How to project the electron density map along 'bc' plane?

[brijith thomas]

Dear all,

I am a beginner in using the EMAN software.

As far as I understood, its possible to project the electron density map on to the surface using e2project3d.py. But is it possible to project it along a particular plane for example 'bc' plane.
I saw the options orientgen to adjust the orientation. But still I couldnt project it along a particular plane.

Can anybody give some insight in to it? Or where I can find something to read about it?

With Regards,

Brijith Thomas

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"Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world. "

Louis Pasteur

 

[Steve Ludtke]

I'm not sure what you mean by "bc" plane. Sounds like you're thinking from a crystallographic perspective. There are no crystals in single particle analysis, so there are are no lattice planes, if that is what you are referring to.  Orientations are specified in EMAN (and most other cryoem software) using Euler angles or Quaternions. e2project3d is really designed to make sets of many projections, not individual projections. It is very inefficient to go through the time to start up a new python script (loading all the libraries) just to make a single projection.  However, if you just need to do this for a 1-off, it is possible:

2project3d.py threed.hdf --outfile projection.hdf --orientgen single:alt=24:az=15:phi=97

You can get more information on orientations here:

http://blake.bcm.edu/emanwiki/Eman2TransformInPython

and in this paper, which explains a bit more about the rotations themselves.

Baldwin, P.R. & Penczek, P.A., 2007, The Transform Class in SPARX and EMAN2, Journal of structural biology, 157(1), pp. 250-61.

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Steven Ludtke, Ph.D.
Professor, Dept. of Biochemistry and Mol. Biol.                Those who do

Co-Director National Center For Macromolecular Imaging            ARE

Baylor College of Medicine                                     The converse
slu...@bcm.edu  -or-  ste...@alumni.caltech.edu               also applies
http://ncmi.bcm.edu/~stevel

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