Module: STAR File To Point Cloud ()

Description:

This is an experimental module from the Xtra Library: https://xtras.amira-avizo.com. This module lets you import motiflists in STAR file format as generated by STOPGAP template matching and convert it into a point cloud object that can be used to display molecules at the detected positions in the specified orientation. The module converts voxel coordinates into real-world coordinates of the attached tomogram and outputs the molecule orientation either in four norm quaternions or three Euler angles.

Connections:

Tomogram [optional]
The tomogram that contains the molecules to be visualized has to be connected in order to obtain its bounding box and voxel size. The STAR file stores the molecule positions in terms of voxel coordinates of the source tomogram. The real-world coordinates will be calculated using this information. If no tomogram is connected, a voxel size of 1 1 1 is assumed.

Ports:

STAR File

Enter the full path of the STAR file to be converted. Click the Browse button (...) to navigate to the STAR file with a File Browser box. The format of the STAR file is described in the documentation of the STOPGAP software package stopgap_0.7.1_doc.pdf. See e.g.: https://github.com/williamnwan/STOPGAP.

Binning

Enter the binning factor that the attached tomogram has with repect to the tomogram on which the template matching has been performed. If the binning was not an integer multiple of 1, the binning factor can be calculated as voxel_size_orig / voxel_size_binned.

Options

Checking the Output Spreadsheet option creates in addition a spreadsheet object that can be used to view the column values or to export to a spread sheet application.

Orientation Output Format

This port lets you choose the orientation format of the output point cloud. The options are three Euler angles (ZXZ, extrinsic rotations) or four norm quaternions q0, q1, q2, q3 (scalar last convention).