| VO EA | [Vector Operation - Create Evenly Spaced Angles Document file] |
| VO MD | [Vector Operation - angular Document file from 'AP MD' output] |
| AP I | [Alignment - Initialize Rings File ||] |
| AP SH | [Alignment - multi-reference, exhaustive rotation & shift ||*] |
.ENTER TEMPLATE FOR REFERENCE IMAGES: REF***
[Give the template name of the existing file series of
reference images (typically projections).]
.ENTER 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).]
.TRANSLATION SEARCH RANGE (ZERO FOR NONE): 5
[For translational alignment enter limit on translational shift. A
response of '0' will give same alignment as obsolete 'AP MD', 'AP RD' or
'AP RN' operations.]
.FIRST, LAST RING, & RING SKIP: 5, 30, 1
[Only data at radii in the range 5-30 will be analyzed.
If skip=0 or 1, then every radial ring between 5 and 30 will be taken;
for skip=2, every second ring, etc.]
.REFERENCE IMAGES ANGLES DOCUMENT FILE: Refangles
[Optional input file. Enter name of the doc file containing
Eulerian angles (psi, theta, phi) for the reference images.
Enter '*' if you do not have any reference angles doc file.
.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 actual reference image files. 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 a reference-rings file will be created
and used during this alignment run. More than one
SPIDER run can use the same reference-rings file.
Note that old responses 'W', 'Y', & 'N' are now obsolete.
.ENTER TEMPLATE FOR IMAGE SERIES TO BE ALIGNED: data001@****
[Give the template name of the existing file series of
experimental images. These images will be checked for
alignment versus the reference images.]
.ENTER FILE NUMBERS OR SELECTION DOC. FILE NAME: 1-2100
[Enter numbers of experimental image 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).]
.EXPERIMENTAL IMAGES ALIGNMENT DOCUMENT FILE: angles001
[Optional input file. If '*' is given then this operation is
similar to obsolete 'AP MD'. If you desire to restrict the range of
angular search for projections then this doc file is necessary. It
must contain the current Eulerian angles of experimental images
(projections): psi, theta, phi) and optionally the current
inplane rotation, shifts and other alignment parameters.
The output files from 'AP SH' and 'AP REF' contain such info.]
.RANGE OF PROJECTION ANGLE SEARCH & ANGLE CHANGE THRESHOLD: 20.0, 5.0
[Experimental images will be compared with only these
reference images whose normal is within the specified degree range.
If a '0.0' range
is input then there is NO restriction on which of the projections
are compared. The angle change threshold is an optional input which
is used solely to record how many angular projections differ by more
than the specified threshold from their previous orientation.]
.CHECK MIRRORED POSITIONS?, SHIFT AND ROTATE INPUT? (Y/N): Y,N
[Optional check of the mirrored reference image. By using this check and
only providing reference images from one hemisphere of projection
directions, speed can be doubled (See Note: 1 below).
The second answer is an optional request
to rotate and shift input images according to parameters in the
experimental images alignment doc. file before determining alignment.
(If this is 'Y' there is no need for 'dala' files.) For
backward compatibility the legacy '0/1' response is still accepted for
CHECK MIRRORED POSITIONS and second response defaults to 'N'.]
1. Eulerian angle (psi) of nearest reference image.
When no matching projection was found within
the angular range specified, this column will
contain the experimental
image's previous Eulerian angle (if any) or 0.0.
2. Eulerian angle (theta) of nearest reference image.
When no matching projection was found within
the angular range specified, this column will contain
the experimental
image's previous Eulerian angle (if any) or 0.0.
3. Eulerian angle (phi) of nearest reference image.
When no matching projection was found within
the angular range specified, this column will contain
the experimental
image's previous Eulerian angle (if any) or 0.0.
4. Number of the most similar reference projection.
When no matching projection was found within
the angular range specified, this column will contain
a 0.0
5. Experimental projection number.
6. Cumulative In-plane rotation angle (psi).
This is the sum of any rotation from the experimental
images align. document file and the current rotation.
To use in 3D reconstruction programs invert the sign.
7. Cumulative X shift
Cumulative X translation of image. This is the sum
of any shift from the experimental images alignment
doc. file and any current shift.
8. Cumulative Y shift
Cumulative Y translation of image. This is the
sum of any shift from the experimental images
alignment doc. file and any current shift.
9. Number of projections searched.
The number of projections searched can vary when
there is a restriction on angular search.
10. Angular change for projection.
Angular difference between previous and current
projection. This will be -1.0 if the previous
projection angles were not specified.
11. Not-normalized correlation coefficient from
rotational search. Can be used as a similarity measure.
Following values are seldom used by existing procedures:
13. Current X shift
This is the X shift necessary to align the experimental
image with the current reference projection.
14. Current Y shift
This is the Y shift necessary to align the experimental
image with the current reference projection.
15. Shift normalized CC Peak Height & Current Mirroring.
This is the normalized cross correlation peak height
from the totated and shifted image. This value can
be used as a
similarity measure. If mirroring was necessary to
align the experimental image with the reference
projection this value is given a negative sign.
NOTES