Jan H. Jensen jhjensen2

jhjensen2 / Emin.py

Last active December 20, 2015 02:59

A simple energy minimization program that uses steepest descent and a force field to minimize the energy of water in internal coordinates

	# A simple energy minimization program that uses steepest descent
	# and a force field to minimize the energy of water in internal coordinates
	# Written by Jan H. Jensen, 2013, released in the the GNU GPL license

	kOH = 50.0
	rOHe = 0.95
	kHOH = 50.0
	thetaHOHe = 104.5

	c = 0.005

jhjensen2 / Jmol script for fragmentation of protein

Created June 15, 2013 10:59

The Jmol script for the video: http://youtu.be/5BLh1PI2u_Q

	background white;
	load /Users/jan/Dropbox/presentation/BBL/1L2Y.pdb;
	reset;
	center {-1.231 1.8259997 0.04649973};rotate z 2.0; zoom 84.74; translate x 0.04; translate y 0.07;
	spin y;delay 10;spin off;delay 1;
	select all;color atoms amino;delay 1;spin y;delay 10;spin off;delay 3;
	display 1;delay 5;
	display 2;delay 1;
	display 3;delay 1;
	display 4;delay 1;

jhjensen2 / gist:4701339

Created February 3, 2013 11:13

A simple JSmol example The page can be found at http://propka.ki.ku.dk/~jhjensen/jsmoltest.html JSmol can be found at http://chemapps.stolaf.edu/jmol/jsmol/test2.htm

	DOCTYPE html>
	<html>
	<title>A simple Jsmol example</title>
	<head>
	<script type="text/javascript" src="jsmol/JSmoljQuery.js"></script>
	<script type="text/javascript" src="jsmol/JSmolCore.js"></script>
	<script type="text/javascript" src="jsmol/JSmolApplet.js"></script>
	<script type="text/javascript" src="jsmol/JSmolApi.js"></script>
	<script type="text/javascript" src="jsmol/j2s/j2sjmol.js"></script>
	<script type="text/javascript" src="jsmol/JSmol.js"></script>