In order to increase accessibility of computational methods employed by the group, we frequently provide code and scripts as open source, such that anyone may use them. Here, we will also post scripts that you may find helpful.
Our class of structure-based models are available at smog-server.org.
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