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| = EMAN2.1 = EMAN2 is the successor to [[EMAN1]]. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing very large data sets (>100,000 particle) very efficiently (up to 20x faster than EMAN1). |
= EMAN2.2 = Most of the pages are editable by any user that has registered an account on the server. To prevent spam, you need to email sludtke@bcm.edu to get an account on the system if you wish to contribute changes. If you just wish to browse, you don't need an account. EMAN2 is the successor to [[EMAN1]]. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing very large data sets (>100,000 particle) very efficiently. |
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| '''Note for EMAN1 users - ''' If you are still using EMAN1 due to some missing functionality in EMAN2, please email sludtke@bcm.edu or post a message on the Google group telling what you are still doing in EMAN1. We will either explain how to do it in EMAN2, or add it to the list of projects. Please also note that there is an EMAN1->EMAN2 transition guide available below. Thanks ! | === Please Cite === EMAN is free software, supported by NIH Grants. It is critical that you cite EMAN2 when you use it in a publication in any significant way, to help us document usage when trying to renew our funding. Feel free to cite any of these: |
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| '''''UNDER (RE)CONSTRUCTION''''' - Note that the current website contains a bit of a mix of 2.0X and 2.1 information. We are gradually updating things to 2.1 as time goes on. If you find something confusing or self-contradictory, please let us know or ask about it. == Please fill out the EMAN2 User Survey! == It's quite brief, and we'd greatly appreciate your responses: Follow [[https://docs.google.com/forms/d/1vtrgk0uZ4Ycgw0LZEWPkUwJ28IjVb6TiNtuH-AxWWRQ/viewform?usp=send_form|this link]] |
* '''Primary EMAN2 paper:''' * G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke. (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol. 157, 38-46. PMID: 16859925 * '''EMAN2 high resolution refinement methods:''' * J.M. Bell, M. Chen, P.R. Baldwin & S.J. Ludtke. (2016) High Resolution Single Particle Refinement in EMAN2.1. Methods. 100, 25-34. PMC4848122 * '''Methods for analysis of conformational and compositional variability:''' * Ludtke, S. J. "Single-Particle Refinement and Variability Analysis in EMAN2.1." in Methods Enzymol 579159-189 (Elsevier, United States, 2016). PMC5101015 * '''Methods for subtomogram averaging:''' * J.G. Galaz-Montoya, C.W. Hecksel, P.R. Baldwin, E. Wang, S.C. Weaver, M.F. Schmid, S.J. Ludtke & W. Chiu. (2016) Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography. J Struct Biol. 194, 383-394. PMC4846534 |
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| * [[EMAN2/Eman21Release|IMPORTANT notice about EMAN2.1 pre-releases]] * [[http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222|Main EMAN2 Download Page]] |
* [[EMAN2/Eman22Release|EMAN2.2 Release Notes]] * [[http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222|Download EMAN2]] (binaries) * [[https://github.com/cryoem/eman2|Download EMAN2]] (source code) |
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| * [[EMAN2/Install|Installation Instructions and Tips]] * Please check this [[EMAN2/ChangeLog|CHANGELOG]] after upgrading to a new version |
* [[EMAN2/Install|Installation Guides]] (binary and source) * [[EMAN2/Remote|EMAN2 Remote GUI use (for clusters and remote workstations)]] == Get Help == We prefer to provide assistance via the Google group below, since this archives all discussions and makes them searchable. You must join the group to post, but can browse old content anonymously. * http://groups.google.com/group/eman2 (Main discussion list for EMAN2) * http://groups.google.com/group/eman2-developers (Discussions among developers, likely less interesting for users) * [[EMAN2/FAQ|FAQ]] - Please ask your questions in the Google Group which has a searchable archive. This page is somewhat out of date * NOTE - If you are located in a country that blocks Google (China) or prefer not to post publicly, please feel free to email sludtke@bcm.edu directly. The Google Group is used because it creates a persistent searchable archive of past questions, but direct emails are completely acceptable. |
