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Manpage of spikeInit
spikeInit
Section: User Commands (1)
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NAME
spikeInit  Create initial motive list and rotation axes file for
particles ("spikes") on the surface of a sphere or cylinder.
SYNOPSIS
spikeInit model
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
DESCRIPTION
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 protein spikes in the envelope of a
retrovirus for the spherical case, and motor proteins decorating a
microtubule in the cylindrical case. Oddnumbered 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 evennumbered contour must contain
a single point defining the estimated center of the sphere. The
vector from that center to each spike will be taken as the particle's
initial orientation. Similarly, in the cylindrical case, the following
evennumber object must contain a pair of points (typically in 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 initial orientation. In either case, 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 nonlinear 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.
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 the input model.
If 0, the tomogram Y axis will be used as the reference direction.
 flgRandomize = integer

If nonzero (Default = 1), include a random rotation around the
reference axis.
 flgRefine = integer

If nonzero (Default = 1), suppress refinement of the center / axis points
using nonlinear least squares.
 flgReverse = integer (Optional, default = 0);

If nonzero, reverse the polarity of the particle Y axes.
 flgShuffle = integer (Optional, default = 0);

By default, spikeInit will use the same pseudorandom rotations on
each invocation. If both flgShuffle and flgRandomize are nonzero,
different rotations will be chosen at each invocation.
AUTHORS
John Heumann
SEE ALSO
averageAll(1), alignSubset(1), modifyMotiveList(1), PEET(1),
seedSpikes(1), stalkInit(1)
Index
 NAME

 SYNOPSIS

 DESCRIPTION

 AUTHORS

 SEE ALSO

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Time: 21:10:06 GMT, March 20, 2017