|VO EA||[Vector Operation - Create Doc File Containing Evenly Spaced Angles]|
|VO MD||[Vector Operation - angular Document file from 'AP MD' output]|
|VO RAS||[Vector Operation - Rotate Angular doc file & Set angle]|
|AP RN||[Alignment - multi-reference, restricted projections, no mirror check ||]|
|AP C||[Rotation Alignment - classification, unknown references ||]|
|AP MD||[Alignment - Multi reference, rotation ||]|
|AP RA||[Alignment - Reference free, Rotation ||]|
|AP RD||[Alignment - multireference, restricted projections ||]|
|AP SA||[Alignment - reference free, Shift ||]|
|AP SR||[Alignment - reference free, Shift & Rotation ||]|
.FILE NUMBERS OR SELECTION DOC. FILE NAME: SELECTREF
[Enter numbers of reference files. The file numbers can also be read from a selection document file where file numbers are contained in the first register (not the keys).]
.FIRST, LAST RING & SKIP: 5,15,1
[Only rings with radii in the range 5-15 will be analyzed. [If skip=0 or 1, then every ring between 5 and 15 will be taken; for skip=2, every second ring; etc.]
.REFERENCE-RINGS FILE: REF001
[Give name of reference-rings file. If the file exists, SPIDER will read the reference-rings data from this file and will not read the reference image file series. If this file does not exist, SPIDER will create/store the reference-rings data in incore memory. If SPIDER is unable to allocate sufficient memory for the reference-rings data then the reference-rings file must exist. In that case, use operation 'AP I' to create the reference-rings file. More than one SPIDER run can use the same reference-rings file.
Note that old responses 'W', 'Y', & 'N' are now obsolete.
[Give the name of the existing experimental image. This image will be checked for alignment versus the reference images.]
Reg 2. Not-normalized correlation coefficient.
Can be used as a similarity measure.
Reg 3. "-psi" angle.
In-plane rotation angle determined. To use in 3D reconstruction programs invert the sign.