Version = 1.0
Pip = 1
[Field = AlignCommandFile]
short = align
type = FN
usage = Command file for running Tiltalign
tooltip =
manpage = Command file for running Tiltalign(1). If this option is not
entered, the first non-option argument will be used for the name of the
command file.
[Field = NumberOfFiducials]
short = fiducials
type = I
usage = Numbers of fiducial markers (beads) in the alignment model
tooltip =
manpage = Numbers of fiducial markers (beads) in the alignment model. With
this entry, he program will assume that each bead is marked on every view. If this
option is not entered, the program will use the number of contours in the
fiducial model with more than one point, and count up the number of points in
those contours. The latter will give more accurate estimates of the ratio of
measurements to unknowns when there beads marked on only a subset of views.
[Field = NumberOfViews]
short = views
type = I
usage = Number of views in the tilt series
tooltip =
manpage = Number of views in the tilt series. If this option is not entered,
the program will use the number of views in the image file listed in the
command file.
[Field = TargetMeasurementRatio]
short = target
type = F
default = 3.6
usage = Target ratio of measurements to unknown values (default 3.6)
tooltip = Target ratio of measurements to unknown values. Of those
restrictions that give a ratio above the required minimum,
the one that gives a ratio closest to this target will be chosen.
manpage = Target ratio of measurements to unknown values. If two successive
restrictions give a ratio above the minimum required by the \fB-minimum\fR
option, the restriction that gives a ratio closest to this value will be chosen.
The default is 3.6.
[Field = MinMeasurementRatio]
short = minimum
default = 3.2
type = F
usage = Minimum ratio of measurements to unknown values (default 3.2)
tooltip = Minimum ratio of measurements to unknown values. Restrictions will
be applied until at least one ratio rises above this value.
manpage = Minimum ratio of measurements to unknown values. Restrictions will
be applied until at least one ratio rises above this value. The default is
3.2.
[Field = OrderOfRestrictions]
short = order
type = IA
default = 1,4,3,2,5
usage = Order in which possible restrictions should be applied to achieve target
tooltip =
manpage = Order in which possible restrictions should be applied to achieve
the target. The restrictions are numbered as follows:
^ 1: Group rotations
^ 2: Solve for one rotation
^ 3: Fix tilt angles
^ 4: Group magnifications
^ 5: Fix magnifications
^The default order is 1,4,3,2,5, which means rotations will be grouped, then
then magnifications grouped, tilt angles fixed, then one rotation solved for,
then magnifications fixed.
[Field = SkipBeamTiltWithOneRot]
short = skipbeam
type = B
usage = Do not add beam tilt when solving for one rotation angle
tooltip =
manpage = By default, the program will add a solution for beam tilt if and when it
switches to solving for only one rotation angle. (If parameters are already
set to solve for only one rotation angle, this switch does not occur and it
will not add beam tilt.) With this option, it will not add the beam tilt
solution along with this restriction.
[Field = usage]
short = help
type = B
usage = Print help output
tooltip =
manpage =