Manpage of spikeInit
Section: User Commands (1)
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spikeInit - Create initial motive list and rotation axes file for
particles ("spikes") on the surface of a sphere, cylinder, or helix.
spikeInit model type
spikeInit model type iRef
spikeInit model type iRef flgRandomize
spikeInit model type iRef flgRandomize flgRefine
spikeInit model type iRef flgRandomize flgRefine flgShuffle
spikeInit model type iRef flgRandomize flgRefine flgReverse flgShuffle
spikeInit model type iRef flgRandomize flgRefine flgReverse flgShuffle\
spikeInit calculates particle rotation axes, an initial motive list,
and an output spike model from an input IMOD model specifying location
and orientation of "spikes" on the surface of one or more spheres or
cylinders. Examples include retrovirus glycoprotein spikes for the
spherical case, motor-decorated microtubules in the cylindrical
case, and TMV coat proteins in the helical case. Odd-numbered objects of
the input IMOD model should contain a scattered contour with points
defining the centers of the spikes to be aligned and averaged. In
the spherical case, the following even-numbered contour must contain
a single point defining the estimated center of the sphere. By default,
the vector from that center to each spike will be taken as the particle's
initial orientation. In the cylindrical and helical cases, the following
even-number object must contain a pair of points in contour 1 (typically
an open contour) defining the approximate axis of the cylinder. In this case,
the vector perpendicular to and extending from this axis to each spike
will be the spike's default initial orientation. In all cases, an
initial motive list will be created with the Euler angles necessary to
rotate each spike either to the orientation of a specified reference
spike or to that of the Y tomogram axis, in addition to a new model
containing all the spikes (and only the spikes) in object 1.
Rotation from a given spike to the reference only determines 2 of the
3 Euler angles. By default, spikeInit adds a random rotation around the
reference axis to resolve this ambiguity and suppress any possible
orientation bias. Randomization can be disabled by setting
flgRandomize = 0, which results in choosing the most direct rotation
between each spike and the reference. Also by default, improved
estimates of the center (in the spherical case) or the axis (in the
cylindrical case) will be computed with non-linear least squares and
used for subsequent calculations. To suppress this behavior (e.g. if
the center or axis points are very preciesly known), set flgRefine to 0.
Default spike orientations (and rotation axes) are perpendicular to
the surface of the associated sphere or cylinder. For cylinders and
helices, but not spheres, the default may be altered by setting
flgParallel = 1, in which case the spike orientations will be taken
as parallel to the cylinder axis. In most cases, axial randomization
is will not be appropriate when using flgParallel.
Unlike many PEET programs, spikeInit works at the level of a single
model. Thus it is unable to orient particles to match a reference in a
different model. Should this be necessary, use spikeInit to orient each
spike to the Y tomogram axis, and then use modifyMotive list to rotate
to the orientation of the desired reference.
- model = string
The path to the input IMOD model.
- type = < 'sphere' | 'cylinder' >
Specify spherical or cylindrical processing. Default = 'sphere'.
- iRef = integer (Default = 0)
If > 0, the index of reference particle/spike in object 1 of the input
model. If 0, the tomogram Y axis will be used as the reference direction.
- flgRandomize = integer
If non-zero (Default = 1), include a random rotation around the
- flgRefine = integer
If non-zero (Default = 1), suppress refinement of the center / axis points
using non-linear least squares.
- flgReverse = integer (Optional, default = 0);
If non-zero, reverse the polarity of the particle Y axes.
- flgShuffle = integer (Optional, default = 0);
By default, spikeInit will use the same pseudo-random rotations on
each invocation. If both flgShuffle and flgRandomize are non-zero,
different rotations will be chosen at each invocation.
- flgParallel = integer (Optional, default = 0);
By default, spikeInit uses spike axes perpendicular to the surface of
the associated cylinder or sphere. For cylinders only, spike axes
parallel to the cylinder axis can be generated by setting
flgParallel=1. Axial randomization should usually be disabled when
flgParallel is 1.
averageAll(1), alignSubset(1), modifyMotiveList(1), PEET(1),
- SEE ALSO
This document was created by
using the manual pages.
Time: 16:44:59 GMT, March 05, 2018