Manuscript is in: enm_review_revised.docx
Endnote library is in: refs.zip

This is a review paper, so it does not contain a lot of results. Instructions for producing plots and figures are included below.

Figure 1: PDBID: 1WPG and 3RFU was submitted to webnma and vector fields illustarting the third lowest energy mode for each structure was downloaded and the subsequent visualization was made with VMD. PDBs and state files for reproducing the image can be found in: /net/orinoco/reuter_group_repository/results/publications/2014_Fuglebakk_Tiwari_Reuter/Figure1

Figure 2: Made with VMD, rendered with tachyon and compiled to one Figure with ImageMagick. VMD state files, .dat files for Tachyon and commands a makefile for putting it all together is included in /net/orinoco/reuter_group_repository/results/publications/2014_Fuglebakk_Tiwari_Reuter/Figure2

The path for tachyon most be specified in the makefile and the make procedure assumes that ImageMagick 6.8.9-7 is installed and the command line tool "convert" is available in command path.

Figure 3:
Produced by executing:

/net/orinoco/reuter_group_repository/results/publications/2014_Fuglebakk_Tiwari_Reuter/Figure3/fk_plot.r

using R (2.12.0)

Figure 4:
Produced by executing:

/net/orinoco/reuter_group_repository/results/publications/2014_Fuglebakk_Tiwari_Reuter/Figure4/sim_measure.r

using R (2.12.0), requires libraries MASS and ellipse.

Figure 5:
/net/orinoco/reuter_group_repository/results/publications/2014_Fuglebakk_Tiwari_Reuter/Figure5/ contains fasta-formatted alignments and .tar archives with structures and vmd-state files for producing the images.

equations:
latex sources for making equations can be found in: /net/orinoco/reuter_group_repository/results/publications/2014_Fuglebakk_Tiwari_Reuter/equations/

requires packages "amsmath" and documentclass "standalone".