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stalkInit

Section: User Commands (1)
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NAME

stalkInit - Compute an initial motive list and models for particles whose orientations are each given by 2 points in an input model

SYNOPSIS

stalkInit inputModel
stalkInit inputModel iRef
stalkInit inputModel iRef flgRandomize
stalkInit inputModel iRef flgRandomize flgReverse
stalkInit inputModel iRef flgRandomize flgReverse flgShuffle

DESCRIPTION

stalkInit calculates particle rotation axes, an initial motive list, and revised models from an input IMOD model specifying particle location and orientation by 2 specific points within each particle. While the program was initially developed to align particles with a stalk or a tail (e.g. as in ATP synthase or phage T4), it is more broadly applicable. The input model should contain a single object with a unique, 2-point contour for each particle. The first point will be referred to as the head and the second as the tail. The output initial motive list will contain the Euler angles required to rotate each particles to match the orientation of the specified reference. Additionally, stalkInit will create 3 new IMOD models containing the head, centroid, and tail locations in a single scattered contour. By default, stalkInit includes a random rotation around the reference axis; to suppress this behavior, set flgRandomize = 0.

Unlike most PEET programs, stalkInit works at the level of a single model. Thus it is unable to orient particles to match a reference specified in a different model. If this is required, consider using stalkInit to create initial motive list(s) orienting the particles with the z axis (see below), and then using modifyMotiveList to generate new motive list(s) corresponding to the desired reference orientation.

inputModel = string: The path to the input IMOD model.
iRef = integer (Optional, default = 0);: The number of the reference particle. If 0, the tomogram y axis will be used as the reference axis.
flgRandomize = integer (Optional, default = 1);: If non-zero, include a pseudo-random rotation around the reference axis.
flgReverse = integer (Optional, default = 0);: By default, stalkInit by default treats the 1st point in each contour as the head and the 2nd as the tail. To reverse this somewhat counterintuitive convention, set flgReverse to be nonzero.
flgShuffle = integer (Optional, default = 0);: By default, stalkInit 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.

AUTHORS

Rick Gaudette
John Heumann