This analysis began with the PDB entry 6Y2E. The structure has been prepared as follows.

Downloaded from PDB repository.
Opened in PyMOL v0.99.
Symmetry applied; symmetry mate selected to form homodimeric structure; symmetry mate chain reset to B; homodimer saved.
Homodimer processed using the MolProbity website to add hydrogens at electron-cloud positions, including flipping of ambiguous residues where suggested.
Hydrogenated homodimer opened in PyMOL v0.99; heteroatoms, mostly water residues, removed; alternative side chain configurations removed; structure saved as "6y2e.pdb".

Covalent, hydrogen-bond and hydrophobic interactions identified based on structure geometry and saved in files cov.in, hbonds.in, hphobes.in. hphobes.in has been edited to remove a single phobic tether linking ALA285 of each chain, as examination of the structure suggested that this tether was not appropriate as a permanent constraint in the system. This bond analysis was carried out using the SBFIRST utility, a copy of which is included with this data set. The .in files are suitable for use as input to the rigidity analysis software FIRST, from Arizona State University. The stacked.in file is empty (would hold stacked-ring interactions in nucleic acid structures).

Static rigidity analysis of the structure is carried out in the folder Clusters. Normal mode analysis identifying nontrivial low-frequency modes intrinsic to the structure is carried out in the folder Modes. Geometric simulations of flexible motion along the normal mode directions is carried out in the folder Runs, controlled by the bash script file loopFRODA.sh.