Manpage of meshInit
Section: User Commands (1)
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meshInit - Generate a starting model for membrane-associated particles.
meshInit model offset
meshInit model offset flgRandomize
meshInit model offset flgRandomize flgBothSides
meshInit model offset flgRandomize flgBothSides flgReverse
meshInit model offset flgRandomize flgBothSides flgReverse flgShuffle
Generate starting model, initial motive list, and rotation axes files
for particles embedded in and, typically, orthogonal to membrane(s)
(e.g. ion channels, viral fusion proteins, etc.). The resulting files
are suitable as inputs for a PEET alignment. MeshInit is similar to
seedSpikes / spikeInit, but, unlike those programs, it can handle
arbitrary, irregularly shaped membranes. The input model must contain
one or more meshes (in any number of objects) defining the membrane(s).
Particle model points will be placed at each vertex in each mesh, and
the particle y axes will be chosen perpendicular to the mesh surface
at each vertex location. Particles will all be put in object 1 of the
output model, with each mesh in its own contour. The output model,
inital motive list, and rot axes files will be named *_mesh.mod,
*_mesh_initMOTL.csv, and *_mesh_RotAxes.csv, respectively.
Outputs of this type can be useful for semi-automated particle
picking for membrane associated proteins template matching with a
user-supplied template, or via refinement of a single- or multi-particle
Often, it will be desirable to place candidate particles uniformly
across a membrane surface. This can easily be done using 3dmod. Consult
the IMOD / 3dmod documentation for additional details, but, briefly,
one can set the desired spacing in pixels in 3dmod's Edit / Model /
Header dialog, and then draw membrane contours with the middle mouse
button held down. The same spacing should also be used between contours
prior to meshing with the 3dmod's Passes (mkmesh -P) or Skip (-s)
options. You can also chose to generate contours and mesh points
manually or programmatically if you prefer.
While meshInit is primarily intended for use with particles
orthogonal to membranes, it can also be used for membrane-associated
particles with no preferred orientation or rotation axis. In this
case, simply use the resulting output model while discarding the
corresponding initial motive list and rotation axes files.
- model = string
The path to the input IMOD model containing one or more meshes.
- offset = float (signed)
Output particles model points will be shifted from each vertex
by offset voxels along the surface noraml. (Default = 0).
- flgRandomize = boolean
If true (non-zero), randomize rotation around the reference axis.
(Default = true).
- flgBothSides = boolean
If true (non-zero) and offset is non-zero, particles with both postive
and negative offsets will be created at each vertex.
(Default = false).
- flgReverse = integer (Optional, default = 0);
If true (non-zero), reverse the poloarity of the particle Y axes.
- flgShuffle = integer (Optional, default = 0);
By default, meshInit 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.
PEET(1), alignSubset(1), meshInit(1), seedSpikes(1), spikeInit(1),
- SEE ALSO
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Time: 18:16:05 GMT, January 11, 2021