d processor ? Additional Note - The new e2filtertool.py program provides an excellent way to interactively determine good mask parameters ! A: When you produce a 3-D structure using single particle analysis, there is inevitably residual noise left in the final reconstruction. While there is nothing you can do about the noise on top of the particle density itself, noise which is clearly outside the… text/html 2025-07-06T18:37:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_bdbconvert&rev=1751827038&do=diff Converting BDB to other file formats First a quick answer : Where possible we use HDF as an exchange format. Chimera will open it, and it preserves the full model metadata, which MRC cannot. Of course EMAN2 supports most other file formats (see: DataStorage and text/html 2025-07-04T22:43:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_bdberrors&rev=1751669027&do=diff BDB Troubleshooting Please note that the BDB system is no longer used in EMAN2.1, and may not even be supported in EMAN2.2. We STRONGLY encourage all users to upgrade to at least 2.1x Please make sure you have read this first: Warning about BDB use MOST issues that happen with BDB are related to the cache (generally in /tmp/eman2db-<username>) getting unsynchronized with the actual data due to users doing something 'illegal' with database files, or computers crashing in bad ways. Here is a se… text/html 2025-07-04T22:44:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_bdbvstack&rev=1751669067&do=diff Q: Can I make a vstack from another vstack, including only a subset of the images ? What will this do ? A: Describe EMAN2/FAQ/BdbVstack here. The way the vstacks work is quite simple. It's exactly like a regular BDB file, but instead of the binary data being stored in an associated file with a deterministic name, each header has a pointer to the file and location where the binary data resides. That is, for each image within the VSTACK, the data can come from an arbitrary different file. If th… text/html 2025-07-04T22:47:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_changeboxsize&rev=1751669227&do=diff Q: How can I reduce the box size in a project without starting completely from scratch A: You don't need to redo particle picking, and you can use 3D maps generated at the original size as initial models for the new size. You need to: * return to the text/html 2025-07-04T22:15:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_citeeman2&rev=1751667315&do=diff Q: What paper should I cite if I use EMAN2 for a reconstruction ? A: This is the original EMAN2 reference: * Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I. & Ludtke, S.J., 2007, EMAN2: an extensible image processing suite for electron microscopy, Journal of structural biology, 157(1), pp. 38-46. text/html 2025-07-03T03:16:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_computer&rev=1751512611&do=diff What sort of desktop computer should I get for EMAN2 reconstructions People frequently ask what sort of computer they should get for EMAN2 (or other image processing work). This isn't a page for the “minimum required specifications”, but a page of recommendations for a high end workstation for data processing. EMAN2 will run even on a fairly basic 4 core laptop. The tutorials are designed so they can run on most typical laptop computers. However, if you are doing a typical single particle recon… text/html 2025-07-04T22:49:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_fsc&rev=1751669351&do=diff FSC Curve Interpretation If you double click on on one of the items under 'resolution' in the workflow, ideally you will see a curve that looks like : What do we see in this plot ? First, and foremost is the thicker yellow line (not always yellow, but always thick in EMAN2). This curve represent the FSC (Fourier shell correlation) between two maps generated by reconstructing the even and odd halves of the particle data separately. Note I say separately, NOT independently. Ideally to assess … text/html 2025-07-04T22:47:49+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_invertdata&rev=1751669269&do=diff Q: I forgot to invert my particles (they are black on a white background), and I've already done CTF correction. How can I fix it ? A: The following assumes you are using bash or a similar shell. If you use zsh or csh, you may need to alter this a bit: text/html 2025-07-04T22:35:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_nfsbdb&rev=1751668507&do=diff Using BDB with NFS mounted filesystems You should, of course, read this database warning as a first step. Quick advice * Never EVER run EMAN2 commands in the same directory on 2 different computers at the same time ! * If you want to switch from one computer to another, run 'e2bdb.py -c' on the first computer before you start using the second text/html 2025-07-04T22:55:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_spidereuler&rev=1751669725&do=diff Q: Can I convert Euler