Content-type: text/html 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
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 reference axis.
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.


John Heumann  


averageAll(1), alignSubset(1), modifyMotiveList(1), PEET(1), seedSpikes(1), stalkInit(1)




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Time: 18:16:05 GMT, January 11, 2021