Making a 2D radial density average

[vmpr...@uw.edu]

Hello All,

I am looking to calculate a 2D radial density average plot/image for an icosahedral virus structure. Is there a program within the EMAN/EMAN2 package that could help me do this?

Thank you.

Vidya

[Ludtke, Steven J.]

Sure, are you trying make this from a set of raw particles or for a 3-D map (ie - 2-D projection -> rotational average)?

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Vidya Mangala Prasad]

Hello Steve,

Preferably using a 3D map to generate the 2D radial average. I do have access to the raw particle set, but it has been processed using Relion.

Thanks,

Vidya

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/BF283CC1-725D-4E96-9954-B34B4DA55FB7%40bcm.edu.

[Ludtke, Steven J.]

Most general operations like this can be performed with e2proc2d.py (for 2-D images), e2proc3d.py (for 3-D volumes) or e2filtertool.py (for dynamic tuning of parameters).

e2proc3d.py --help 

will give a list of all of the program options, but many things you can do is via "processors"

e2help.py processors

What you are trying to do would be 

e2proc3d.py <input map> <out text file> --calcradial <0 or 1>

if you give it 0, it will compute radial amplitudes, which is probably what you want (1 will compute radial "intensity", which mainly makes sense in Fourier space)

You can use any plotting program you like, of course, but:

e2display.py --plot <text file>

then middle-click for the control panel. This will allow you to select which column to use for the x and y axes easily. The text file will contain 

radius mean min max sigma

for each radial shell

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/00C6F08C-CE9A-4266-8C79-82F364C4119C%40uw.edu.

[Vidya Mangala Prasad]

Dear Steve,

Thank you very much for your response and for explaining the different options available. I will use them accordingly.

With Best Wishes,

Vidya

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/21F4DFB1-2573-4153-95FB-F4F071C36EBB%40bcm.edu.