https://blake.bcm.edu/emanwiki/ 2026-05-10T00:25:20+00:00 https://blake.bcm.edu/emanwiki/ https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2025-07-04T19:52:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular:aligners&rev=1751658766&do=diff Aligners To get a current list of Aligners, run e2help.py aligner or for more detailed information e2help.py aligner -v 2. For single particle analysis, we currently recommend using rotate_translate_flip for first stage alignment, and refine for second-stage alignment. text/html 2025-07-04T20:02:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular:analyzers&rev=1751659356&do=diff Analyzers To get a current list of Analyzers, run e2help.py analyzer or for more detailed information e2help.py analyzer -v 2. text/html 2025-07-04T19:53:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular:averagers&rev=1751658805&do=diff Averagers To get a current list of Averagers, run e2help.py averager or for more detailed information e2help.py averager -v 2. Currently for EMAN2 refinements, these are the recommended choices: * ctfw.auto - (recommended) CTF corrected average with Wiener filtration. Note that the text/html 2025-07-04T19:52:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular:cmps&rev=1751658724&do=diff Comparators (cmp) To get a current list of Comaparators, run e2help.py cmp or for more detailed information e2help.py cmp -v 2. The most commonly used comparators and options are: * ccc - simple cross correlation coefficient (dot product). Causes orientation bias for some particles, but generally good for initial coarse alignments. text/html 2025-07-04T20:03:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular:orientgens&rev=1751659431&do=diff OrientGens To get a current list of available orientation generators, please run e2help.py orientgens or for more detail, e2help.py orientgens -v 2. A typical orientation generator looks like this: * eman:delta=2.0:inc_mirror=0 Note that the perturb text/html 2025-07-04T19:49:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular:processors&rev=1751658582&do=diff Processors To get a current list of Processors, run e2help.py processor or for more detailed information e2help.py processor -v 2. These are algorithms for masking, filtering and performing other basic image processing operations. They are used in a wide range of different situations, but most often are specified to text/html 2025-07-04T19:54:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular:projectors&rev=1751658863&do=diff Projectors To get a current list of Projectors, run e2help.py projector or for more detailed information e2help.py projector -v 2. For the moment, standard is the only projector we recommend for use in EMAN2 refinements. text/html 2025-07-04T19:55:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular:reconstructors&rev=1751658908&do=diff Reconstructors To get a current list of Recosntructors, run e2help.py reconstructor or for more detailed information e2help.py reconstructor -v 2. At present we recommend either of these: * wiener_fourier - (recommended unless using m3dsetsf) Standard EMAN2 direct Fourier inversion, with true 3-D Wiener filtration based on micrograph SSNR estimates. That this will (properly) undo any 2-D Wiener filtration prior to reconstruction. text/html 2025-07-04T20:03:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:modular:symmetries&rev=1751659387&do=diff Symmetries To get a current list of Symmetries, run e2help.py symmetry or for more detailed information e2help.py symmetry -v 2. See also Symmetry