The loopFRODA script in the directory above automates the exploration of motion parallel and antiparallel (indicated as pos and neg, for positive and negative) to each of a given list of normal modes (here, modes 7 to 16, the ten lowest frequency nontrivial modes of motion) using the constraint network and structural rigidity appropriate to each of a given list of hydrogen bond energy cutoffs. In this case only a cutoff of -3.0 kcal/mol has been used, after examination of the structural rigidity as a function of cutoff in the Clusters folder.

Each trajectory is found in a folder Mode[NN]-[dir]-[cut]

The FRODA engine iteratively projects the protein structure along the mode direction while constraining the local geometry to match that of the original protein structure. Frames along each such trajectory are written out as numbered PDB files. Rigid cluster membership information is recorded in the b-factor columns of these files, as in the Clusters folder.

The unifyPosNegPML.sh script included here writes out a pml file instructing PyMOL to load files from the negative and positive directions of a given mode number as an ordered sequence. The resulting .pml files here can be used with PyMOL to easily visualise motions of the all-atom protein structures exploring the low-frequency modes of motion (flexible motions) of the protein structure.