In EMAN2, e2refine2d.py will compute and save Eigenimages from the aligned particle stack in each iteration as r2d_01/basis_XX.hdf
or
e2refine2d.py --help
alternatively, if you want to just use a single alignment reference then compute Eigenimages:
e2a2d_align.py ptclstack.hdf align_ref.hdf,3 --threads=8 --saveali
where ptclstack.hdf contains the phase-flipped particle stack (note that you may still get Eigenimages related to defocus differences),
align_ref.hdf is a particle stack (or single image) containing the alignment reference and "3" is the image number to use as a reference (0 is the first image),
--threads is the number of cores on the machine
e2msa.py m2d_01/aliptcls_01.hdf basis.hdf --nbasis 12
will compute the first 12 Eigenimages and save them in basis.hdf
As with other EMAN2 programs you can use any file format you prefer for input...
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Steven Ludtke, Ph.D. <
[log in to unmask]> Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology (
www.bcm.edu/biochem)
Hi all,
I am trying to compute the eigenimages of my particles and first I think I need to align my particles. Does anyone know which software will be the best to do the alignment? My particles are segmented helices and I do have some 2D class averages.
Best,
Yangqi