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| Single Particle Tomography in EMAN2 === Wed PM Practical === |
= Single Particle Tomography in EMAN2 = == Wed PM Practical == |
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| The session will cover: |
== OUTLINE == |
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| * 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]. | * 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]. |
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| /!\ ''PLEASE NOTE that "particle" and "sub-volume" are used interchangeably'' | |
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| == SOFTWARE == | |
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| == RAW DATA == | |
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| == BOXING == | |
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| 1) Directly, by typing e2tomoboxer.py followed my the path to the tomogram file on the commandline: | 1) Directly, by typing e2tomoboxer.py followed my the path to the tomogram file at the commandline. |
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| {{{ e2tomoboxer.py e15phaseplate.rec }}} |
2) Or you can launch e2workflow.py from the commandline and access a tomogram through the browser in the tomographic menu. |
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| 2)Or you can launch e2workflow.py from the commandline and access a tomogram through the browser in tomographic menu. [In theory, you can open a tomogram for contemplation purposes by typing: "e2display.py <my_tomogram_path_name_goes_here>" at the commandline, but this is NOT recommendable, unless you have a grossly large (VERY, VERY large) amount of virtual memory on your computer; otherwise, things will crash]. |
[In theory, you can open a tomogram for contemplation purposes by typing: "e2display.py <my_tomogram_path_name_goes_here>" at the commandline. /!\ This is NOT recommendable, unless you have a grossly large (VERY, VERY large) amount of virtual memory on your computer; otherwise, catastrophe WILL befall upon you]. |
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| OPENING A TOMOGRAM DIRECTLY WITH e2tomoboxer.py | === OPENING A TOMOGRAM DIRECTLY WITH e2tomoboxer.py === |
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
OUTLINE
- 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.
![/!\](/emanwiki/moin_static197/modern/img/alert.png "/!\")
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 PLEASE NOTE that "particle" and "sub-volume" are used interchangeably
SOFTWARE
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
RAW DATA
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:
BOXING
You have two options for opening the tomogram for purposes of boxing it.
1) Directly, by typing e2tomoboxer.py followed my the path to the tomogram file at the commandline.
2) Or you can launch e2workflow.py from the commandline and access a tomogram through the browser in the tomographic menu.
[In theory, you can open a tomogram for contemplation purposes by typing: "e2display.py <my_tomogram_path_name_goes_here>" at the commandline. This is NOT recommendable, unless you have a grossly large (VERY, VERY large) amount of virtual memory on your computer; otherwise, catastrophe WILL befall upon you].
Let's explore the FIRST APPROACH.