README

rna_distmap is just the simplest possible script to plot a distance matrix. It uses scipy's spatial.distance function to compute the distance matrix of all atom-to-atom distances.

Version

This is version 0.2 created on October 30, 2012 while postducking at Kar. Inst. in tze Zveeden.

Setup

1. Clone the repository

git clone https://github.com/esguerra/rna_distmap.git

Usage

To run the program just call it from the prompt:

./rna_distmap.py 1ehz

It will make a picture just like the one in Yathindra and Malathi's 1982 paper [1] for the crystal structure of phenylalanine tRNA at 1.93 Angstrom resolution.

[1] R. Malathi and N. Yathindra, Secondary and tertiary structural foldings in tRNA, Biochemistry Journal, 1982, 205, 457-460