. Author manuscript; available in PMC: 2011 Jun 1.

Published in final edited form as: J Struct Biol. 2010 Jun 15;172(3):407–412. doi: 10.1016/j.jsb.2010.06.010

Table 1.

List of primary FREALIGN subroutines that can be parallelized

	Subroutine	Description
Refinement	cc3m()	Calculate overall phase residue in Fourier space
	ccp()	Calculate cross-correlation in Fourier space
Reconstruction	pinsert_s()	Interpolate a particle image into 3D Fourier transform of the volume being reconstructed
Other	sigma2()	Calculate correlation coefficient in real space
	presb()	Calculate amplitude correlation coefficient in Fourier space
	ccoef()	Calculate correlation coefficient in real space