Script to generate PORCUPINE PLOTS ---------------------------------- Introduction: This ready to use perlscript generates plots as described in Haider et al., Biophys J. 2008 Jul;95(1):296-311. (Molecular dynamics and principal components analysis of human telomeric quadruplex multimers) Input for this script is the animated output file (anim.pdb) from PCZdump. It then extracts two models whose coordinates are furthest apart. (Model 6 and 16 are defaults from PCZdump). It then draws arrows between the two corresponding coordinates. The direction of the arrow represents the direction of the eigenvector and the length of the arrow represents the magnitude of motion. All one needs to do is to edit names of output files in the script (marked by 'EDIT' flag) to suit ones purpose. The useage is ./porcupine.pl The output file that is generated can be used directly in vmd using the command vmd -e porcupine.vmd License: These tools are provided under the terms of the Gnu Public License (GPL). If you have any problems or just wish to say how good this works for you then you can always drop me an email. Please dont be shy. Shozeb Haider 6th October 2008 BioMolecular Structure Group The London School of Pharmacy 29-39 Brunswick Square London WC1N 1AX UK