Place Object

Place Object is a plugin for UCSF Chimera to visualize the spatial distribution of subtomograms within the tomogram as described in this publication:

Qu K., Glass B., Dolezal M., Schur F.K.M., Murciano B., Rein A., Rumlova M., Ruml T., Kraeusslich H.-G., Briggs J.A.G. (2018) Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences of the United States of America. 115:E11751-E11760.

It has capabilities for marking and displaying points that are similar to the EMPackage[1]. A geometric object or a down-sampled surface of the high-resolution reference is translated and rotated according to the parameters determined for each subtomogram and displayed in the same volume space as the tomogram. Each object can be coloured according to classes or the Cross-Correlation Coefficient (CCC).

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

Coordinate File

Currently the plugin only supports the coordinate file in EM (.em) format. 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[2,3].

Row	Required Inputs
1	Cross-Correlation Coefficient
2	(optional)
3	(optional)
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

Objective Style

The shape, Voxel-size, Z-Offset and Phi-Offset of the object can be specified. A customized object file in STL format can be converted from a 3D map in Chimera. Open the 3D map in a new Chimera session. In the Volume Viewer ... Features ... Coordinates, change the Origin index to the centre of the 3D box. Make sure that the Voxel size is consistent with the coordinate file and/or the tomogram at the given bin. Set a favourable isosurface level, and then click Center and Orient. In the main GUI of Chimera, generate the STL object in File ... Export Scene.

Colour Style

Class: Objects are coloured in different classes. The class information is assigned in Row-No. in Colour Range.
Cross-Correlation: The colour of objects denotes the CCC of alignment on a scale from low (red) to high (green).
Custom Colour: Specify the colour of objects in Chimera Colour Editor.

Colour Range

Row-No.: The colour scale of each class is extracted from the Nth row. The default row is 20.
CC-Range: The CCC range is set between the minimum and the maximum CCC values by default. It is also user defined.

Visualization

All: Display all objects.
None: Hide all objects.
One: Display one object specified by Particle Number.
Cross-Correlation: Display objects with CCC values between the thresholds defined in Lower CC Threshold and Upper CC Threshold.
Class-number: Display the specified class only in Class Number.

Particle Number

Set the object number.

Lower CC Threshold

Set the lowest CCC value cut-off.

Upper CC Threshold

Set the highest CCC value cut-off.

Class Number

Set the class number.

Apply

Display objects that meet the conditions.

Focus

Focus on visible objects.

Save

Save visible objects into a new MOTIVELIST file.

Delete

Close all objects.

References

[1] Pruggnaller S, Mayr M, Frangakis AS (2008) A visualization and segmentation toolbox for electron microscopy. Journal of Structural Biology 164(1):161-165.
[2] Nickell S, et al. (2005) TOM software toolbox: acquisition and analysis for electron tomography. Journal of Structural Biology 149(3):227-234.
[3] Förster F, Hegerl R (2007) Structure Determination In Situ by Averaging of Tomograms. Methods in Cell Biology 79:741-767.

Heidelberg 2016