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| == Single Particle Tomography in EMAN2 == | Single Particle Tomography in EMAN2 |
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| 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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| This is a relatively new feature in EMAN2. This session will cover the beta version of a small fraction of the Single Particle Tomography (SPT) capabilities that will eventually be available. | This session will cover the beta version of a small fraction of the SPT |
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| 1) Sub-volume extraction from tomograms using e2tomoboxer.py 2) Preparation of extracted particles for alignment 3) Reference based alignment and averaging |
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| The software is provided as part of EMAN2 (already installed). | * 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. [Details later. For a myriad of reasons, it is NOT recommendable to align and average sub-volumes directly after extraction without "preparing" them first]. * 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]] |
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| We have prepared some sample data. The tomogram in the link below comes from a tilt series of epsilon15 virion particles recorded using Zernike phase-plate technology: |
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: |
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| The following tomogram also comes from a tilt series of epsilon15 virion particles but was recorded under conventional cryoEM imaging conditions: | The following tomogram also comes from a tilt series of epsilon15 viruses in vitro but was recorded under conventional cryoEM imaging conditions: |
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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
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. [Details later. For a myriad of reasons, it is NOT recommendable to align and average sub-volumes directly after extraction without "preparing" them first].
- 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:
