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| Single Particle Tomography in EMAN2 | = Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX = |
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| === Wed PM Practical === SPT (single particle tomography) capabilities are relatively new in EMAN2. They were inspired by Michael Schmid's studies on sub-volume averaging (mostly on viruses), and a stubborn student insisting on doing extensive sub-volume averaging on chaperons. |
The SPT page has move to http://blake.bcm.edu/emanwiki/SPT/Spt |
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| This session will cover the beta version of a small fraction of the SPT capabilities EMAN2 will eventually make available. | This is just an archaic page with the version of the tutorial used in the EMAN2 Workshop in March 2011. |
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| The session will cover: | == OLD E2SPT USERS' GUIDE == |
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| * 1) SPT processing through EMAN2's workflow: e2workflow.py * 2) Sub-volume extraction from tomograms using e2tomoboxer.py * 3) "Preparation" of extracted particles for alignment {{{#!wiki caution For a myriad of reasons, it is NOT recommendable to align and average sub-volumes directly after extraction. }}} * 4) Reference based alignment and averaging |
* Single particle tomography USER'S GUIDE (March 2011). |
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| All necessary software is provided as part of EMAN2. If you don't have EMAN2 installed, you can download the most updated version (for your specific platform, Windows, Linux or Mac), from here: http://ncmi.bcm.edu/ncmi/software/counter_222/software_86 | [[attachment:e2spt_users_guide_03_2011_workshop.pdf| e2spt_users_guide_03_2011_workshop.pdf |&do=get]] |
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| We have prepared sample data for this tutorial. The tomogram in the link below comes from a tilt series of epsilon15 virus particles in vitro, recorded using Zernike phase-plate technology: | == DATA == Epsilon 15 virus data, used since the EMAN2 Workshop in 2010. |
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| [[attachment:e15phaseplate.rec]] The following tomogram also comes from a tilt series of epsilon15 viruses in vitro but was recorded under conventional cryoEM imaging conditions: [[attachment:e15normal.rec]] {{attachment:imagefile.png|text describing image|width=100}} |
[[http://blake.grid.bcm.edu/wikifiles/SPT/e2spt_data.zip|e2spt_data.zip]] |
Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX
The SPT page has move to http://blake.bcm.edu/emanwiki/SPT/Spt
This is just an archaic page with the version of the tutorial used in the EMAN2 Workshop in March 2011.
OLD E2SPT USERS' GUIDE
* Single particle tomography USER'S GUIDE (March 2011).
e2spt_users_guide_03_2011_workshop.pdf
DATA
Epsilon 15 virus data, used since the EMAN2 Workshop in 2010.