Ribosome PyMOL Plugin
| Type | PyMOL Plugin |
|---|---|
| Download | plugins/ribosome_plugin.py |
| Author(s) | abelew |
| License | GPLv2 |
| This code has been put under version control in the project Pymol-script-repo | |
Description
A small plugin containing functions to make working with multi-pdb structures easier, most notably ribosomes. The menu options include a call-out to a csv file containing all (as of ~2012) the extant pdb entries with ribosomal structures. It includes functionality to color modified bases (pseudouridines and methyls) for those species I found referenced annotations. Similarly, it includes helix definitions using the comparative rna web site: http://www.rna.icmb.utexas.edu/ for those species that I wanted to play with the tRNA entrance tunnel.
Example of use
Perform a git pull using the instructions at: https://github.com/abelew/ribosome_pymol Depending on your installation of pymol, you may need to set the environment variable 'PYMOL_HOME' in order for the plugin installer to succeed. Once complete, click on 'Plugin -> Ribosome' and to view my favorite ribosome:
'Ribosomes by species' -> 'Saccharomyces cerevisiae' -> 'Yusupov 2011'
"The Eukaryotic Ribosome at 3.0A resolution." For extra fun, click 'Helices' and take a tour of the yeast ribosome!