angles from e2initialmodel.py from EMAN convention to Spider (or other) convention ? A: Similar to supporting the various available file-formats, EMAN2 also supports most of the available Euler angle conventions (see Eman2TransformInPython and Symmetry) but there is currently no tool in the text/html 2025-07-04T22:45:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:faq_symmetry&rev=1751669128&do=diff Q: What symmetry should I specify during refinement if I don't know what it is ? A: There is no single good answer to this question. It can be a very complicated issue. Take the case of TriC/CCT, for example: <http://www.pnas.org/content/107/11/4967.abstract> In this case, the object in question really has no symmetry, or at most D1 symmetry, since it is constructed of 8 unique proteins. However, these proteins have extremely high homology, and in fact, at resolutions worse than 4-6 A, the st… text/html 2025-06-19T03:36:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:galleries&rev=1750304193&do=diff Gallery * Test images * e2display features * e2desktop ---------- Capabilities of em3Dfonts.py text/html 2025-07-03T03:20:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:galleries_testimages&rev=1751512828&do=diff AdvancedTutorials Archive of weekly EMAN2/Python discussion session For a while we were holding weekly EMAN2 programming discussion sessions, and some of these are archived on YouTube. Here is one to get you started: * July 15, 2022 - Using the new filter.helix processor to investigate objects with helical symmetry, some use of Jupyter EMAN2 plugins and e2filtertool.py. text/html 2025-06-19T03:29:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:gpu&rev=1750303763&do=diff GPGPU Computing As of 6/2025 EMAN2 uses primarily TensorFlow code for anything GPU related. This has transitioned to JAX in EMAN3, and some specific EMAN2 programs may use JAX as well. The installation instructions now include details on installing GPU libraries. Use is automatic for programs that support it, though some behaviors can be impacted by environment settings. text/html 2025-07-04T19:23:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:hdf5format&rev=1751656985&do=diff HDF5 HDF5 is a general purpose scientific data storage file format adopted by numerous scientific disciplines. In the CryoEM community, it is used by EMAN2/SPARX/SPHIRE, Chimera (2 different variants), and may(?) have some support in recent IMOD versions. text/html 2025-06-19T15:29:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:imageformats&rev=1750346995&do=diff Table of supported image formats in EMAN2 Type Extension Read Write 3D Image Stacks Volume Stacks Bit Trunc. Region I/O Comments Primary EMAN2 Format HDF5 hdf Y Y Y Y Y Y Y HDF5 is an international standard for scientific data (<http://www.hdfgroup.org/HDF5/>). It supports arbitrary metadata (header info) and is very portable. This is the standard interchange format for EMAN2. Chimera can read EMAN2 style HDF files. text/html 2025-06-19T03:04:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:important&rev=1750302240&do=diff Important Information For Everyone * Working with Images - EMAN2 has many general image processing methods, and the list is continuously expanding. Use e2help.py to get lists of the different operations, then use them with e2proc2d.py, e2proc3d.py or e2filtertool.py. * Help - You can give any program the text/html 2025-07-04T19:37:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:infometadata&rev=1751657847&do=diff Metadata Stored in JSON files JSON files in the info folder JSON files are human-readable and editable text files, which are also software-friendly. This is rapidly becoming one of the most common formats used in the web-development community. They have a '.json' extension, and can be opened in any text-editor. text/html 2025-07-06T03:35:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:install_binaryinstall&rev=1751772920&do=diff All platforms Note that the instructions on this page should only be followed if you specifically need to install this version of EMAN2. Current releases use a completely different scheme. Note for International use - We lack sufficient manpower at present for any real internationalization support. In particular some users have reported problems with the use of ',' rather than '.' in numbers. The only known solution at present is to set English to your language. text/html 2025-07-06T03:32:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:install_binaryinstallanaconda_2.2&rev=1751772778&do=diff Binary Installation Instructions Note that the instructions on this page should only be followed if you specifically need to install this version of EMAN2. Current releases use a completely different scheme. Mac OS X Note: the neural network code in EMAN2 works best on GPUs, which are available only on the Linux installations. It can still run on Mac, but will be quite slow. text/html 