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meshInit

Section: User Commands (1)
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NAME

meshInit - Generate a starting model for membrane-associated particles.

SYNOPSIS

meshInit Model
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

DESCRIPTION

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 reference.

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.

AUTHORS

John Heumann