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

Jmol script for fragmentation of protein

 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;
 display 5;delay 0.5;
 display 6;delay 0.5;
 display 7;delay 0.5;
 display 8;delay 0.5;
 display 9;delay 0.5;
 display 10;delay 0.5;
 display 11;delay 0.5;
 display 12;delay 0.5;
 display 13;delay 0.5;
 display 14;delay 0.5;
 display 15;delay 0.5;
 display 16;delay 0.5;
 display 17;delay 0.5;
 display 18;delay 0.5;
 display 19;delay 5;
 display 18,19;delay 10;
 display 17,19;delay 10; 
 display 17,18,19;delay 1;
 display 16,17,18,19;delay 0.5;
 display 15,16,17,18,19;delay 0.5;
 display 14,15,16,17,18,19;delay 0.5;
 display 13,14,15,16,17,18,19;delay 0.5;
 display 12,13,14,15,16,17,18,19;delay 0.5;
 display 11,12,13,14,15,16,17,18,19;delay 0.5;
 display 10,11,12,13,14,15,16,17,18,19;delay 0.5;
 display 9,10,11,12,13,14,15,16,17,18,19;delay 0.5;
 display 8,9,10,11,12,13,14,15,16,17,18,19;delay 0.5;
 display 7,8,9,10,11,12,13,14,15,16,17,18,19;delay 0.5;
 display 6,7,8,9,10,11,12,13,14,15,16,17,18,19;delay 0.5;
 display 5,6,7,8,9,10,11,12,13,14,15,16,17,18,19;delay 0.5;
 display 4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19;delay 0.5;
 display 3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19;delay 0.5;
 display 2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19;delay 0.5;
 display 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19;delay 0.5;
 delay 3; select all; color atoms cpk; delay 1; spin y