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| * Upcoming Live Tutorials * [[EMAN2/Live/Upcoming|Thu June 19, 2014 at 9:00AM - 10AM CDT ]] - EMAN2 from Python |
* Tutorials * [[https://www.youtube.com/c/SteveLudtke|YouTube Tutorials]] (Archived video tutorials and mini-tutorials) * [[EMAN2/Tutorials|Tutorials]] (Full PDF tutorials with data covering many different tasks) * User Documentation * [[EMAN2/DirectoryStructure|File Descriptions]] (Folders and files in an EMAN2 Project) * [[EMAN2/Concepts|Standards]] (File Formats, Symmetry, Box Size, etc.) * [[EMAN2/Programs|Programs]] (Individual Program Documentation) * [[EMAN2/Parallel|Clusters]] (Running EMAN2 on clusters and multi-core workstations) * [[EMAN2/Gpu|GPGPU Computing]] (use the graphics processor for image processing) * [[EMAN2/Galleries|Galleries]] * [[EMAN2/Eman1Transition|EMAN1 -> EMAN2 Transition Guide]] * [[EMAN2/Obsolete|Old Docs]] (Out of date documentation) |
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| * User Documentation * [[EMAN2/Eman1Transition|EMAN1 -> EMAN2 Transition Guide]] * [[EMAN2/Tutorials|EMAN2 Tutorials (START HERE!)]] * [[EMAN2/VideoTutorials|EMAN2 Video Tutorials]] * [[EMAN2/DirectoryStructure|Standard Folders in an EMAN2 Project]] * [[EMAN2/Concepts|File Formats, Image Processing Functions, Mathematical Conventions]] * [[EMAN2/Programs|Individual Program Documentation]] * [[EMAN2/ProgramFiles|Output file descriptions and details]] * [[EMAN2/Parallel|Parallel Computing (multiple cores, linux clusters, sets of workstations)]] * [[EMAN2/Gpu|GPGPU Computing (use the graphics processor for image processing)]] * [[EMAN2/Galleries|Galleries]] * [[EMAN2/Obsolete|Obsolete Pages]] * Advanced Users & Programmers * [[EMAN2/Library|Python/C++ Programmers Documentation]] * [[http://blake.grid.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|Direct link to docs for EMData (image) class]] * [[http://blake.grid.bcm.edu/eman2/doxygen_html/classEMAN_1_1Transform.html|Direct link to docs for Transform (orientation/Euler angle) class]] * [[EMAN2/FAQ|FAQ]] - Please ask your questions in the Google Group, answers to common questions will be posted here as well as in the Group * Mailing list for EMAN2 discussions: * http://groups.google.com/group/eman2 * eman2@googlegroups.com (must join the group before you can post) * http://groups.google.com/group/eman2-developers (This is the group for discussions among developers, likely less interesting for users) |
== Advanced Users & Programmers (Python) == * [[EMAN2/GitTutorials|GitHub (Transitioning from CVS to Git)]] * [[EMAN2/Library|Python/C++ Programmers Documentation]] * [[http://blake.grid.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|Direct link to docs for EMData (image) class]] * [[http://blake.grid.bcm.edu/eman2/doxygen_html/classEMAN_1_1Transform.html|Direct link to docs for Transform (orientation/Euler angle) class]] |
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| EMAN2 is now a fully usable reconstruction package, including parallelism support. However, in case you aren't ready to abandon EMAN1 yet, EMAN1 and EMAN2 can be installed in the same user account with no conflicts. All EMAN2 programs, including GUI programs, are written in the easy-to-learn Python scripting language. This permits knowledgeable end-users to customize any of the code with unprecedented ease. If you aren't an advanced user, you can still make use of the integrated GUI and all of EMAN2's command-line programs. Any programs in EMAN2 with an EMAN1 equivalent are likely substantially improved over their EMAN1 equivalents. For example e2pdb2mrc.py is ~10x faster than the EMAN1 pdb2mrc. 3-D refinements are typically 5-25x faster than in EMAN1 (with the correct options). | All EMAN2 programs, including GUI programs, are written in the easy-to-learn Python scripting language. This permits knowledgeable end-users to customize any of the code with unprecedented ease. If you aren't an advanced user, you can still make use of the integrated GUI and all of EMAN2's command-line programs. |
EMAN2.2
Most of the pages are editable by any user that has registered an account on the server. To prevent spam, you need to email sludtke@bcm.edu to get an account on the system if you wish to contribute changes. If you just wish to browse, you don't need an account.
EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing very large data sets (>100,000 particle) very efficiently.
Please also note that this is not the (related) EMEN2 electronic notebook, but is EMAN2, a scientific image processing suite.
Please Cite
EMAN is free software, supported by NIH Grants. It is critical that you cite EMAN2 when you use it in a publication in any significant way, to help us document usage when trying to renew our funding. Feel free to cite any of these:
Primary EMAN2 paper:
G. Tang, L. Peng, P.R. Baldwin, D.S. Mann, W. Jiang, I. Rees & S.J. Ludtke. (2007) EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol. 157, 38-46. PMID: 16859925
EMAN2 high resolution refinement methods:
J.M. Bell, M. Chen, P.R. Baldwin & S.J. Ludtke. (2016) High Resolution Single Particle Refinement in EMAN2.1. Methods. 100, 25-34. PMC4848122
Methods for analysis of conformational and compositional variability:
- Ludtke, S. J. "Single-Particle Refinement and Variability Analysis in EMAN2.1." in Methods Enzymol 579159-189 (Elsevier, United States, 2016). PMC5101015
Methods for subtomogram averaging:
J.G. Galaz-Montoya, C.W. Hecksel, P.R. Baldwin, E. Wang, S.C. Weaver, M.F. Schmid, S.J. Ludtke & W. Chiu. (2016) Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography. J Struct Biol. 194, 383-394. PMC4846534
Download EMAN2
Download EMAN2 (binaries)
Download EMAN2 (source code)
Install EMAN2
Installation Guides (binary and source)
Get Help
We prefer to provide assistance via the Google group below, since this archives all discussions and makes them searchable. You must join the group to post, but can browse old content anonymously.
http://groups.google.com/group/eman2 (Main discussion list for EMAN2)
http://groups.google.com/group/eman2-developers (Discussions among developers, likely less interesting for users)
FAQ - Please ask your questions in the Google Group which has a searchable archive. This page is somewhat out of date
NOTE - If you are located in a country that blocks Google (China) or prefer not to post publicly, please feel free to email sludtke@bcm.edu directly. The Google Group is used because it creates a persistent searchable archive of past questions, but direct emails are completely acceptable.
Documentation
- Tutorials
YouTube Tutorials (Archived video tutorials and mini-tutorials)
Tutorials (Full PDF tutorials with data covering many different tasks)
- User Documentation
File Descriptions (Folders and files in an EMAN2 Project)
Standards (File Formats, Symmetry, Box Size, etc.)
Programs (Individual Program Documentation)
Clusters (Running EMAN2 on clusters and multi-core workstations)
GPGPU Computing (use the graphics processor for image processing)
Old Docs (Out of date documentation)
Advanced Users & Programmers (Python)
About EMAN2
EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. Image processing in a suite like EMAN differs from consumer image processing packages like Photoshop in that pixels in images are represented as floating-point numbers rather than small (8-16 bit) integers. In addition, image compression is avoided entirely, and there is a focus on quantitative analysis rather than qualitative image display.
All EMAN2 programs, including GUI programs, are written in the easy-to-learn Python scripting language. This permits knowledgeable end-users to customize any of the code with unprecedented ease. If you aren't an advanced user, you can still make use of the integrated GUI and all of EMAN2's command-line programs.
