#Needed vmd packages: lappend auto_path /Users/alberto/TAR/VMD/la1.0 lappend auto_path /Users/alberto/TAR/VMD/orient #Follow this link to prepare: http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

#Changes paths in analyze_ENM.py: /Users/alberto/DillLab/flex/Scripts/align_CA_all_atom.pl /Users/alberto/DillLab/flex/Scripts/align_and_draw_ENM.tcl

#EXECUTING: cd Example ../analyze_ENM.py --pdb new_template.pdb --reference new_crystal.pdb

#Results: new_template.pdb 8.08 8.13 12.85

second column is RMSD, gives geometric information about the two structures First term is energy in kcal/(mol Residue) to deform from "reference" to "pdb" using the flexible directions of "reference" Second term is energy in kcal/(mol Residue) to deform from "pdb" to "reference" using the flexible directions of "pdb"

There will be a figure rendered: paper_fig.tga and there will be a state_paper.vmd which can be used with vmd to load the state that was used with the paper_fig.tga