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:

• Go to the Find Similar Structures Tool.
• Follow the prompts to indicate which structure you would like to compare. Let's call this the "reference" structure.
• When you hit "submit" you will be given a list of all available structures, and their similarities with the designated reference structure.
• To visualize any two structures of interest and create animations that depict the differences in rotation, tilt and translation, you will want to use the RADtool plugin for VMD, as described here.

If you want to compare an unpublished structure with all published structures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

• Install VMD and RADtool on your machine. Instructions can be found here.
• Follow the example below for how to "Detect rRNA in local files". This will allow you to calculate the RAD angles for your model. This step is performed entirely on your machine (i.e. there are no file uploads or downloads).
• Use the Find Similar Structures Tool to see if any published structures have similar orientations. For this, you will provide the RAD angles and the webtool will calculate the difference, in terms of Euler-Rodrigues angles, for the head and/or body of every structure in the database.
• If you find structures are similar to yours, you can also visually compare the orientations with the RADtool plugin.

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.

• Installing VMD in Windows
• Installing VMD in OSX
• Installing VMD in Linux
• Installing VMD in Linux (without admin access)

Launching RADtool

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

• Single-use start - This may be your preference if you only plan on running RADtool occassionally. With this approach, each time you want to analyze a ribosome, you will have to manually launch RADtool from within VMD.
• Persistent installation - If you plan to use RADtool frequently, it can be helpful to set up VMD so that RADtool will be accessible through a dropdown menu. This only takes a few extra steps and some basic knowledge of the command line. This is not required, but it can be worth the extra steps if you regularly use RADtool.

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.

• Automatic structure downloads - With this approach, RADtool will retrieve any structure from the RCSB database, identify the rRNA segments and analyze all ribosomes included under the same accession code.
• Detect rRNA in local files - With this approach, you can analyze structure files that are already on your machine. RADtool will try to automatically identify and analyze all rRNA chains present in the provided set of files.
• User-specified chains - (less common) If RADtool is unable to automatically determine which chains are rRNA, or if you only want to analyze a single ribosome contained in a bundle of files, you can use this approach to explicitly indicate which files and chains should be analyzed.

Animation options

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

• Animate from the reference E. coli structure - This shows how to animate the reference E. coli structure by separately applying a rotation, tilt and translation, in order to reach the structure being analyzed.
• Animate between any two structures - This explains how to generate an animation between any two structures that have been analyzed in RADtool.

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.