2025-07-06T03:29:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:install_binaryinstallanaconda_2.3&rev=1751772588&do=diff Binary Installation Instructions v2.3 Note that the instructions on this page should only be followed if you specifically need to install this version of EMAN2. Current releases use a completely different scheme. All Systems Official releases are in reverse chronological order. The text/html 2025-07-06T03:32:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:install_binaryinstallanaconda_2.21&rev=1751772727&do=diff Binary Installation Instructions Note that the instructions on this page should only be followed if you specifically need to install this version of EMAN2. Current releases use a completely different scheme. Mac OS X Note: the neural network code in EMAN2 works best on GPUs, which are available only on the Linux installations. It can still run on Mac, but will be quite slow. text/html 2025-07-06T03:31:00+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:install_binaryinstallanaconda_2.22&rev=1751772660&do=diff Binary Installation Instructions Note that the instructions on this page should only be followed if you specifically need to install this version of EMAN2. Current releases use a completely different scheme. All Systems Official releases are in reverse chronological order. The text/html 2025-07-06T03:28:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:install_binaryinstallanaconda_2.31&rev=1751772537&do=diff Binary Installation Instructions v2.31 (Legacy) All Systems Note that the instructions on this page should only be followed if you specifically need to install this version of EMAN2. Current releases use a completely different scheme. Official releases are in reverse chronological order. The text/html 2025-06-19T17:46:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:jsstorage&rev=1750355197&do=diff JSON Files (BDB Replacement) JSON files replace the much despised BDB database mechanism for storing metadata in EMAN2. These files offer a number of advantages over BDB, but there are also a few tradeoffs. Advantages: * Human-readable, and human-editable. text/html 2025-06-14T21:13:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:jupyter&rev=1749935592&do=diff EMAN2 and JupyterLab This page describes how to use EMAN2 interactive display widgets (2-D images, 3-D volumes, plots, etc.) from within a JupyterLab session. This (the features and the documentation) are a work in progress as of early 2022, targeted for release in EMAN3. To use these features you should compile EMAN2 from source using master on Github or use a recent binary snapshot version. text/html 2025-06-29T23:48:29+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:library&rev=1751240909&do=diff Documentation for Python or C++ Programmers Introductory concepts * EMAN2 Python Programming Style Guide * EMAN2 python programming quickstart * Image Formats in EMAN2 * EMAN2 data storage & format conversion * Using NumPy with EMAN2 * EMAN2 JSON file access from Python * Parameters/Metadata appearing in EMData attributes (and stored on disk with the image), accessed with get_attr and set_attr * Limited Table of translations from EMAN1 functions -> EMAN2 * Modifying the EMAN2… text/html 2025-06-19T17:48:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:metadata&rev=1750355313&do=diff Parameters/Metadata stored in EMData Objects The EMData object, and its representation on disk in the BDB local database, XML files, and when serialized in Python using 'pickle', supports the concept of arbitrary header parameters also known as metadata. This metadata are key/value pairs. The keys are always simple ascii text, and the values may be virtually anything represented as an EMObject, including simple ints, floats and strings, as well as more complicated objects such as Transform cla… text/html 2025-07-04T17:26:52+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular_overview&rev=1751650012&do=diff Overview of modular functions in EMAN2 EMAN2's modular function interface is one of its most powerful features, permitting a wide range of different algorithms to be selected through a single common interface. It also means new algorithms can be added to the system without making any changes to the end-user programs. For example, if you have an idea for a new alignment algorithm, (and you know a little C++), you can easily inset the algorithm in EMAN2's core library, and it will immediately bec… text/html 2026-03-05T14:35:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:negativestain&rev=1772721314&do=diff Negative Stain Single Particle Analysis There are some special problems which can arise when processing negative stain data. EMAN2 was primarily designed to work with Cryo data, so you may need to do things a little differently to get good results with negative stain. text/html 2025-06-19T21:03:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:new3ditem&rev=1750366987&do=diff