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| = Single Particle Tomography in EMAN2 = == Wednesday March 16, 2011 - P.M. Practical EMAN2 SPT tutorial == 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's insistence on doing extensive sub-volume averaging on chaperons. |
= Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX = |
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| This session will cover the beta version of a small fraction of the SPT possibilities EMAN2 will eventually offer. | The SPT page has move to http://blake.bcm.edu/emanwiki/SPT/Spt |
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| == 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. /!\ 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'' |
This is just an archaic page with the version of the tutorial used in the EMAN2 Workshop in March 2011. |
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| == 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]] |
== OLD E2SPT USERS' GUIDE == |
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| == 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: |
* Single particle tomography USER'S GUIDE (March 2011). |
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| [[attachment:e15phaseplate.rec]] | [[attachment:e2spt_users_guide_03_2011_workshop.pdf| e2spt_users_guide_03_2011_workshop.pdf |&do=get]] |
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| The following tomogram also comes from a tilt series of epsilon15 viruses ''in vitro'' but was recorded under conventional cryoEM imaging conditions: | == DATA == Epsilon 15 virus data, used since the EMAN2 Workshop in 2010. |
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| [[attachment:e15normal.rec]] == 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. === OPENING A TOMOGRAM DIRECTLY WITH e2tomoboxer.py === |
[[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.