Pick Particle

Pick Particle is a plugin for UCSF Chimera to calculate the initial coordinates and orientations of subtomograms on the surface of spherical or tubular objects in the tomogram as described in the publication below:

Qu K., Ke Z., Zila V., Anders-Oesswein M., Glass B., Muecksch F., Mueller R., Schultz C., Mueller B., Kraeusslich H.-G., Briggs J.A.G. Maturation of the matrix and viral membrane of HIV-1. Science 373, 700-704 (2021).

This package is distributed under the GPL v.3 for academic and non-commercial use.

STARTUP AND INPUT

Open the tomogram in Volume Viewer and change the Origin index and Voxel size in Features ... Coordinates to 1. In this way, the shift and rescale of the tomogram are reset. Pick Particle only considers the absolute coordinates of subtomograms.
The centre of a sphere (one marker) or the axis of a tube (at least two markers) are placed in Volume Tracer. Multiple spheres can be saved in either one or several marker sets. But each tube must possess a New marker set.
Pick Particle saves the parameters of objects and subtomograms in EM (.em) files. The following parameters are stored in the matrix MOTIVELIST of dimension (20, NPARTICLES). The coordinates and Euler angles correspond to the definition in TOM/AV3 toolbox[1,2].

Row	Required Inputs
1	Cross-Correlation Coefficient
2	Marker set id
3	Sphere/Tube radius
4	Particle number
5	Running number of tomogram
6	Index of feature in tomogram
7	Tomogram number
8	X-coordinate in full tomogram
9	Y-coordinate in full tomogram
10	Z-coordinate in full tomogram
11	X-shift in subvolume
12	Y-shift in subvolume
13	Z-shift in subvolume
14	(optional)
15	(optional)
16	(optional)
17	Phi-rotation along Z (in degree)
18	Psi-rotation along Z (in degree)
19	Theta-rotation along X (in degree)
20	Class number

Tomogram ID

Tomogram ID is saved in the 5th and 7th rows for subtomogram extraction, wedge-mask reweighting, CTF correction and etc in various packages.

Marker File

The plugin takes the cmm file as input from Volume Tracer.

Objective Style

The morphology of object in the tomogram must be specified as either sphere or tube.

Sampling

The spacing of subtomograms is defined by the tangential distance on a sphere or by the tangential and axial distances on a tube. The distance is measured in voxels. The Phi angle of subtomograms can be randomized if required.

BUTTONS AND OPTIONS

Display

Display spherical or tubular object.

Save

The radius (row 3) and the centre of sphere or the axis of tube (row 8-10) are saved in MarkerName.em.
The coordinates of subtomograms are saved in MarkerName_sphere/tube.em as defined in the table above.
The two EM files can be displayed in Place Object to check the positioning of subtomograms.

Reset

Close all objects.

Options

Combine Coordinates: Combine multiple coordinate files of subtomograms in different tomograms into one EM file. Sequential numbering of subtomograms in row 4 can be applied permissively.
Shift Coordinates: Manipulate the coordinates of each subtomograms. Rescaling is applied after translations if both are acquired.

References

[1] Nickell S, et al. (2005) TOM software toolbox: acquisition and analysis for electron tomography. Journal of Structural Biology 149(3):227-234.
[2] Förster F, Hegerl R (2007) Structure Determination In Situ by Averaging of Tomograms. Methods in Cell Biology 79:741-767.

Cambridge 2017