Creating a new Item3D widget for use in EMScene3D To create a new Item3D widget use must inherit from EMItem3D (you will need to import this class from emitem3d). EMItem3D is a new style class so you don't need to multiply inherit from object. To make a valid object you must re-implement several method and redefine two attributes 1. class(static) attribute: text/html 2025-06-19T17:43:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:numpy&rev=1750355014&do=diff Using EMAN2 with NumPy NymPy interoperability is well supported, and with EMAN3 modules, JAX as well. Note that converting an EMData object to a NumPy array produces an object which shares the memory of the EMData array, but when converting NumPy to EMAN2 a copy is made : text/html 2025-06-19T03:37:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:obsolete&rev=1750304254&do=diff These pages relate to older versions of EMAN2 * Please read this Important Warning (pre 2.1) text/html 2025-07-04T19:41:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:otherfiles&rev=1751658108&do=diff Other Miscellaneous Files While EMAN2 prefers HDF and JSON files for most tasks, there are a few other formats which are supported and used in specific contexts. .lst files LST files and LSTX files originated in EMAN1. They are text files containing a list of image filenames and numbers, which EMAN2 will treat as if they contained actual images. These files follow the following format: text/html 2025-06-19T03:02:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:othertutorials&rev=1750302147&do=diff Tutorials on Related Topics Under Construction * FFT Synthesis on Google Colab - Similar to the e2fftsynth.py in EMAN2 demos, but doesn't require EMAN2 installation text/html 2025-06-19T01:45:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:oxfordws2012&rev=1750297510&do=diff EMAN2 This page contains an EMAN2 reconstruction tilt validation tutorial using real data. Tutorial In this tutorial, we will validate the Ip3R structure or the PRD1 Virus(your choice): You MUST use the EMAN2 nightly build for this tutorial. In the future, we will put out EMAN2.1, which will be sufficient for EM validation. Follow this link to download the EMAN2 Nightly build: text/html 2025-06-19T03:10:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:parallel&rev=1750302608&do=diff Parallel Processing in EMAN2 EMAN2 uses a modular strategy for running commands in parallel. That is, you can choose different ways to run EMAN2 programs in parallel, depending on your environment. Which option is best ? If you are running on a single machine/node, then Threaded is by far the most efficient option, and the easiest to use as well. If you are running on a few nodes on a single cluster, use MPI. In many cases a single cluster node has enough cores that using Threaded paralleli… text/html 2025-07-03T01:34:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:parallel_distributed&rev=1751506467&do=diff THIS METHOD IS NO LONGER WORKING IN EMAN>2.1 - This method is effectively retired. It was quite powerful and useful many years ago, but rarely makes sense in the current linux cluster ecosystem. If you are actively using it, we'd very much like to discuss the issue, and understand what motivates this in your setup. text/html 2025-07-03T01:33:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:parallel_mpi&rev=1751506397&do=diff Note that this topic is somewhat deprecated. Most EMAN2 jobs run perfectly well on a single workstation with a decent number of cores, a single GPU and a fast hard drive. Using MPI is much more difficult than threads/GPU and requires that you have Pydusa installed and working properly. text/html 2025-07-03T01:27:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:parallel_threaded&rev=1751506067&do=diff Threaded Parallelism in EMAN2 Most modern computers have at a minimum 4 cores. A decade or two ago this would have been called 4 CPUs, however, now you may still have 2 physical CPUs in your computer, but each may have multiple cores, effectively multiple CPUs in a single package. For that reason, we often make the distinction between the CPU (the physical package) and the number of cores (the effective number of CPUs). Typical computers in 2025 will have 4-12 text/html 2025-06-19T21:04:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:pmcustomization&rev=1750367056&do=diff Customizing the e2projectmanager workflow tree: Unlike, e2workflow.py, e2projectmanager can be easily customized. The SPR and Tomo workflow trees are constructed using the JSON files, spr.json and tomo.json, respectively. These files reside in lib/pyemtbx or in the source code, libEM/pmconfig, and can be edited to customize the tree. The JSON file contains a list of dictionaries, which represents a toplevel(root/base) item in the workflow tree. Each dictionary must contain(except for those mar… text/html 2025-07-06T03:00:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:pmworkflow&rev=1751770802&do=diff