EMAN Wiki

e2gmm_rigidbody

muyuanchen (muyuanchen@undisclosed.example.com) — 2026-09-29T23:42:44+00:00

GMM-based focused refinement for single particle analysis (2026) * Most programs are available in EMAN2 builds after 2026-06, but newer versions are typically better. * The tutorial is only tested on Linux with Nvidia GPU and CUDA. * For reference of the method, see the

gmm_trpv_mov1.gif - created

muyuanchen (muyuanchen@undisclosed.example.com) — 2026-09-29T23:42:28+00:00

movie1_loop.gif - created

muyuanchen (muyuanchen@undisclosed.example.com) — 2026-09-29T23:41:25+00:00

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muyuanchen (muyuanchen@undisclosed.example.com) — 2026-09-29T23:33:40+00:00

gmm_trpv_focus.png - created

muyuanchen (muyuanchen@undisclosed.example.com) — 2026-09-29T22:46:48+00:00

gmm_trpv_mask.png - created

muyuanchen (muyuanchen@undisclosed.example.com) — 2026-09-29T22:38:03+00:00

gmm_trpv_global.png - created

muyuanchen (muyuanchen@undisclosed.example.com) — 2026-09-29T22:14:26+00:00

cmake1 - created

steveludtke (steveludtke@undisclosed.example.com) — 2026-09-23T00:57:39+00:00

Your system does not have a library named “ncurses”. Install this package first, then compile cmake again, you will get ccmake. (or configure isn't finding ncurses properly, you may need to manually tell configure in the cmake package where curses is)

faq

steveludtke (steveludtke@undisclosed.example.com) — 2026-09-23T00:56:47+00:00

FAQ This is the new EMAN Frequently Asked Questions page : * YOU MUST CREATE AN ACCOUNT FOR YOURSELF TO EDIT THIS PAGE. Click on the Login button above, then follow the UserPreferences link. * Create a new link below by copying an existing one, and put a summary of your question as the description

faq_eman_using_13 - created

steveludtke (steveludtke@undisclosed.example.com) — 2026-09-23T00:48:51+00:00

Question: What paper should I cite if I use EMAN1 in published results ? Answer: This one: Ludtke, S.J., Baldwin, P.R., and Chiu, W. (1999). EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128, 82-97.

library - created

steveludtke (steveludtke@undisclosed.example.com) — 2026-09-23T00:46:39+00:00

EMAN1 Programmer Docs // Under Construction //

programs - created

steveludtke (steveludtke@undisclosed.example.com) — 2026-09-23T00:45:45+00:00

EMAN1 Individual Programs There are over 200 command-line programs in EMAN, this list contains more detailed documentation for the most commonly used programs. See the fixed documentation for a full list. GUI Programs eman Image browser and tutorial interface boxer Manual particle picking ctfit CTF parameter determination and simulation

spaoverview - created

steveludtke (steveludtke@undisclosed.example.com) — 2026-09-23T00:44:49+00:00

Single Particle Reconstruction in EMAN1 under construction For the moment, please continue to use the tutorial interface in the 'eman' program. Just run 'eman' and hit 'step 1'.

eman_compile_unix - created

steveludtke (steveludtke@undisclosed.example.com) — 2026-09-23T00:43:58+00:00

EMAN depend on some third party libraries: Some dependency libraries are mandatory, like fftw2, gsl, and cmake for eman compilation. Some others are optional, like boost.python, Python if you need run Pyhton program in EMAN or want to program in Python with EMAN, you can turn this option off by switching ENABLE_PYTHON to off. And

install - created

steveludtke (steveludtke@undisclosed.example.com) — 2026-09-23T00:42:22+00:00

EMAN1 Installation and Tips IMPORTANT NOTE FOR WINDOWS USERS : EMAN1 is NOT fully windows compatible. The GUI programs should largely work without problems, and many of the command line utility programs, like proc2d and proc3d will work fine, but you cannot run refinements under windows. This includes 'refine2d.py', 'refine' and 'multirefine'. You will need to use Linux or a Mac if you wish to run these programs. In EMAN2 we are attempting to provide full Windows support for all aspects of the …

tomoseg - created

steveludtke (steveludtke@undisclosed.example.com) — 2026-09-23T00:40:05+00:00

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,

eman2 - [UPDATE 7/7/25]

steveludtke (steveludtke@undisclosed.example.com) — 2026-08-31T18:55:28+00:00

EMAN2.99.47 UPDATE 7/7/25 The EMAN2 wiki was undergoing a massive hacker attack, and we were forced to update to a newer Wiki system. The transition is largely complete, but there may still be a few missing (red) links around, If you find one you need just email sludtke@bcm.edu and we'll manually restore it. The URLs for links are using a new style so pre-2025 bookmarks are broken. To fix you will need to navigate to the pages again and re-bookmark.

computer - created

steveludtke (steveludtke@undisclosed.example.com) — 2026-07-24T03:19:36+00:00

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…

e2tomo_atpsyn

muyuanchen (muyuanchen@undisclosed.example.com) — 2026-06-11T16:19:34+00:00

EMAN2 tomography - ATP synthase in mitochondria (2026) This tutorial uses a public in situ CryoET dataset ( EMPIAR-11830) of Chlamydomonas reinhardtii prepared using cryo-plasmaFIB milling. Here, we use 5 tilt series and target the structure and dynamics of ATP synthase inside mitochondria. In the end, from this small dataset, we will produce monomer structure at (slightly) sub-nanometer resolution, and characterize the rotary movement of the F1 head domain. Using a larger dataset, it is possi…

atpsyn_map_back.jpg - created

muyuanchen (muyuanchen@undisclosed.example.com) — 2026-06-11T16:18:42+00:00