RiboKit : RiboVis

PyMOL Commands by the Das Lab Style


1q9a Example Image

RiboVis is a set of useful and short Python functions for rendering RNA and proteins in PyMOL in our ‘lab style’. For a quick preview:

Function Description
rr() For RNA: renders 2′-OH as spheres, bases as filled rings, and backbone as cartoon ribbons, rainbow-colored from 5′ to 3′. No hydrogens, white background.
rd() For proteins: side chains are all-atom and colored CPK, backbone is rainbow cartoon from N to C terminus.
sa() Superimposes all models to the first one. Thanks to Kyle Beauchamp for this one

And more, including coloring 3D structures by chemical mapping data and other rendering options!


To install RiboVis, simply:

git clone https://github.com/ribokit/RiboVis.git
import sys
run /path/to/RiboVis/ribovis.py

To quickly test RNA rendering, run:

fetch 1q9a



Copyright © of RiboVis Source Code is described in LICENSE.md.

Developed by Das lab, Leland Stanford Junior University.

README by t47, April 2016, edits by Clarence Cheng, May 2016.

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