Comparison of SPIDER Alignment Operations

Operation Multiple images Multiple references Shift Rotation Restricted Projections Check Mirrored position Source code Notes

'AP SHC' + + + + +/- +/- apmaster.f & apsh_psc.f Exhaustive optimal search of rotations and shifts. Faster than: 'AP SH' and has increased search range restriction capability.

'AP SH' + + + + +/- +/- apmaster.f, apsh_ps.f, apsh_ss.f Exhaustive optimal search of rotations and shifts. Replaced legacy operations: 'AP MQ', 'AP MQ R', 'AP NQ', 'AP RQ', & 'AP RQ N'.

'AP REF' +/- + +/- + +/- +/- apmaster.f, dsgr_pm.f, dsfs_p.f Search of rotations followed by shifts for optimal rotation.
Replaced legacy operations: 'AP MD', 'AP RD', & 'AP RN', & 'AP RNS'.

'AP I' - - - - - - apmaster.f, aprings.f Create rings file for 'AP SH' & 'AP REF'

'AP MS' + + + - - - multishift.f Also checks 180
degree rotation.

'AP SA' + - + - - - saqb.f Reference free.

'AP SR' + - + + - - gali.f Reference free.

'AP RA' + - - + - - falb.f Self-alignment.

'AP C' + - - + - +/- hali.f & hali_p.f Also classifies images into groups. Replaces 'AP CA', 'AP CM'.

'AP TOOL' + + + + +/- +/- apmaster_tool.f & apsh_tool.f Atool for investigating selection of search parameters. Compares different shifts and ring settings to see effect on choice of best alignment.

'OR A' - - + + - +/- oracfmsk.f, oracfmskm.f, frng.f Self-correlation.

'OR Q' + + + + - +/- oracfmskm.f, frng.f Self-correlation.

'OR SH' - - + + - +/- apmaster.f, apsh_ss.f Same method as 'AP SH'. Replaces 'OR MQ', 'OR NQ'.

'OR R' - - - + - x ormd.f, ormd_p.f Same method as 'AP SH' without shifts. Replaces 'OR 2' & 'OR 2M'.

Operation	Multiple images	Multiple references	Shift	Rotation	Restricted Projections	Check Mirrored position	Source code	Notes
'AP SHC'	+	+	+	+	+/-	+/-	apmaster.f & apsh_psc.f	Exhaustive optimal search of rotations and shifts. Faster than: 'AP SH' and has increased search range restriction capability.
'AP SH'	+	+	+	+	+/-	+/-	apmaster.f, apsh_ps.f, apsh_ss.f	Exhaustive optimal search of rotations and shifts. Replaced legacy operations: 'AP MQ', 'AP MQ R', 'AP NQ', 'AP RQ', & 'AP RQ N'.
'AP REF'	+/-	+	+/-	+	+/-	+/-	apmaster.f, dsgr_pm.f, dsfs_p.f	Search of rotations followed by shifts for optimal rotation. Replaced legacy operations: 'AP MD', 'AP RD', & 'AP RN', & 'AP RNS'.
'AP I'	-	-	-	-	-	-	apmaster.f, aprings.f	Create rings file for 'AP SH' & 'AP REF'
'AP MS'	+	+	+	-	-	-	multishift.f	Also checks 180 degree rotation.
'AP SA'	+	-	+	-	-	-	saqb.f	Reference free.
'AP SR'	+	-	+	+	-	-	gali.f	Reference free.
'AP RA'	+	-	-	+	-	-	falb.f	Self-alignment.
'AP C'	+	-	-	+	-	+/-	hali.f & hali_p.f	Also classifies images into groups. Replaces 'AP CA', 'AP CM'.
'AP TOOL'	+	+	+	+	+/-	+/-	apmaster_tool.f & apsh_tool.f	Atool for investigating selection of search parameters. Compares different shifts and ring settings to see effect on choice of best alignment.
'OR A'	-	-	+	+	-	+/-	oracfmsk.f, oracfmskm.f, frng.f	Self-correlation.
'OR Q'	+	+	+	+	-	+/-	oracfmskm.f, frng.f	Self-correlation.
'OR SH'	-	-	+	+	-	+/-	apmaster.f, apsh_ss.f	Same method as 'AP SH'. Replaces 'OR MQ', 'OR NQ'.
'OR R'	-	-	-	+	-	x	ormd.f, ormd_p.f	Same method as 'AP SH' without shifts. Replaces 'OR 2' & 'OR 2M'.

NOTE: 'AP SH' differs from 'AP REF' in that the former has an exhaustive search of all specified rotations and shifts, while the latter first finds the optimal rotation and then finds optimal shift for that rotation only.

There is a comprehensive discussion and examples of different ways that these alignment operations can be used to solve alignment problems in: Methodology of 2D particle alignment.

Source file: align_overview.html Updated: 16 Sep. 2013 ArDean Leith