In order to increase accessibility of computational methods employed by the group, we frequently provide open-source code and scripts.
The Noel-Onuchic-Whitford class of structure-based models are available at smog-server.org. smog-server has both a web interface (smog 1), as well as a more versatile standalone version (smog 2, highly recommended). If you find these tools are limited, let us know. These tools are constantly being expanded to support the most challenging researcher questions.
Ribosome Rotation Angles
We have been very interested in developing systematic measures of subunit rotation in ribosomes. In order to unambiguously define any rigid body rotation, we use Euler Angles (as described in Nguyen and Whitford, 2016). Since calculating rigid-body rotations can be quite complex, we provide an easy-to-use VMD tcl script that will calculate the tilt angle, tilt direction and rotation angle for the 30S head and body, given a PDB structure. We also provide instructions with the download. Download Ribosome Rotation Script This script only supports E. coli numbered structures.
We are preparing to release the next version of this script that is capable of handling ribosomes from any organism. If you are interested in beta testing the next version, let us know.