Manpage of stalkInit
Section: User Commands (1)
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stalkInit - Compute an initial motive list and models for particles
whose orientations are each given by 2 points in an input model
stalkInit inputModel iRef
stalkInit inputModel iRef flgRandomize
stalkInit inputModel iRef flgRandomize flgReverse
stalkInit inputModel iRef flgRandomize flgReverse flgShuffle
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.
averageAll(1), alignSubset(1), modifyMotiveList(1), PEET(1), spikeInit(1)
- SEE ALSO
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Time: 16:44:59 GMT, March 05, 2018