https://blake.bcm.edu/emanwiki/ 2026-06-25T11:47:42+00:00 https://blake.bcm.edu/emanwiki/ https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2026-06-11T16:19:34+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=eman2:e2tomo_atpsyn&rev=1781194774&do=diff 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… text/html 2026-06-11T16:18:42+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_map_back.jpg&ns=eman2&rev=1781194722&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=e3cdeb&amp;media=eman2:atpsyn_map_back.jpg" alt="atpsyn_map_back.jpg" loading="lazy" width="500" height="500" /> text/html 2026-06-06T03:09:58+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_f1_motion.gif&ns=eman2&rev=1780715398&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=cede0a&amp;media=eman2:atpsyn_f1_motion.gif" alt="atpsyn_f1_motion.gif" loading="lazy" width="500" height="500" /> text/html 2026-06-06T03:09:43+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_cmp_focus_refine.png&ns=eman2&rev=1780715383&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=7c8ce0&amp;media=eman2:atpsyn_cmp_focus_refine.png" alt="atpsyn_cmp_focus_refine.png" loading="lazy" width="500" height="500" /> text/html 2026-06-06T03:09:21+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_bad_ptcls.png&ns=eman2&rev=1780715361&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=df6921&amp;media=eman2:atpsyn_bad_ptcls.png" alt="atpsyn_bad_ptcls.png" loading="lazy" width="500" height="500" /> text/html 2026-06-06T03:08:57+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_euler_view.png&ns=eman2&rev=1780715337&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=a544cc&amp;media=eman2:atpsyn_euler_view.png" alt="atpsyn_euler_view.png" loading="lazy" width="500" height="500" /> text/html 2026-06-06T03:08:38+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_c2_refine.png&ns=eman2&rev=1780715318&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=64d432&amp;media=eman2:atpsyn_c2_refine.png" alt="atpsyn_c2_refine.png" loading="lazy" width="500" height="500" /> text/html 2026-06-06T03:07:38+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_temp_pick.png&ns=eman2&rev=1780715258&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=93235a&amp;media=eman2:atpsyn_temp_pick.png" alt="atpsyn_temp_pick.png" loading="lazy" width="500" height="500" /> text/html 2026-06-06T03:04:57+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_init_model.png&ns=eman2&rev=1780715097&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=392405&amp;media=eman2:atpsyn_init_model.png" alt="atpsyn_init_model.png" loading="lazy" width="500" height="500" /> text/html 2026-06-06T03:03:06+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_pick_ptcls.png&ns=eman2&rev=1780714986&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=23ca2d&amp;media=eman2:atpsyn_pick_ptcls.png" alt="atpsyn_pick_ptcls.png" loading="lazy" width="500" height="500" /> text/html 2026-06-06T03:01:50+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_eval_tomo.png&ns=eman2&rev=1780714910&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=0f911c&amp;media=eman2:atpsyn_eval_tomo.png" alt="atpsyn_eval_tomo.png" loading="lazy" width="500" height="500" /> text/html 2026-06-06T02:42:18+00:00 muyuanchen (muyuanchen@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?image=eman2%3Aatpsyn_tilt_series.jpg&ns=eman2&rev=1780713738&tab_details=history&media_do=diff&do=media <img src="https://blake.bcm.edu/emanwiki/lib/exe/fetch.php?w=500&amp;h=500&amp;tok=dad805&amp;media=eman2:atpsyn_tilt_series.jpg" alt="atpsyn_tilt_series.jpg" loading="lazy" width="500" height="500" /> text/html 2026-04-24T00:13:24+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:startup&rev=1776989604&do=diff Running EMEN2 at system boot For systems that will run EMEN2 continuously, I highly recommend creating a dedicated “emen2” account. This will run EMEN2 using regular user-level permissions instead of as root. Please see your operating system documentation for creating a new account. text/html 2026-04-24T00:12:41+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:emen2ctl&rev=1776989561&do=diff EMEN2 control script (emen2ctl) Similar to Apache's “apachectl” script, EMEN2 includes an “emen2ctl” script. This can be used to start and stop the server and perform some basic administration tasks. Running emen2ctl Note: Depending on how you installed EMEN2, emen2ctl may not be in your $PATH. On Linux, using the recommended installation, it will probably be $$HOME/test.db") or by setting the $ text/html 2026-04-24T00:11:12+00:00 steveludtke (steveludtke@undisclosed.example.com) https://blake.bcm.edu/emanwiki/doku.php?id=emen2:install&rev=1776989472&do=diff Installing and configuring EMEN2 EMEN2 has a number of dependencies, which are described on the dependencies page. However, because EMEN2 is often used with EMAN2, we have packaged all of the EMEN2 dependencies along with binary builds of EMAN2, which greatly simplifies installation. See the $HOME/EMAN2, you would use $