Tutorial to aid adding a new e2program to the e2projectmanager.py This tutorial covers the necessary steps to incorporate a e2program into the projectmanager. Modifications to the e2program itself Canonical e2programs must maintain the following standards 1. Options are handled via EMArgumentParser, which is a subclass of Python's argparse module (version 2.7 and higher). For more information on argparse, see the python documentation. text/html 2025-06-19T20:46:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:progoverview&rev=1750365982&do=diff Extending EMAN2 or connecting EMAN2 to external software Let me clarify the possible ways of having external code interact with EMAN2/SPARX to see if that helps the discussions any... 1. Use EMAN2/SPARX as a C++ library for an external package, to gain access to some of its image processing capabilities 2. Use EMAN2/SPARX at the Python level, and interact with other software with Python wrapping 3. Write a wrapper module to permit EMAN2/SPARX to exchange images/metadata between packages 4.… text/html 2025-06-19T15:24:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:progquickstart&rev=1750346675&do=diff EMAN2 Programming Quickstart This page contains some example sessions to get you started using EMAN2 from Python. This is not aimed at mainstream users, but is for those wanting to move into programming in EMAN2. Here is a sample EMAN2 session: e2.py # this runs ipython (provided with EMAN2 binaries) and does 'from EMAN2 import *' >>> a=test_image() >>> display(a) # Use the middle mouse on the image for controls, right mouse to pan >>> b=[test_image(),test_… text/html 2026-03-25T14:24:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programfiles&rev=1774448686&do=diff EMAN2 Output Files This page documents all of the various files produced by various tasks and workflows in EMAN2. While the format of the actual files will be one of the standard EMAN2 supported image formats in most cases, these pages will explain the contents of files with specific standard names. text/html 2025-06-19T21:11:49+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programmingpm&rev=1750367509&do=diff This page illustrates the working of e2projectmanager.py The new GUI for EMAN2 is known as e2projectmanager.py and is mainly used to organize electron microscopy projects, and execute e2programs. The projectmanager can be run in two modes, SPR(single particle reconstruction) and tomo (tomogramphic). Other modes can be added and this page describes how to do that. Each mode has a JSON file describing the workflow of a mode. The workflow is a tree that describes a flow of data from raw to final f… text/html 2025-06-19T01:16:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs_convnet_pickparticle&rev=1750295813&do=diff Particle Picking with Convolution Neural Network Update 2018-1-24 EMAN2.21 * Now we train two networks, one for boxing particles from micrographs, another for excluding obvious bad particles (ice etc). * Use Good Refs to pick particle references, text/html 2025-07-04T18:17:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs_e2filtertool&rev=1751653022&do=diff e2filtertool This program allows you to interactively construct sequences of processors and apply them to both 2-D and 3-D data. For example, if you need to determine the best parameters for automasking a 3-D volume, or if you wish to play with low-pass filtering your data with different options, this program provides an easy interface. text/html 2025-07-06T16:17:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs_e2refine&rev=1751818670&do=diff e2refine This program is the heart of single particle reconstruction in EMAN2. It embodies the concept of an iterative 3-D single particle reconstruction in a single step, starting with a 3-D starting model and a set of preprocessed particle data. The overall strategy is similar to that used in text/html 2025-07-04T19:20:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs_e2refine2d&rev=1751656813&do=diff e2refine2d e2refine2d.py runs in much the same way as EMAN1's refine2d.py, though it has been improved in a number of subtle ways This program will take a set of boxed out particle images and perform iterative reference-free classification to produce a set of representative class-averages. The point of this process is to reduce noise levels, so the overall shape of the particle views present in the data can be better observed. Generally cryo-EM single particles are noisy enough that it is diff… text/html 2025-07-04T18:13:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:programs_tomoseg&rev=1751652814&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 2025-07-04T19:16:16+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:projectionfiles&rev=1751656576&do=diff projections_xx Generated by e2project3d.py These files contain a set of projections of the map from the previous iteration of refinement: threed_filt_(xx-1) The distribution of orientations is controlled by the --orientgen= command-line option. Note: If you are running 2-stage classification, you will additionally see proj_stg1_xx files. These files represent averages of aligned sets of projection images after classification, and are used to do the first-stage classification of the particles… text/html 2025-06-19T15:22:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:pythonstyleguide&rev=1750346533&do=diff EMAN2 Python Programming Style Guide This document describes the structure of programs distributed with EMAN2. If you plan to write a program for inclusion with EMAN2 in the 'bin' directory, you must follow the following general guidelines. Python Style text/html 2025-06-19T01:45:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:rcttutorial&rev=1750297558&do=diff Tutorials on Random Conical Tilt Random conical tilt is a method for determining 3-D structure using tilt-pairs. Typically this is done with an untilted image and a second image tilted to 45-60 degrees. Unfortunately, this strategy leads to structures which always have a 'missing cone'. An alternative strategy is the +/- 45 degree tilt method, where images are collected at -45 degrees and +45 degrees. Since they are then 90 degrees apart, it is possible to do a reconstruction without a missing … text/html 2025-06-19T20:37:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:reconstructors&rev=1750365447&do=diff Using Reconstructors from Python Reconstructors are modular objects which take a set of images and assemble them in some way into a single higher dimensional image. Normally this means taking 2-D projections in known orientations and producing a single 3-D volumetric reconstruction, but the concept extends to taking 1-D projections and producing 2-D reconstructions, or even other algorithms which do not work with projections. text/html 2025-06-19T03:08:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:remote&rev=1750302492&do=diff EMAN2 on a remote computer EMAN uses OpenGL for all of its graphical display windows. This is separate from the X-windows protocol which supports basic remote windowing operations. In many configurations, logging in via ssh and doing remote display will not work properly, due to broken remote OpenGL capabilities. Even if remote EMAN does work perfectly (including OpenGL) at your site, it may not be the best strategy to use for several reasons. There are two sections below. The first is a good s… text/html 2025-07-04T19:16:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:simmxfiles&rev=1751656611&do=diff Similarity Matrix Image Files Generated by: e2simmx.py or e2simmx2stage.py These files, normally named bdb:refine_XX#simmx_YY are produced during e2refine.py runs. One such file should appear in each iteration. If the --twostage option is being used, then two additional files simmx_stg1_YY and proj_simmx_YY will also be produced with the same general format, though some of these files will not be completely filled in (not exhaustive). text/html 2025-07-04T18:16:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:simulateddata&rev=1751652986&do=diff Making Simulated Single Particle Data If your goal is to develop software and have a good test data set where you know the ground truth, just give up now. All simulated data sets I have ever seen fall short of real data. That is, any reasonable algorithm will perform extremely will even with very noisy simulated data, much more so than with real data. text/html 2025-06-19T02:50:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:spt_spt&rev=1750301431&do=diff Last update: February 10, 2016. Single Particle Tomography in EMAN2 RECOMMENDATIONS Get comfortable with the command-line. The pipeline through e2projectmanager.py is very limited and less robust. You can try to average subtomograms with EMAN2's stable release (EMAN2.12 from October 19, 2015); however, I recommend using the daily build. Download the easy-to-install binaries from EMAN2's download page: text/html 2025-07-06T02:59:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:standardparms&rev=1751770747&do=diff Standard Program Parameters These are command-line options used in multiple programs. Feel free to add to this list where appropriate, but note that these are only parameters which are used in multiple programs with the same meaning. --verbose -v Level of verboseness when printing output to the console. All programs must accept this option. text/html 2025-07-04T17:58:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:symmetry&rev=1751651914&do=diff Quick Summary Supported symmetries in EMAN2/SPARX are : * Cn - single rotational n-fold symmetry axis * Dn - dihedral rotational n-fold, eg - GroEL is ~D7 * icos - icosahedral, (5,3,2) * oct - octahedral, symmetry of a cube (4,3,2) * tet - tetrahedral, (3,2) text/html 2025-07-04T19:46:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:theory_ctf&rev=1751658402&do=diff