Ribosome PyMOL Plugin: Difference between revisions
(Created page with "{{Infobox script-repo |type = plugin |filename = plugins/ribosome_plugin.py |author = abelew |license = GPLv2 }} ==Description== A small plugin conta...") |
(fix download link) |
||
| Line 1: | Line 1: | ||
{{Infobox script-repo | {{Infobox script-repo | ||
|type = plugin | |type = plugin | ||
| | |download = https://github.com/abelew/ribosome_pymol | ||
|author = [[User:abelew|abelew]] | |author = [[User:abelew|abelew]] | ||
|license = GPLv2 | |license = GPLv2 | ||
| Line 28: | Line 28: | ||
[[Category:Plugins]] | [[Category:Plugins]] | ||
[[Category:Coloring]] | [[Category:Coloring]] | ||
Latest revision as of 10:23, 24 July 2015
| Type | PyMOL Plugin |
|---|---|
| Download | https://github.com/abelew/ribosome_pymol |
| Author(s) | abelew |
| License | GPLv2 |
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!