Tool: Orthopick

Orthopick contains settings for the mouse mode named orthopick, developed for picking particles in cryo-electron tomograms with the mouse. The orthopick mode shows three orthogonal slices of a small area of the map centered at the clicked point as well as laid out in a plane for easy viewing without rotation.

For an example of use, details, and discussion, see Membrane Complexes. See also: Volume Viewer

Orthopick can be started from the Volume Data section of the Tools menu and moved, resized, etc. like other tool windows. Starting Orthopick automatically assigns the mode to the right mouse button (= trackpad + Alt on Windows, trackpad + on Mac). Other ways to assign the mode are by clicking the orthopick icon in the Toolbar or by using the mousemode command. By default, the orthopick icon is not shown in the Toolbar, but it can be added to the Home tab using the Toolbar Settings.

In the orthopick mode,

• clicking shows orthogonal red (cryo-EM-beam-aligned XY), green (XZ), and blue (YZ) slices centered on the click, as well as copies of the slices laid out in a plane, as shown in the figure
• each of the slice planes can be dragged to see different cross-sections
• dragging with the Shift key held down translates (recenters) the box delimiting the orthoplanes

Settings:

• Particle size (Angstroms) [default 200] – orthoplanes box size in each dimension
• Orient to membrane surface [surface-model] – if a surface model is specified, use the plane of the surface as the reference for aligning the box; if no surface model is specified, the box will be aligned to the XYZ axes of the tomogram
• Average slab density, thickness (Angstroms) [default 50] – color the slice planes based on average density values through a slab of the specified thickness

Buttons:

• Show particle surface – show 3D contour surface inside the box instead of intersecting orthoplanes; the slices laid out in a plane will still be shown, however, as in the righthand image above. The contour level can be changed by clicking and dragging with the orthopick-assigned mouse button on the particle surface.
• Save particle map – save an MRC file of the map inside the box, including the origin and rotation to apply if the file is opened in ChimeraX; other programs may honor the origin, but not the rotational information, as the latter is not a defined part of the MRC format
• Help – show this page in the Help Viewer