CTF Correction in EMAN2 Under Construction This page describes the CTF correction model used in EMAN2 (not yet published). The core theory of image formation and correction is very similar to that used in EMAN1, but the method for characterizing images has changed substantially. text/html 2025-07-04T19:19:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:threedfiles&rev=1751656772&do=diff threed_xx Produced by - e2make3d.py sometimes postprocessed There are 3 types of 3-D files produced during refinement. * threed_xx - The minimally processed 3-D reconstruction. It is filtered, but not masked or normalized. * threed_filt_xx - This is the masked version of the 3-D reconstruction, and is used as input for the next round of refinement. Based on the mass you provided, 1.0 should be the correct isosurface for viewing, but you will find that this depends a lot on resolution. text/html 2025-06-19T01:21:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:tomosymmetry&rev=1750296083&do=diff Symmetric Particles in Subtomogram Averaging (new pipeline) Symmetric biomolecules really aren't (symmetric). At some limiting resolution, the symmetry will always be broken. Consider 3 examples: * small rigid enzyme - symmetry breaking might be at the level of independent individual sidechain motion, may only impact at 3-5 Å resolution text/html 2025-07-06T03:39:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:transforminpython&rev=1751773193&do=diff Transforms in Python The center of the image ---------- The center of the image for purposes of rotations is different for odd and even sized images. For even images, the center is at $(nx/2,ny/2)$ where the first pixel is at $(0,0)$. For odd sized images, the center is at $((nx-1)/2,(ny-1)/2)$$\mathrm{Tr}$$$\mathrm{Tr} = M T S R$$$M$$T$$S$$R$$\begin{bmatrix}\cos phi&\sin phi& 0\\-\sin phi&\cos phi&0\\0&0&1\end{bmatrix}$$\begin{bmatrix}1&0&0\\0& \cos alt& \sin alt\\0& -\sin alt& \cos alt\end{… text/html 2026-03-20T05:23:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:tutorials&rev=1773984195&do=diff EMAN2 Introductory Tutorials Please note that we are continuously developing and updating the tutorials. 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 text/html 2025-07-04T16:22:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:tutorials_addandmultiply&rev=1751646121&do=diff The following example shows various ways of adding, subtracting, multiplying and dividing images. The given example uses 2D images but the functionality generalizes for 3D images. Adding and multiplying images First I make different two example images that have the same dimensions text/html 2025-07-04T16:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:tutorials_iter_pixels&rev=1751646954&do=diff Iterating through the pixels in the EMData object In your Python script you can use commands like this to iterate through the pixels in an EMData object a = test_image() for k in xrange(a["nz"]): for j in xrange(a["ny"]): for i in xrange(a["nx"]): pixel_value = a[i,j,k] # get the pixel value a[i,j,k]=pixel_value*3 # set the pixel value text/html 2025-07-04T16:37:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:tutorials_make_a_projection&rev=1751647053&do=diff Quickly make a projection To make a projection you must have your 3D model loaded into python, and you must be able to define your projection direction as a Transform object. See Using the EMAN2 Transform class and the Transform turorial page for more information on the Transform object. Also, for more information on Euler angles see the text/html 2025-07-04T16:32:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:tutorials_ri2ap&rev=1751646724&do=diff Changing image format from real/imaginary to amplitude/phase format in EMAN2 is a straightforward procedure. To illustrate the process start with a test image and perform an inplace Fourier transform on it as follows: [someone@localhost] e2.py Welcome to EMAN2 Prompt provided by IPython Enter '?' for ipython help In [3]: e = EMData(32,32,32) In [4]: e.process_inplace("testimage.axes") In [5]: e.do_fft_inplace() text/html 2025-07-03T03:21:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:tutorials_rotatetranslate&rev=1751512913&do=diff Transforming Images (Applying Rotation, Translation, Scale and Mirroring) What follows is a very simply demonstration of using the Transform object to transform EMData (image) objects. A very thorough explanation of using the Transform is presented in text/html 2025-07-16T23:15:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:unreal_render&rev=1752707702&do=diff Render structures using Unreal Engine This is not strictly EMAN2 related, but I have been showing short videos around (example and biorxiv) and people ask how to make them. So here is a simple tutorial. To start, * Install Unreal Engine 5. * Start a new blank project. text/html 2025-06-19T20:57:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:using3dwidget&rev=1750366674&do=diff