subtomo PCA classification

[tomca...@gmail.com]

Hello,

I have a question about interpreting the output from e2spt PCA classification - I am trying to map each particle to its point in the PCA plot, to visualise the division of classes in the plot by colouring the points for each particle according to class. As far as I can tell, the output ptcls_clsXX.lst files tell me which particles are in which class, but I cannot find a way to relate them to their PCA values - is this information retrievable? The pca_ptcls.txt file seems to have particle indices in the first column but I am not sure how to identify each particle based on this.

The classification was run in version 2.31.

Thanks,

Tom

[Ludtke, Steven J.]

Hi Tom,

that's part of a pretty old pipeline, and due to missing wedge issues PCA based classification of subtomograms has an unfortunate tendency to split things based on the wedge orientation despite efforts to fill the wedge. That isn't to say it can't work at all, just that it is generally a lot less effective than the new programs in post EMAN2.91. ie - starting with:

https://eman2.org/e2TomoSmall

having said that, the pca_ptcls.txt file should be indexed to the particle numbers in the input file. ie - 0 is the first image in the input to the program. That program doesn't give a lot of options in controlling how the classification works based on the PCA vectors. You can use "e2display.py --plot pca_ptcls.txt" to visualize the PCA vectors. Use the control panel (middle click) to select which 2 axes to display. The 3d plot will let you display 3 components of the vector at once if you prefer...

--------------------------------------------------------------------------------------
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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[tomca...@gmail.com]

Thanks for the quick response Steve! I will have a look at the particle orientations to check that they were not split by missing wedge orientation. 

So to map each particle to its PCA values, I just go through the pca_ptcls.txt file, indexing in the same order as the input particle_parms_XX.json file. 

Thanks,

Tom