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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\

flgParallel

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.

- NAME
- SYNOPSIS
- DESCRIPTION
- AUTHORS
- SEE ALSO

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