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| The necessary software is provided through EMAN2. All the data you need is inside a .zip file below which contains: a) Two tomograms of epsilon15 virus (e15) b) 3 e15 "references" (an asymmetric one, and one with icosahedral symmetry, both prepared for alignment; and a raw one, straight from the EMDB) c) 1 text file (a small "coordinates file") |
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| There is no Wiki version of the tutorial as of now. You MUST download it as a PDF or word document, provided below. | Download the written tutorial provided through the PDF file below. |
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| The links SHOULD work directly (it is safe to do right-click followed by "save as"). If not, once you click on the link it will take you to another page where you'll see a "DOWNLOAD" link. Click on that to get the corresponding file. | [The links SHOULD work directly (it is safe to do right-click followed by "save as"); if not, once you click on the link it will take you to another page where you'll see a "DOWNLOAD" link; click on that to get the corresponding file]. |
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| ||<style="color: #FF0000; font-weight: bold;"> PDF || | |
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| ||<style="color: #FF0000; font-weight: bold;"> WORD 2008 || [[attachment:eman2_spt_tutorial.docx| eman2_spt_tutorial.docx|&do=get]] === You should have downloaded ALL the data BEFORE the workshop starts; if you didn't, the tutorial document will lead you through downloading files as needed === . . . . . == 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 == 1) [[attachment:e15tomogram_phaseplate_bin4.rec| e15tomogram_phaseplate_bin4.rec|&do=get]] This first tomogram was reconstructed from a tilt series of epsilon15 virus particles in vitro, recorded using Zernike phase-plate technology. [Liu and Murata et al, 2010]. 2) [[attachment:e15tomogram_phaseplate_bin2.rec| e15tomogram_phaseplate_bin2.rec|&do=get]] It’s the same as the previous one, but shrunk by a factor of 2. 3) [[attachment:e15tomogram_normal_bin4.rec| e15tomogram_normal_bin4.rec|&do=get]] This tomogram also comes from a tilt series of epsilon15 viruses in vitro, but was recorded under “conventional” cryoET imaging conditions. [Liu and Murata et al, 2010]. 4) [[attachment:e15tomogram_normal_bin2.rec| e15tomogram_normal_bin2.rec|&do=get]] (Again, the previous tomogram shrunk by 2). |
== DATA == |
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== REFERENCES == [[attachment:e15ref_prep_icos_bin4.hdf| e15ref_prep_icos_bin4.hdf|&do=get]] cubical box, side length = 70; icosahedrally symmetric model [[attachment:e15ref_prep_icos_bin2.hdf| e15ref_prep_icos_bin2.hdf|&do=get]] cubical box, side length = 140; icosahedrally symmetric model [[attachment:e15ref_prep_asym_bin4.hdf| e15ref_prep_asym_bin4.hdf|&do=get]] cubical box, side length = 70; asymmetric model [[attachment:e15ref_prep_asym_bin2.hdf| e15ref_prep_asym_bin2.hdf|&do=get]] cubical box, side length = 140; asymmetric model [[attachment:e15ref_raw.hdf| e15ref_raw.hdf|&do=get]] cubical box, side length = 576; asymmetric model [[attachment:e15references.zip| e15references.zip|&do=get]] Get all the references listed above in a zip file == PREPARED COORDINATES FILES == [[attachment:e15phaseplate_coords.txt| e15phaseplate_coords.txt|&do=get]] [[attachment:e15normal_coords.txt| e15normal_coords.txt|&do=get]] |
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| = ANYTHING BELOW THIS MARK IS DEPRECATED = This session will cover the beta version of a small fraction of the possibilities for SPT processing EMAN2 will eventually offer. |
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| = ANYTHING BELOW THIS MARK IS DEPRECATED = | |
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| This session will cover the beta version of a small fraction of the possibilities for SPT processing EMAN2 will eventually offer. |
Single Particle Tomography in EMAN2
Wednesday March 16, 2011 - P.M.
This session will be about extracting sub-volumes from a tomogram, preparing them for alignment, aligning them, and averaging them. The necessary software is provided through EMAN2. All the data you need is inside a .zip file below which contains: a) Two tomograms of epsilon15 virus (e15) b) 3 e15 "references" (an asymmetric one, and one with icosahedral symmetry, both prepared for alignment; and a raw one, straight from the EMDB) c) 1 text file (a small "coordinates file")
Download the written tutorial provided through the PDF file below.
[The links SHOULD work directly (it is safe to do right-click followed by "save as"); if not, once you click on the link it will take you to another page where you'll see a "DOWNLOAD" link; click on that to get the corresponding file].
TUTORIAL DOCUMENT
DATA
e15tomograms.zip Get all the tomograms listed above in a zip file
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ANYTHING BELOW THIS MARK IS DEPRECATED
This session will cover the beta version of a small fraction of the possibilities for SPT processing EMAN2 will eventually offer.
RESULTS UH
OUTLINE
- 1) SPT processing through EMAN2's workflow (e2workflow.py)
- 2) Sub-volume extraction from tomograms using EMAN2's 3D particle picking tool (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
BOXING
There are 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
To launch the GUI that will show you the tomogram (you're free to choose whichever you prefer, "e15normal.rec" or "e15phaseplate.rec") type the following COMMAND #001 at the commandline:
COMMAND #001 |
e2tomoboxer.py e15normal.rec --yshort --inmemory
EXPLANATION
To specify --yshort, or not to
- This option will FLIP the orientation of your tomogram respect to the Y and Z coordinates. You should ONLY specify it IF the tomogram has its smallest/slimmest dimension running along the Y-axis, so that it becomes parallel to the Z-axis instead.
Ok... but WHY? What does this mean?
Some tomograms are built with the slimmest part of the 3D volume (that corresponding to the "ice thickness" in cryoEM) running along the Y-axis. BUT in EMAN2 volumes are displayed such that the Z-axis is perpendicular to the screen. If you open one of these tomograms "as is", you'll be looking at it "from the side". Most of the time you want the slimmest part of the volume to be aligned along Z (NOT Y), so you can see the tomogram "from the TOP", and look at the entire CCD-captured area in the XY plane slice by slice, as you go through the volume.
--inmemory
- This option pre-loads your tomogram to memory, allowing to box particles (or do whatever you want to do in e2tomoboxer) more smoothly (faster), because reading data from memory is faster than reading it from disk. You can get the entire list of options that e2tomoboxer.py takes (not many at this point) and some sort of explanation of what they're for by typing the following at the commandline:
e2tomoboxer.py -h
If you ran the command and took a leap of faith in skipping the explanation, you will probably have already clicked a few things in the GUI (Graphical User Interface with nice 'clickable' buttons) that popped up. (I hope you did; extensive explanations really ought to be read only when following the execution boxes doesn't work smoothly, when you're confused, when you have a lot of time to spare and nothing better to do, or when you're a purist [slightly OCD] about reading manuals in their entirety with the noble purpose of getting the most out of them).
USING THE WORKFLOW FOR SPT
The e2tomoboxer.py GUI should look like this: 
This window is called You will notice...