RiboVis

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!

Installation

To install RiboVis, simply:

git clone https://github.com/ribokit/RiboVis.git

import sys
sys.path.append('/path/to/RiboVis')
run /path/to/RiboVis/ribovis.py

Replace /path/to/ with the actual path to your RiboVis folder.
Optionally, you can create or edit a .pymolrc file in your home directory (on Mac; on Windows, create or edit .pymolrc in ‘C:\Program Files\PyMOL\PyMOL'), and add the above commands. This will automatically load ribovis.py whenever PyMOL is started.

To quickly test RNA rendering, run:

fetch 1q9a
rr()

Developed by Das lab, Leland Stanford Junior University.

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