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| This is a relatively new feature in EMAN2, and is ... | 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. |
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| The software is provided as part of EMAN2 (already installed) | This session will cover the beta version of a small fraction of the SPT capabilities EMAN2 will eventually make available. |
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| We have prepared some sample data | The session will cover: * 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 }}} |
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| [[attachment:spt_demo_2011.tgz]] | 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 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: [[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]] |
Single Particle Tomography in EMAN2
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.
This session will cover the beta version of a small fraction of the SPT capabilities EMAN2 will eventually make available.
The session will cover: * 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
(for a myriad of reasons, it is NOT recommendable to align and average sub-volumes directly after extraction). * 4) Reference based alignment and averaging
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
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:
The following tomogram also comes from a tilt series of epsilon15 viruses in vitro but was recorded under conventional cryoEM imaging conditions: