Tutorials and Examples

To make it easier to use this resource, we have prepared a set of video tutorials and example analysis pipelines.

Example Usage Cases

If you want to compare published structures

You may want to know how a structure compares to other structures that were not mentioned in a manuscript. Or, you may read an older article and want to know how those structures compare to later models. For this purpose, here is an example workflow:

If you want to compare an unpublished structure with all published structures

When preparing a manuscript, you may want to check and see how different/similar your structure is to other published structures. Here is an example for how to use this resource for that purpose.

Step-by-step video demonstrations with the RADtool plugin

These short tutorials provide step-by-step instructions on how to configure and run various forms of analysis with the GUI-based interface. If you prefer to use the command-line interface, see the README file for instructions.

Installing VMD

VMD is a powerful visualization and analysis tool that is developed by researchers at UIUC. While VMD is generally easy to install, we also provide some introductory installation instructions to help you get started. Once you have installed VMD, you can launch the RADtool plugin.

Launching RADtool

Detailed instructions for launching RADtool are provided in the README file, as well as in these short videos.

Analyzing ribosome structures

RADtool provides various methods for loading and analyzing ribosome structures. Here, we provide demonstrations of the three main approaches that are accessible through the RADtool GUI. For more advanced capabilities, including the analysis of simulations, see the README.

Animation options

RADtool allows users to generate animations that show the decomposition of rotation, tilt, tilt direction and translation.

Need more help?

If you find these tutorials are insufficient, we are always happy to provide direct assistance, as well as prepare additional example videos.

Page created and maintained by the Whitford Group at the Center for Theoretical Biological Physics, Northeastern University.