EMAN2 3D Widget for Python applications: The 3D widget is a python class allowing display of 3D items in EMAN2. These include isosurafces, volume slices, volumes, in additon to text and shapes for annotation. The 3D object is arranged in a tree datastructure for easy data grouping and control. The scene itself can be save for later analysis and snapshots can be taken for publication. text/html 2025-06-19T21:28:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:usingcudafromc&rev=1750368507&do=diff This page is historical/obsolete. EMAN now uses TensorFlow/JAX for any GPU operations using the EMAN2 CUDA api EMAN2 includes support for CUDA processing. To use CUDA in EMAN2 you must set the flag ENABLE_EMAN2_CUDA using ccmake, then recompile. This step defines the identifier text/html 2025-06-19T20:49:29+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:usingftgl&rev=1750366169&do=diff Compiling EMAN2 with FTGL support To compile EMAN2 with FTGL support set ENABLE_FTGL to ON in cmake setup. This may also require you to install FTGL on your machine. For more information contact an EMAN2 developer. Using FTGL in python Programmers have to create an instance of an EMFTGL object. A platform independent solution to getting a font renderer is available and is the recommended approach text/html 2025-06-19T02:33:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:utmbworkshop2019&rev=1750300435&do=diff Sealy Center for Structural Biology/UTMB Workshop on CryoEM Data Processing May 6-9 2019 Sessions will alternate between theory talks and tutorial sessions. Participants will need to use their own laptops to participate in the tutorials (see below). text/html 2025-06-19T02:57:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:videotutorials&rev=1750301874&do=diff Video Tutorials for EMAN2 We are now hosting periodic live video-conferences/telecasts to discuss specific EMAN2 topics, in addition to some short tutorial videos. These telecasts are available live, and are recorded for later viewing on YouTube as well as directly on this site. text/html 2025-07-06T02:41:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:videotutorialslocal&rev=1751769692&do=diff Videos for Direct Streaming from BCM Some of our videos are also available for direct streaming from our site. YouTube will generally give you more flexibility, and won't eat up BCM's bandwidth, so we prefer if you use VideoTutorials. However if you are in China or another location that often blocks YouTube, you are welcome to use the links on this page: text/html 2025-07-06T02:39:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:ws2011_eman2&rev=1751769579&do=diff EMAN2 This page contains an EMAN2 single particle reconstruction tutorial using real data. This page is part of the 2011 workshop. Tutorial Here are the two parts of the tutorial (linked from the workshop agenda page): Part 1 Part 2 You MUST use a current version of EMAN2 for these tutorials, not an older release. If you have an old version installed, please upgrade to 2.01 or newer, and be sure to run 'e2bdb.py -c' under the old version BEFORE installing the new version ! text/html 2025-06-19T02:54:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:ws2012_eman2&rev=1750301657&do=diff Tutorial from the CryoEM Workshop at NUS (Singapore) This workshop covers several different aspects of image processing associated with biological transmission electron microcsopy experiments. These range from single particle reconstruction, which typically focuses on determining the high resolution structure of a highly structurally homogeneous molecule/assembly text/html 2025-06-19T02:53:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:ws2013_eman2&rev=1750301614&do=diff International Workshop of Advanced Image Processing of Cryo-Electron Microscopy Institute of Biophysics, Chinese Academy of Sciences, Beijing These tutorial materials are for the workshop hosted by the Chinese Academy of Sciences in Beijing in July 2013. Each day of the workshop is devoted to a different software package. The material on this page is the training material for EMAN2. text/html 2025-06-19T02:52:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:ws2014&rev=1750301559&do=diff EMAN2.1 Workshop Tutorial, Summer 2014 The final release of EMAN2.1 is out. This tutorial was designed for EMAN2.1beta4, but the differences are quite minimal. It should be possible to finish this tutorial in a few hours on a reasonable desktop PC. text/html 2025-06-19T02:47:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:ws2015&rev=1750301241&do=diff NCMI Workshop on Single Particle Reconstruction, Structural Variability and Modeling Oct 30 - Nov 2, 2015 We strongly recommend bringing a 3 button (or 2 button+scroll) mouse. While it is possible to survive with a trackpad or one button mouse, there are many things in EMAN and Chimera where having additional mouse buttons is VERY useful.