Normal mode analysis TSD Journal

Back to task.

Input

PDB file 2gk1 was used as input. Chain A was extracted and two files prepared, one containing only the protein part and one also containing the ligand NGT as ATOMs (instead of HETATMs). All other HETATMs were removed in both cases.

WEBnm@

createWEBnmaPNGs.pml creates a PNG for every frame of the animation. createAnimationsWEBnma.sh will create the final animated gif from these PNGs.

To color the picture according to the fluctuations colorFluctuations.pl was used. It is important to note that all residues have to be mapped back onto the structure again. Here the gap between 74 and 89 needs special adjustment as it is ignored in the WEBnm@ output.

elNemo

elNomo was run at the respective webserver at default parameters except that the cutoff for elastic interactions was increased to 10 from the default 8.

createPNGs.pml will perform every necessary task inside Pymol to create a PNG for every frame of the animation. createAnimations.sh will create the final animated gif from these PNGs.

plotRMS.R will plot the mean square distance in R, and createMSDPlots.sh will perform all the necessary pre- and postprocessing.